CAP Profiles

Bio

Bio

Dr Hernandez-Boussard is an Associate Professor in Surgery, Medicine (Biomedical Informatics), and Biomedical Data Science at the Stanford University School of Medicine. Dr. Hernandez-Boussard's background and expertise is in the field of computational biology, with concentration on accountability measures, population health, and health policy. A key focus of her research is the application of novel methods and tools to large clinical datasets for hypothesis generation, comparative effectiveness research, and the evaluation of quality healthcare delivery.

Academic Appointments

Administrative Appointments

  • Director, Surgical Health Services Research Unit (2015 - Present)

Honors & Awards

  • Innovation Award in Population Science, Stanford University (2011-2012)
  • Innovation Award in Population Science, Stanford University (2012-2013)

Boards, Advisory Committees, Professional Organizations

  • Member, VA BD-Step Executive Committee (2015 - Present)
  • Member, Stanford Precision Health Committee (2015 - Present)
  • Member, Stanford Surgical Council Committee (2015 - Present)
  • Member, AHRQ Quality Indicators wrokgroup (2013 - 2015)
  • Member, AHRQ Quality Indicator™ ICD-10-CM/PCS Conversion Project (2012 - 2013)

Professional Education

  • M.S., Stanford University, Health Services Research (2013)
  • Ph.D., University Claude Bernard, Lyon 1, Computational Biology (1999)
  • M.P.H., Yale University, Epidemiology (1993)
  • B.A., University California, Irvine, Psychology (1991)
  • B.S., University of California, Irvine, Biology (1991)

Community and International Work

  • International Quality Improvement, Bologna, Italy

    Topic

    Quality Measurement

    Partnering Organization(s)

    Bologna University

    Location

    International

    Ongoing Project

    Yes

    Opportunities for Student Involvement

    Yes

Contact

Research & Scholarship

Current Research and Scholarly Interests

My background and expertise is in the field of computational biology, with concentration in health services research. A key focus of my research is to apply novel methods and tools to large clinical datasets for hypothesis generation, comparative effectiveness research, and the evaluation of quality healthcare delivery. My research involves managing and manipulating big data, which range from administrative claims data to electronic health records, and applying novel biostatistical techniques to innovatively assess clinical and policy related research questions at the population level. This research enables us to create formal, statistically rigid, evaluations of healthcare data using unique combinations of large datasets.

Projects

  • Improving Quality of Postoperative Pain Care Through use of Electronic Health Records, Agency for Healthcare Research and Quality (AHRQ) (September 1, 2015 - 6/30/2020)

    Millions of Americans undergo surgery every year and postoperative pain is common and often poorly managed. Poorly managed postoperative pain may cause severe functional impairment, impaired care of the underlying diseases, transition to chronic pain, and decreased quality of life. Many controlled studies have demonstrated a variety of interventions that benefit postoperative pain, yet their application in a large and more diverse population is unknown and a nationally endorsed, concise quality process metric for postoperative pain management does not exist. One roadblock is that postoperative pain and its related outcomes are complex. The gathering of evidence from electronic health data, which draw from and inform real-world practice, could bypass this roadblock and inform decisions that lead to effective and efficient postoperative pain management. This project seeks to measure quality of care for postoperative pain, assess proposed evidence-based interventions from randomized controlled trails, lay the ground work for systematic pain-related research using EMRs, and produce population-based evidence for a nationally-endorsed postoperative pain management quality metric. To achieve these objectives, this project has three specific aims: (1) to develop standardized electronic definitions of pain-related care processes and outcomes (e.g. prolonged opioid use, readmission for pain, etc.); (2) to extract clinically meaningful data from both structured data and free text in electronic medical records (EMR) and examine the relationship between recommended care processes and outcomes for postoperative pain using EMRs; (3) to validate pain-related process-outcome relationships at a national level and to develop a National Quality Forum submission and evaluation form for a postoperative pain quality metric(s). This project will achieve these aims by developing data capture algorithms on Palo Alto Veterans Administration (VA) Healthcare data, refining algorithms at a tertiary academic hospital, and validating algorithms on the National VA healthcare system. Data will be identified and extracted from the EMR using an extended version of our validated data-mining workflow. Established experience with quality metric development and NQF endorsement will facilitate the dissemination of this work. These approaches are the basis of a learning healthcare system and the proposed research directly aligns with AHRQ’s mission and goals to improve healthcare quality through health information technology and data resources.

    Location

    Stanford University

    Collaborators

    • Catherine Curtin, Associate Professor, Stanford University
    • Steven Asch, Professor, Stanford University / VA
    • Ian Carroll, Assistant Professor, Stanford University
    • Kathryn McDonald, Executive Director & Senior Scholar, Medicine - Med/PCOR, School of Medicine
    • Todd Wagner, Consulting Professor, Medicine - General Medical Disciplines, VA
    • Nigam Shah, Associate Professor of Medicine (Biomedical Informatics Research), Stanford University
  • Utilizing Electronic Health Records to Measure and Improve Prostate Cancer Care, National Cancer Institute (NCI) (7/1/2015 - 6/30/2020)

    Prostate cancer is the most common malignancy in men. Newly diagnosed men face complex treatment choices, each with different risks of acquired morbidities, including patient-centered outcomes (PCOs). The widespread implementation of electronic health records (EHRs) provides opportunities to incorporate PCOs into healthcare quality metric evaluations. However, efforts to assess quality metrics in EHRs have been limited because most relevant data are not reliably captured in structured formats. Our proposal innovates in three ways. First, we will develop an EHR prostate cancer database that will allow for clinical care data to be analyzed alongside diagnostic details. Second, we will create novel ontological representations of quality metrics that will be public and reliably calculable across EHR-systems. Third, we will assemble a robust data-mining workflow that expands on existing quality assessment methods by focusing on ontology-based dictionaries to annotate free text. Combining this set of innovative components will uniquely allow us to use existing EHRs to efficiently study the association between treatment processes and outcomes. Our methods are applicable not only to prostate cancer, but any disease with associated quality metrics. Our primary hypothesis is important prostate cancer PCOs will differ significantly across treatments (i.e. robotic surgery, open prostatectomy, and radiation therapy). To gather data to test our hypothesis, we assemble a data-mining workflow to extract quality metrics from both structured and free-text components of EHRs. In Aim 1 we will create the building blocks needed to identify quality metric data in the EHR. We will develop an EHR-database, map quality metrics to medical vocabularies and ontologies, and create quality metric phenotypes. This will be the first endeavor to generate structured representations of quality metrics. In Aim 2 we will expand our workflow to gather data relevant to quality metrics from EHRs. This will allow us to identify and validate a comprehensive set of quality metrics from the EHR. We will validate our technologies in 3 different EHR systems to ensure transportability. In Aim 3 we will develop a web-based risk assessment tool to compare PCOs across prostate cancer treatments. Our proposal will be the largest assessment of patient-centered quality metrics. It will produce a validated list of structured quality metrics, data-mining workflow, clinician documentation feedback reports, and risk assessment tool. Given the current state of prostate cancer treatment and research, these results will significantly impact clinical care, providing clinicians and patients with evidence needed to balance the risks and benefits of different treatment options. Our work is consistent with our nation’s focus on EHR meaningful use and the comprehensive and systematic assessment of healthcare delivery, and with NCI’s focus on improving the quality of cancer care delivery.

    Location

    Stanford University

    Collaborators

    • James Brooks, Professor, Stanford University
    • Douglas Blayney, Professor, Stanford University
    • Kathryn McDonald, Executive Director & Senior Scholar, Medicine - Med/PCOR, School of Medicine
    • Nigam Shah, Associate Professor of Medicine (Biomedical Informatics Research), Stanford University
    • Robert Tibshirani, Professor of Health Research and Policy (Biostatistics) and of Statistics, Stanford University
  • Surgical Health Services Research, Stanford University

    Location

    Arastradero, Stanford University

    Collaborators

Teaching

2016-17 Courses

Stanford Advisees

Publications

All Publications

  • Relationship of Affordable Care Act Implementation to Emergency Department Utilization Among Young Adults ANNALS OF EMERGENCY MEDICINE Hernandez-Boussard, T., Morrison, D., Goldstein, B. A., Hsia, R. Y. 2016; 67 (6): 714-720

    Abstract

    The 2010 provision of the Patient Protection and Affordable Care Act (ACA) extended eligibility for health insurance for young adults aged 19 to 25 years. It is unclear, however, how expanded coverage changes health care behavior and promotes efficient use of emergency department (ED) services. Our objective was to use population-level emergency department data to characterize any changes in diagnoses seen in ED among young adults since the implementation of the ACA dependent coverage expansion.We performed a difference-in-differences analysis of 2009 to 2011 ED visits from California, Florida, and New York, using all-capture administrative data to determine how the use of ED services changed for clinical categories after the ACA provision among young adults aged 19 to 25 years compared with slightly older adults unaffected by the provision, aged 26 to 31 years.We analyzed a total of 10,158,254 ED visits made by 4,734,409 patients. After the implementation of the 2010 ACA provision, young adults had a relative decrease of 0.5% ED visits per 1,000 people compared with the older group. For the majority of diagnostic categories, young adults' rates and risk of visit did not change relative to that of slightly older adults after the implementation of the ACA. However, although young adults' ED visits significantly increased for mental illnesses (2.6%) and diseases of the circulatory system (eg, nonspecific chest pain) (4.8%), visits decreased for pregnancy-related diagnoses and diseases of the skin (eg, cellulitis, abscess) compared with that of the older group (3.7% and 3.1%, respectively).Our results indicate that increased coverage has kept young adults out of the ED for specific conditions that can be cared for through access to other channels. As EDs face capacity challenges, these results are encouraging and offer insight into what could be expected under further insurance expansions from health care reform.

    View details for DOI 10.1016/j.annemergmed.2015.11.034

    View details for Web of Science ID 000377424400007

    View details for PubMedID 26778281

  • New Paradigms for Patient-Centered Outcomes Research in Electronic Medical Records: An Example of Detecting Urinary Incontinence Following Prostatectomy. EGEMS (Washington, DC) Hernandez-Boussard, T., Tamang, S., Blayney, D., Brooks, J., Shah, N. 2016; 4 (3): 1231

    Abstract

    National initiatives to develop quality metrics emphasize the need to include patient-centered outcomes. Patient-centered outcomes are complex, require documentation of patient communications, and have not been routinely collected by healthcare providers. The widespread implementation of electronic medical records (EHR) offers opportunities to assess patient-centered outcomes within the routine healthcare delivery system. The objective of this study was to test the feasibility and accuracy of identifying patient centered outcomes within the EHR.Data from patients with localized prostate cancer undergoing prostatectomy were used to develop and test algorithms to accurately identify patient-centered outcomes in post-operative EHRs - we used urinary incontinence as the use case. Standard data mining techniques were used to extract and annotate free text and structured data to assess urinary incontinence recorded within the EHRs.A total 5,349 prostate cancer patients were identified in our EHR-system between 1998-2013. Among these EHRs, 30.3% had a text mention of urinary incontinence within 90 days post-operative compared to less than 1.0% with a structured data field for urinary incontinence (i.e. ICD-9 code). Our workflow had good precision and recall for urinary incontinence (positive predictive value: 0.73 and sensitivity: 0.84).Our data indicate that important patient-centered outcomes, such as urinary incontinence, are being captured in EHRs as free text and highlight the long-standing importance of accurate clinician documentation. Standard data mining algorithms can accurately and efficiently identify these outcomes in existing EHRs; the complete assessment of these outcomes is essential to move practice into the patient-centered realm of healthcare.

    View details for DOI 10.13063/2327-9214.1231

    View details for PubMedID 27347492

  • The Affordable Care Act reduces emergency department use by young adults: evidence from three States. Health affairs Hernandez-Boussard, T., Burns, C. S., Wang, N. E., Baker, L. C., Goldstein, B. A. 2014; 33 (9): 1648-1654

    Abstract

    The Affordable Care Act (ACA) extended eligibility for health insurance for young adults ages 19-25. This extension may have affected how young adults use emergency department (ED) care and other health services. To test the impact of the ACA on how young adults used ED services, we used 2009-11 state administrative records from California, Florida, and New York to compare changes in ED use in young adults ages 19-25 before and after the ACA provision was implemented with changes in the same period for people ages 26-31 (the control group). Following implementation of the ACA provision, the younger group had a decrease of 2.7 ED visits per 1,000 people compared to the older group-a relative change of -2.1 percent. The largest relative decreases were found in women (-3.0 percent) and blacks (-3.4 percent). This relative decrease in ED use implies a total reduction of more than 60,000 visits from young adults ages 19-25 across the three states in 2011. When we compared the probability of ever using the ED before and after implementation of the ACA provision, we found a minimal decrease (-0.4 percent) among the younger group compared to the older group. This suggests that the change in the number of visits was driven by fewer visits among ED users, not by changes in the number of people who ever visited the ED.

    View details for DOI 10.1377/hlthaff.2014.0103

    View details for PubMedID 25201671

  • Protecting Nipple Perfusion by Devascularization and Surgical Delay in Patients at Risk for Ischemic Complications During Nipple-Sparing Mastectomies ANNALS OF SURGICAL ONCOLOGY Bertoni, D. M., Dung Nguyen, D., Rochlin, D., Hernandez-Boussard, T., Meyer, S., Choy, N., Gurtner, G. C., Wapnir, I. L. 2016; 23 (8): 2665-2672

    Abstract

    Indications for nipple-sparing mastectomy (NSM) are expanding; however, high-risk patients have more ischemic complications. Surgical devascularization of the nipple-areolar complex (NAC) prior to NSM can reduce complications. This study reports perfusion patterns and complications in high-risk patients undergoing 2-stage NSM.Surgical devascularization of the NAC was performed 3-6 weeks prior to NSM in 28 women. Risk factors included ptosis, obesity, smoking, prior breast surgery, and radiation. Using indocyanine green (ICG)-based fluorescence and an infrared camera, blood inflow was visualized intraoperatively. NAC perfusion patterns were classified as: V1, underlying breast; V2, surrounding skin; V3 = V1 + V2, or V4, capillary fill following devascularization. Ischemic complications were analyzed.Baseline perfusion for 54 breasts was 35 % V1, 32 % V2, and 33 % V3. Increasing ptosis was associated with V1 pattern: 86 % for grade 3, 31 % for grade 2, and 18 % for grade 1. Postdevascularization epidermolysis was observed in 63 % of V1 baseline, 41 % of V2, and 22 % of V3 (P = .042) and after NSM in 26 % for V1, 7 % for V2, and 6 % for V3 (P = .131). Ptosis was significantly associated with epidermolysis postdevascularization (P = .002) and NSM (P = .002). Smoking and BMI ≥30 were related to increased ischemic complications. Two or more risk factors were associated with postdevascularization ischemic changes (P = .026), but were not significant after NSM. Nipple loss was not observed, but 2 patients underwent partial areolar resection.Adaptive circulatory changes after devascularization allow tissues to tolerate the additional ischemic challenge of mastectomy. Our findings support extending 2-staged operations to high-risk women previously considered unsuitable for NSM.

    View details for DOI 10.1245/s10434-016-5201-8

    View details for Web of Science ID 000379189900044

    View details for PubMedID 27038458

  • Analyzing treatment aggressiveness and identifying high-risk patients in diabetic foot ulcer return to care. Wound repair and regeneration Remington, A. C., Hernandez-Boussard, T., Warstadt, N. M., Finnegan, M. A., Shaffer, R., Kwong, J. Z., Curtin, C. 2016; 24 (4): 731-736

    Abstract

    Rates of diabetes and its associated comorbidities have been increasing in the United States, with diabetic foot ulcer treatment representing a large cost to the patient and healthcare system. These ulcers often result in multiple hospital admissions. This study examined readmissions following inpatient care for a diabetic foot ulcer and identified modifiable factors associated with all-cause 30-day readmissions to the inpatient or emergency department (ED) setting. We hypothesized that patients undergoing aggressive treatment would have lower 30-day readmission rates. We identified patient discharge records containing International Classification of Disease ninth revision codes for both diabetes mellitus and distal foot ulcer in the State Inpatient and Emergency Department databases from the Agency for Healthcare Research and Quality, Healthcare Cost and Utilization Project in Florida and New York, 2011-2012. All-cause 30-day return to care visits (ED or inpatient) were analyzed. Patient demographics and treatment characteristics were evaluated using univariate and multivariable regression models. The cohort included 25,911 discharges, having a mean age of 63 and an average of 3.8 comorbidities. The overall rate of return to care was 30%, and 21% of subjects underwent a toe or midfoot amputation during their index stay. The most common diagnosis codes upon readmission were diabetes mellitus (19%) and infection (13%). Patients with a toe or midfoot amputation procedure were less likely to be readmitted within 30 days (odds ratio: 0.78; 95% confidence interval: 0.73, 0.84). Presence of comorbidities, black and Hispanic ethnicities, and Medicare and Medicaid payer status were also associated with higher odds of readmission following initial hospitalization (p < 0.05). The study suggests that there are many factors that affect readmission rates for diabetic foot ulcer patients. Understanding patients at high-risk for readmission can improve counseling and treatment strategies for this fragile patient population.

    View details for DOI 10.1111/wrr.12439

    View details for PubMedID 27144893

  • Robot-assisted versus open radical prostatectomy utilization in hospitals offering robotics. Canadian journal of urology Yanamadala, S., Chung, B. I., Hernandez-Boussard, T. M. 2016; 23 (3): 8279-8284

    Abstract

    Prostate cancer is an extremely prevalent cause of morbidity and mortality among American men. Several different treatments exist, but differences in utilization between these treatments are not well understood.We performed an observational study using administrative datasets linked to hospital survey data, which included non-metastatic prostate cancer patients receiving robot-assisted radical prostatectomy (RARP) or open radical prostatectomy (ORP) in California, Florida, or New York from 2009-2011. We developed two hierarchical regression models with fixed effect accounting for hospital clustering and physician clustering to determine factors associated with utilization of RARP versus ORP at hospitals offering robotic surgery.A total of 36,694 patients were identified, with 77.13% receiving RARP and 22.87% receiving ORP. African American patients had lower RARP rates than White patients (OR = 0.80, p < 0.001). Patients using Medicare (OR = 0.91, p = 0.028), Medicaid (OR = 0.68, p < 0.001), or self-pay (OR = 0.72, p = 0.046) had lower RARP rates than patients using private insurance. Patients in Florida had lower RARP rates than patients in California (OR = 0.48, p = 0.010). Patients treated at teaching hospitals had lower RARP rates than patients treated at non-teaching hospitals (OR = 0.50, p = 0.006). The average cost of RARP was $13,614.83, and the average cost of ORP was $12,167.44 (p < 0.001).This population based study suggests that both patient and hospital characteristics are associated with utilization of RARP versus ORP in hospitals where robotic surgery is offered.

    View details for PubMedID 27347621

  • Robot-assisted versus open radical prostatectomy utilization in hospitals offering robotics CANADIAN JOURNAL OF UROLOGY Yanamadala, S., Chung, B. I., Hernandez-Boussard, T. M. 2016; 23 (3): 8280-8285

    View details for Web of Science ID 000379635800006

  • Risks of adverse events in colorectal patients: population-based study JOURNAL OF SURGICAL RESEARCH Hernandez-Boussard, T. M., McDonald, K. M., Morrison, D. E., Rhoads, K. F. 2016; 202 (2): 328-334

    Abstract

    Postoperative (PO) outcomes are rapidly being integrated into value-based purchasing programs and associated penalties are slated for inclusion in the near future. Colorectal surgery procedures are extremely common and account for a high proportion of morbidity among general surgery. We sought to assess adverse events in colorectal surgical patients.We performed a retrospective study using the Nationwide Inpatient Sample database, 2008-2012. Patients were identified using International Classification of Diseases, Ninth Revision, Clinical Modification codes and classified based on procedure indication: colon cancer, benign polyps, diverticulitis, inflammatory bowel disease, and ischemic colitis. The outcome of interest was inpatient adverse event identified by Agency for Healthcare Research and Quality's patient safety indicators (PSIs).We identified 1,100,184 colorectal patients who underwent major surgery; 2.7% developed a PSI during their hospital stay. Compared to all colorectal patients, those with ischemic colitis had significantly higher risk-adjusted rates per 1000 case for pressure ulcer (50.20), failure to rescue (211.30), central line bloodstream infection (2.33) and PO DE/deep vein thrombosis (16.02), and sepsis (46.99), whereas benign polyps were associated with significantly lower risk-adjusted rates per 1000 cases for pressure ulcer (11.48), failure to rescue (84.79), central line bloodstream infection (0.97) and PO pulmonary embolism/deep vein thrombosis (4.81), and sepsis (11.23). Compared to both patient demographic and clinical characteristics, the procedure indication was the strongest predictor of any PSI relevant to colorectal surgery; patients with ischemic colitis had higher odds of experiencing a PSI (odds ratio, 1.84; 95% confidence interval, 1.71-1.99) compared with cancer patients.Among colorectal surgery patients, inpatient events were not uncommon. We found important differential rates of adverse events by diagnostic category, with the highest odds ratio occurring in patients undergoing surgery for ischemic colitis. Our work elaborates the need for rigorous risk adjustment, quality improvement strategies for high-risk populations, and attention to detail in calculating financial incentives in emerging value-based purchasing programs.

    View details for DOI 10.1016/j.jss.2016.01.013

    View details for Web of Science ID 000376334700013

    View details for PubMedID 27229107

  • Electronic Health Records and Quality of Care: An Observational Study Modeling Impact on Mortality, Readmissions, and Complications MEDICINE Yanamadala, S., Morrison, D., Curtin, C., McDonald, K., Hernandez-Boussard, T. 2016; 95 (19)

    Abstract

    Electronic health records (EHRs) were implemented to improve quality of care and patient outcomes. This study assessed the relationship between EHR-adoption and patient outcomes.We performed an observational study using State Inpatient Databases linked to American Hospital Association survey, 2011. Surgical and medical patients from 6 large, diverse states were included. We performed univariate analyses and developed hierarchical regression models relating level of EHR utilization and mortality, readmission rates, and complications. We evaluated the effect of EHR adoption on outcomes in a difference-in-differences analysis, 2008 to 2011.Medical and surgical patients sought care at hospitals reporting no EHR (3.5%), partial EHR (55.2%), and full EHR systems (41.3%). In univariate analyses, patients at hospitals with full EHR had the lowest rates of inpatient mortality, readmissions, and Patient Safety Indicators followed by patients at hospitals with partial EHR and then patients at hospitals with no EHR (P < 0.05). However, these associations were not robust when accounting for other patient and hospital factors, and adoption of an EHR system was not associated with improved patient outcomes (P > 0.05).These results indicate that patients receiving medical and surgical care at hospitals with no EHR system have similar outcomes compared to patients seeking care at hospitals with a full EHR system, after controlling for important confounders.To date, we have not yet seen the promised benefits of EHR systems on patient outcomes in the inpatient setting. EHRs may play a smaller role than expected in patient outcomes and overall quality of care.

    View details for DOI 10.1097/MD.0000000000003332

    View details for Web of Science ID 000376927000010

    View details for PubMedID 27175631

  • The Ontology for Biomedical Investigations PLOS ONE Bandrowski, A., Brinkman, R., Brochhausen, M., Brush, M. H., Bug, B., Chibucos, M. C., Clancy, K., Courtot, M., Derom, D., Dumontier, M., Fan, L., Fostel, J., Fragoso, G., Gibson, F., Gonzalez-Beltran, A., Haendel, M. A., He, Y., Heiskanen, M., Hernandez-Boussard, T., Jensen, M., Lin, Y., Lister, A. L., Lord, P., Malone, J., Manduchi, E., McGee, M., Morrison, N., Overton, J. A., Parkinson, H., Peters, B., Rocca-Serra, P., Ruttenberg, A., Sansone, S., Scheuermann, R. H., Schober, D., Smith, B., Soldatova, L. N., Stoeckert, C. J., Taylor, C. F., Torniai, C., Turner, J. A., Vita, R., Whetzel, P. L., Zheng, J. 2016; 11 (4)

    Abstract

    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

    View details for DOI 10.1371/journal.pone.0154556

    View details for Web of Science ID 000375212600038

    View details for PubMedID 27128319

  • Performance Measures in Neurosurgical Patient Care Differing Applications of Patient Safety Indicators MEDICAL CARE Moghavem, N., McDonald, K., Ratliff, J. K., Hernandez-Boussard, T. 2016; 54 (4): 359-364

    Abstract

    Patient Safety Indicators (PSIs) are administratively coded identifiers of potentially preventable adverse events. These indicators are used for multiple purposes, including benchmarking and quality improvement efforts. Baseline PSI evaluation in high-risk surgeries is fundamental to both purposes.Determine PSI rates and their impact on other outcomes in patients undergoing cranial neurosurgery compared with other surgeries.The Agency for Healthcare Research and Quality (AHRQ) PSI software was used to flag adverse events and determine risk-adjusted rates (RAR). Regression models were built to assess the association between PSIs and important patient outcomes.We identified cranial neurosurgeries based on International Classification of Diseases, Ninth Revision, Clinical Modification codes in California, Florida, New York, Arkansas, and Mississippi State Inpatient Databases, AHRQ, 2010-2011.PSI development, 30-day all-cause readmission, length of stay, hospital costs, and inpatient mortality.A total of 48,424 neurosurgical patients were identified. Procedure indication was strongly associated with PSI development. The neurosurgical population had significantly higher RAR of most PSIs evaluated compared with other surgical patients. Development of a PSI was strongly associated with increased length of stay and hospital cost and, in certain PSIs, increased inpatient mortality and 30-day readmission.In this population-based study, certain accountability measures proposed for use as value-based payment modifiers show higher RAR in neurosurgery patients compared with other surgical patients and were subsequently associated with poor outcomes. Our results indicate that for quality improvement efforts, the current AHRQ risk-adjustment models should be viewed in clinically meaningful stratified subgroups: for profiling and pay-for-performance applications, additional factors should be included in the risk-adjustment models. Further evaluation of PSIs in additional high-risk surgeries is needed to better inform the use of these metrics.

    View details for DOI 10.1097/MLR.0000000000000490

    View details for Web of Science ID 000372935200004

    View details for PubMedID 26759981

  • Lymph Node Ratio Analysis After Neoadjuvant Chemotherapy is Prognostic in Hormone Receptor-Positive and Triple-Negative Breast Cancer. Annals of surgical oncology Tsai, J., Bertoni, D., Hernandez-Boussard, T., Telli, M. L., Wapnir, I. L. 2016; 23 (10): 3310-6

    Abstract

    Lymph node ratios (LNR), the proportion of positive lymph nodes over the number excised, both defined as ranges and single ratio values are prognostic of outcome. Little is known of the prognostic value of LNR after neoadjuvant chemotherapy (NAC) according to molecular subtype.From 2003 to 2014, patients who underwent definitive surgery after NAC were identified. LNR was calculated for node-positive patients who received axillary dissection or had at least 6 nodes removed. DFS was calculated using the Kaplan-Meier log rank test for yp N0-3 status, LNR categories (LNRC) ≤0.20 (low), 0.21-0.65 (intermediate), >0.65 (high), and single LNR values.Of 428 NAC recipients, 263 were node negative and 165 (38.6 %) node positive: ypN1 = 97 (58.8 %), ypN2 = 43 (26.1 %), and ypN3 = 25 (15.2 %). Among node-positive cancers, the median number of LN removed was 14 (range, 6-51) and the median LNR was 0.22 (range, 0.03-1.0). Nodal stage was inversely associated with 5-year DFS: 91.5 % (ypN0), 74.5 % (ypN1), 49.8 % (ypN2), and 50.7 % (ypN3) (p < 0.001). LNRC was similarly inversely associated with DFS: 69.1 % (low), 71.4 % (intermediate), 49.3 % (high) (p < 0.001). Significant associations between LNRC and DFS were demonstrated in hormone receptor (HR)-positive and triple negative breast cancer (TNBC) subtypes, p = 0.02 and p = 0.003. A single-value LNR ≤ 0.15 in node-positive, HR-positive (94.1 vs 67.7 %; p = 0.04) and TNBC (94.1 vs 47.8 %; p = 0.001) groups was also significant.Residual nodal disease after NAC, analyzed by LNRC or LNR = 0.15 cutoff value, is prognostic and can discriminate between favorable and unfavorable outcomes for HR-positive and TNBC cancers.

    View details for DOI 10.1245/s10434-016-5319-8

    View details for PubMedID 27401442

  • Characterization of Young Adult Emergency Department Users: Evidence to Guide Policy. The Journal of adolescent health : official publication of the Society for Adolescent Medicine Burns, C., Wang, N. E., Goldstein, B. A., Hernandez-Boussard, T. 2016

    Abstract

    The purpose of this study was to characterize young adult patients aged 19-25 years who are emergency department (ED) frequent users and study factors associated with frequent ED use.ED visits among 19- to 25-year olds were identified from administrative records in California, Florida, Iowa, Massachusetts, and New York, 2010. Patients were analyzed for 12 months to study the frequency of their ED utilization. ED visits were categorized according to primary diagnosis. Patients were stratified by frequency of ED use: one visit (single users), two to four visits (infrequent users), and five or more visits (frequent users) in a 1-year period.We identified 1,711,774 young adult patients who made 3,650,966 ED visits. Sixty-six percent of patients were single users, 29% were infrequent users, and 4.6% were frequent users. Frequent users accounted for a disproportionate 28.8% of visits within the population studied. Frequent users had the largest proportion of visits for complications of pregnancy (13.6%) compared to single users (6.1%) and Medicaid (42.6%) compared to private insurance (17.3%). There was an increased risk of frequent ED use associated with females (odds ratio [OR]: 1.77), Medicaid (OR: 3.21), and Medicare insurance (OR: 4.22) compared to private insurance, and diseases of the blood (OR: 3.36) and mental illness (OR: 1.99) compared to injury and poisoning.Frequent users comprise a significant portion of the young adult ED population and present with a large proportion of visits for complications of pregnancy. Policies targeting this population might focus on improved access to primary and urgent care, acute obstetric care, and better coordination of care.

    View details for DOI 10.1016/j.jadohealth.2016.07.011

    View details for PubMedID 27613220

  • Risk-adjustment models for heart failure patients' 30-day mortality and readmission rates: the incremental value of clinical data abstracted from medical charts beyond hospital discharge record. BMC health services research Lenzi, J., Avaldi, V. M., Hernandez-Boussard, T., Descovich, C., Castaldini, I., Urbinati, S., Di Pasquale, G., Rucci, P., Fantini, M. P. 2016; 16: 473

    Abstract

    Hospital discharge records (HDRs) are routinely used to assess outcomes of care and to compare hospital performance for heart failure. The advantages of using clinical data from medical charts to improve risk-adjustment models remain controversial. The aim of the present study was to evaluate the additional contribution of clinical variables to HDR-based 30-day mortality and readmission models in patients with heart failure.This retrospective observational study included all patients residing in the Local Healthcare Authority of Bologna (about 1 million inhabitants) who were discharged in 2012 from one of three hospitals in the area with a diagnosis of heart failure. For each study outcome, we compared the discrimination of the two risk-adjustment models (i.e., HDR-only model and HDR-clinical model) through the area under the ROC curve (AUC).A total of 1145 and 1025 patients were included in the mortality and readmission analyses, respectively. Adding clinical data significantly improved the discrimination of the mortality model (AUC = 0.84 vs. 0.73, p < 0.001), but not the discrimination of the readmission model (AUC = 0.65 vs. 0.63, p = 0.08).We identified clinical variables that significantly improved the discrimination of the HDR-only model for 30-day mortality following heart failure. By contrast, clinical variables made little contribution to the discrimination of the HDR-only model for 30-day readmission.

    View details for DOI 10.1186/s12913-016-1731-9

    View details for PubMedID 27600617

  • Cataract Surgery Complications and Revisit Rates among 3 States. American journal of ophthalmology Pershing, S., Morrison, D. E., Hernandez-Boussard, T. 2016

    Abstract

    To characterize population-based 30-day procedure-related readmissions (revisits) following cataract surgery.Ambulatory cataract surgery performed in California, Florida, or New York DESIGN: Retrospective cohort study.This study used all-capture state administrative datasets. Cataract procedures from CA, FL, and NY state ambulatory surgery settings were identified using ICD-9-CM and CPT codes. Thirty-day readmissions (revisits) were identified in inpatient, ambulatory, and emergency department settings across each state RESULTS: Across the three states, the all-cause 30-day readmission rate was 6.0% and the procedure-related readmission (revisit) rate was 1.0%. Procedure-related revisits were highest for patients aged 20-29 (2.9%) and 30-39 (2.3%) and lowest for patients aged 70-79 (0.9%). Multivariate associations between clinical characteristics and 30-day procedure-related revisits included age 20-29 (Odds Ratio [OR]: 3.13; 95% Confidence Intervals [CI]: 2.33-4.20) and age 30-39 (OR: 2.35; CI: 1.91-2.89) compared to age 70-79, male gender (OR: 1.29; CI: 1.24-1.34), races black (OR: 1.37; CI: 1.27-1.48) and Hispanic (OR: 1.16; CI: 1.08-1.24) compared to white, and Medicaid insurance (OR: 1.18, CI: 1.07-1.30) compared to Medicare. Diabetes was also associated with increased 30-day procedure-related revisits (OR: 1.093, CI: 1.024-1.168).Cataract surgery is a common and, in aggregate, expensive procedure. Complication-related revisits follow a similar trend as surgical complications in large-scale population data, and may be useful as a preliminary, screening, outcome measure. Our results highlight the importance of age as a risk factor for cataract surgery readmissions, and suggest a relationship between black or Hispanic race, Medicaid insurance, and diabetes associated with higher risk for cataract surgery complications.

    View details for DOI 10.1016/j.ajo.2016.08.036

    View details for PubMedID 27615607

  • Evaluating patient safety indicators in orthopedic surgery between Italy and the USA. International journal for quality in health care : journal of the International Society for Quality in Health Care / ISQua Tedesco, D., Hernandez-Boussard, T., Carretta, E., Rucci, P., Rolli, M., Di Denia, P., McDonald, K., Fantini, M. P. 2016

    Abstract

    To compare patient safety in major orthopedic procedures between an orthopedic hospital in Italy, and 26 US hospitals of similar size.Retrospective analysis of administrative data from hospital discharge records in Italy and Florida, USA, 2011-13. Patient Safety Indicators (PSIs) developed by the Agency for Healthcare Quality and Research were used to identify inpatient adverse events (AEs). We examined the factors associated with the development of each different PSI, taking into account known confounders, using logistic regression.One Italian orthopedic hospital and 26 hospitals in Florida with ≥ 1000 major orthopedic procedures per year.Patients ≥ 18 years who underwent 1 of the 17 major orthopedic procedures, and with a length of stay (LOS) > 1 day.Patient Safety management between Italy and the USA.Patient Safety Indicators.A total of 14 393 patients in Italy (mean age = 59.8 years) and 131 371 in the USA (mean age = 65.4 years) were included. US patients had lower adjusted odds of developing a PSI compared to Italy for pressure ulcers (odds ratio [OR]: 0.21; 95% confidence interval [CI]: 0.10-0.45), hemorrhage or hematoma (OR: 0.42; CI 0.23-0.78), physiologic and metabolic derangement (OR: 0.08; CI 0.02-0.37). Italian patients had lower odds of pulmonary embolism/deep vein thrombosis (OR: 3.17; CI 2.16-4.67) compared to US patients.Important differences in patient safety events were identified across countries using US developed PSIs. Though caution about potential coding differences is wise when comparing PSIs internationally, other differences may explain AEs, and offer opportunities for cross-country learning about safe practices.

    View details for DOI 10.1093/intqhc/mzw053

    View details for PubMedID 27272404

  • Pediatric Patient and Hospital Characteristics Associated With Treatment of Peritonsillar Abscess and Peritonsillar Cellulitis CLINICAL PEDIATRICS Nguyen, T., Haberland, C. A., Hernandez-Boussard, T. 2015; 54 (13): 1240-1246

    Abstract

    Objective. To identify patient and hospital characteristics associated with the choice of treatment for pediatric patients who present in the acute setting with peritonsillar abscess/cellulitis (PTA/PTC). Study Design. A retrospective cohort study was performed using Healthcare Cost and Utilization Project emergency department, ambulatory, and inpatient state databases for the years 2010 and 2011. Children aged 0 to 17 years were identified using International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) diagnosis code for PTA/PTC. The main outcome of interest was treatment received, which included medical therapy alone, incision and drainage (IND) or tonsillectomy. Multiple logistic regression analyses were conducted to model non-clinical factors associated with treatment received after adjusting for age, hospital state, race, primary expected payer, existing chronic condition(s), and type of hospital. Results. We identified 2994 patients who presented with PTA/PTC. The most common treatment choice was medical therapy alone (30.8%), followed by IND (30.5%) and tonsillectomy (9.4%). There were significant associations between treatment choice and race, primary payer status, and type of hospital (P < .05). We found that Hispanic patients, those with Medicaid as their primary expected payer, and those treated at a designated children's hospital were 3 nonclinical factors independently associated with an increase in likelihood of receiving tonsillectomy as treatment. Conclusion. There are important nonclinical factors associated with treatment of children who present in the acute setting with PTA/PTC. Additional research is recommended to understand these observed differences in care and how they may affect health outcomes.

    View details for DOI 10.1177/0009922814565884

    View details for Web of Science ID 000363063800002

    View details for PubMedID 25589309

  • The Effect of Moving Carpal Tunnel Releases Out of Hospitals on Reducing United States Health Care Charges JOURNAL OF HAND SURGERY-AMERICAN VOLUME Nguyen, C., Milstein, A., Hernandez-Boussard, T., Curtin, C. M. 2015; 40 (8): 1657-1662

    Abstract

    To better understand how perioperative care affects charges for carpal tunnel release (CTR).We developed a cohort using ICD9-CM procedure code 04.43 for CTR in the National Survey of Ambulatory Surgery 2006 to test perioperative factors potentially associated with CTR costs. We examined factors that might affect costs, including patient characteristics, payer, surgical time, setting (hospital outpatient department vs. freestanding ambulatory surgery center), anesthesia type, anesthesia provider, discharge status, and adverse events. Records were grouped by facility to reduce the impact of surgeon and patient heterogeneity. Facilities were divided into quintiles based on average total facility charges per CTR. This division allowed comparison of factors associated with the lowest and highest quintile of facilities based on average charge per CTR.A total of 160,000 CTRs were performed in 2006. Nearly all patients were discharged home without adverse events. Mean charge across facilities was $2,572 (SD, $2,331-$2,813). Patient complexity and intraoperative duration of surgery was similar across quintiles (approximately 13 min). Anesthesia techniques were not significantly associated with patient complexity, charges, and total perioperative time. Hospital outpatient department setting was strongly associated with total charges, with $500 higher charge per CTR. Half of all CTRs were performed in hospital outpatient departments. Facilities in the lowest quintile charge group were freestanding ambulatory surgery centers.Examination of charges for CTR suggests that surgical setting is a large cost driver with the potential opportunity to lower charges for CTRs by approximately 30% if performed in ASCs.Economic/decision analysis II.

    View details for DOI 10.1016/j.jhsa.2015.04.023

    View details for Web of Science ID 000359511100019

  • Cranial neurosurgical 30-day readmissions by clinical indication JOURNAL OF NEUROSURGERY Moghavem, N., Morrison, D., Ratliff, J. K., Hernandez-Boussard, T. 2015; 123 (1): 189-197

    Abstract

    OBJECT Postsurgical readmissions are common and vary by procedure. They are significant drivers of increased expenditures in the health care system. Reducing readmissions is a national priority that has summoned significant effort and resources. Before the impact of quality improvement efforts can be measured, baseline procedure-related 30-day all-cause readmission rates are needed. The objects of this study were to determine population-level, 30-day, all-cause readmission rates for cranial neurosurgery and identify factors associated with readmission. METHODS The authors identified patient discharge records for cranial neurosurgery and their 30-day all-cause readmissions using the Agency for Healthcare Research and Quality (AHRQ) State Inpatient Databases for California, Florida, and New York. Patients were categorized into 4 groups representing procedure indication based on ICD-9-CM diagnosis codes. Logistic regression models were developed to identify patient characteristics associated with readmissions. The main outcome measure was unplanned inpatient admission within 30 days of discharge. RESULTS A total of 43,356 patients underwent cranial neurosurgery for neoplasm (44.23%), seizure (2.80%), vascular conditions (26.04%), and trauma (26.93%). Inpatient mortality was highest for vascular admissions (19.30%) and lowest for neoplasm admissions (1.87%; p < 0.001). Thirty-day readmissions were 17.27% for the neoplasm group, 13.89% for the seizure group, 23.89% for the vascular group, and 19.82% for the trauma group (p < 0.001). Significant predictors of 30-day readmission for neoplasm were Medicaid payer (OR 1.33, 95% CI 1.15-1.54) and fluid/electrolyte disorder (OR 1.44, 95% CI 1.29-1.62); for seizure, male sex (OR 1.74, 95% CI 1.17-2.60) and index admission through the emergency department (OR 2.22, 95% CI 1.45-3.43); for vascular, Medicare payer (OR 1.21, 95% CI 1.05-1.39) and renal failure (OR 1.52, 95% CI 1.29-1.80); and for trauma, congestive heart failure (OR 1.44, 95% CI 1.16-1.80) and coagulopathy (OR 1.51, 95% CI 1.25-1.84). Many readmissions had primary diagnoses identified by the AHRQ as potentially preventable. CONCLUSIONS The frequency of 30-day readmission rates for patients undergoing cranial neurosurgery varied by diagnosis between 14% and 24%. Important patient characteristics and comorbidities that were associated with an increased readmission risk were identified. Some hospital-level characteristics appeared to be associated with a decreased readmission risk. These baseline readmission rates can be used to inform future efforts in quality improvement and readmission reduction.

    View details for DOI 10.3171/2014.12.JNS14447

    View details for Web of Science ID 000356981200025

  • Patient Safety in Plastic Surgery Identifying Areas for Quality Improvement Efforts ANNALS OF PLASTIC SURGERY Hernandez-Boussard, T., McDonald, K. M., Rhoads, K. F., Curtin, C. M. 2015; 74 (5): 597-602

    Abstract

    Improving quality of health care is a global priority. Before quality benchmarks are established, we first must understand rates of adverse events (AEs). This project assessed risk-adjusted rates of inpatient AEs for soft tissue reconstructive procedures.Patients receiving soft tissue reconstructive procedures from 2005 to 2010 were extracted from the Nationwide Inpatient Sample. Inpatient AEs were identified using patient safety indicators (PSIs), established measures developed by Agency for Healthcare Research and Quality.We identified 409,991 patients with soft tissue reconstruction and 16,635 (4.06%) had a PSI during their hospital stay. Patient safety indicators were associated with increased risk-adjusted mortality, longer length of stay, and decreased routine disposition (P < 0.01). Patient characteristics associated with a higher risk-adjusted rate per 1000 patients at risk included older age, men, nonwhite, and public payer (P < 0.05). Overall, plastic surgery patients had significantly lower risk-adjusted rate compared to other surgical inpatients for all events evaluated except for failure to rescue and postoperative hemorrhage or hematoma, which were not statistically different. Risk-adjusted rates of hematoma hemorrhage were significantly higher in patients receiving size-reduction surgery, and these rates were further accentuated when broken down by sex and payer.In general, plastic surgery patients had lower rates of in-hospital AEs than other surgical disciplines, but PSIs were not uncommon. With the establishment of national basal PSI rates in plastic surgery patients, benchmarks can be devised and target areas for quality improvement efforts identified. Further prospective studies should be designed to elucidate the drivers of AEs identified in this population.

    View details for DOI 10.1097/SAP.0b013e318297791e

    View details for Web of Science ID 000353475100016

  • The TRANSFORM Patient Safety Project: A Microsystem Approach to Improving Outcomes on Inpatient Units JOURNAL OF GENERAL INTERNAL MEDICINE Braddock, C. H., Szaflarski, N., Forsey, L., Abel, L., Hernandez-Boussard, T., Morton, J. 2015; 30 (4): 425-433

    Abstract

    Improvements in hospital patient safety have been made, but innovative approaches are needed to accelerate progress. Evidence is emerging that microsystem approaches to quality and safety improvement in hospital care are effective.We aimed to evaluate the effects of a multifaceted, microsystem-level patient safety program on clinical outcomes and safety culture on inpatient units.A 1-year prospective interventional study was conducted, followed by a 6-month sustainability phase.Four medical and surgical inpatient units within an academic university medical center were included, with registered nurses and residents representing study participants.In situ simulation training; debriefing of medical emergencies; monthly patient safety team meetings; patient safety champion role; interdisciplinary patient safety conferences; recognition program for exemplary teamwork.Hospital-acquired severe sepsis/septic shock and acute respiratory failure; unplanned transfers to higher level of care (HLOC); weighted risk-adjusted mortality. Safety culture was measured using a widely accepted, validated survey.Rates of hospital-acquired severe sepsis/septic shock and acute respiratory failure decreased on study units, from 1.78 to 0.64 (p = 0.04) and 2.44 to 0.43 per 1,000 unit discharges (p = 0.03), respectively. The mean number of days between cases of severe sepsis/septic shock increased from baseline to the intervention period (p = 0.03). Unplanned transfers to HLOC increased from 715 to 764 per 1,000 unit transfers (p = 0.08). The weighted risk-adjusted observed-to-expected mortality ratio on all study units decreased from 0.50 to 0.40 (p < 0.001). Overall scores of safety culture on study units improved after the 1-year intervention, significantly for nurses (p < 0.001), but not for residents (p = 0.06). Scores significantly improved in nine of twelve survey dimensions for nurses, compared to in four dimensions for residents.A multifaceted patient safety program suggested an association with improved hospital-acquired complications and weighted, risk-adjusted mortality, and improved nurses' perceptions of safety culture on inpatient study units.

    View details for DOI 10.1007/s11606-014-3067-7

    View details for Web of Science ID 000351664000014

  • Ambulatory surgery center utilization by vitreoretinal surgeons: 1999-2011. Ophthalmic surgery, lasers & imaging retina Vaziri, K., Moshfeghi, D. M., Hernandez-Boussard, T., Callaway, N. F., Moshfeghi, A. A. 2015; 46 (3): 355-361

    Abstract

    To evaluate the utilization rates of ambulatory surgery centers (ASCs) in the state of Florida for vitreoretinal, cataract, and glaucoma surgical procedures over a 13-year period from 1999 through 2011.Retrospective analysis utilizing the State Ambulatory Surgery Databases (SASD) for Florida from 1999 through 2011. ICD-9 codes for vitreoretinal, cataract, and glaucoma procedures were queried. Joinpoint regression was used to calculate average annual percent change (APC) in ASC utilization by these procedures over the 13-year study period and also separately for the years 2007 to 2011.From 1999 through 2011, APC in ambulatory surgery center utilization was +26.4% (P = .0039) for vitreoretinal, +21.3% (P = .012) for cataract, and +20.9% (P = .0063) for glaucoma surgery. The APC from 2007 through 2011 was -1.2% for vitreoretinal (P = .47), -9.2% for cataract (P = .0039), and -17.3% for glaucoma surgery (P = .008).A significant overall increase in ASC utilization by vitreoretinal, cataract, and glaucoma surgeons over the study period was seen; however, the most recent 5-year data show that these trends may have begun to reverse. [Ophthalmic Surg Lasers Imaging Retina. 2015;46:355-361.].

    View details for DOI 10.3928/23258160-20150323-10

    View details for PubMedID 25856823

  • Ambulatory Surgery Center Utilization by Vitreoretinal Surgeons: 1999-2011 OPHTHALMIC SURGERY LASERS & IMAGING RETINA Vaziri, K., Moshfeghi, D. M., Hernandez-Boussard, T., Callaway, N. F., Moshfeghi, A. A. 2015; 46 (3): 355-361

    View details for DOI 10.3928/23258160-20150323-10

    View details for Web of Science ID 000359291400011

  • Impact of histological subtype on long-term outcomes of neuroendocrine carcinoma of the breast BREAST CANCER RESEARCH AND TREATMENT Cloyd, J. M., Yang, R. L., Allison, K. H., Norton, J. A., Hernandez-Boussard, T., Wapnir, I. L. 2014; 148 (3): 637-644

    View details for DOI 10.1007/s10549-014-3207-0

    View details for Web of Science ID 000345370600018

  • Restrictive blood transfusion practices are associated with improved patient outcomes. Transfusion Goodnough, L. T., Maggio, P., Hadhazy, E., Shieh, L., Hernandez-Boussard, T., Khari, P., Shah, N. 2014; 54 (10): 2753-2759

    Abstract

    Blood transfusion has been cited as one of the five most overutilized therapeutic procedures in the United States. We assessed the impact of clinical decision support at computerized physician order entry and education on red blood cell (RBC) transfusions and clinical patient outcomes at our institution.Clinical patient outcomes and RBC transfusions were assessed before and after implementation of a best practice alert triggered for transfusions when the hemoglobin level was higher than 7 g/dL for all inpatient discharges from January 2008 through December 2013. Retrospective clinical and laboratory data related to RBC transfusions were extracted: case-mix complexity, patient discharges and selected surgical volumes, and patient outcomes (mortality, 30-day readmissions, length of stay).There was a significant improvement in RBC utilization as assessed by RBC units transfused per 100 patient-days-at-risk. Concurrently, hospital-wide clinical patient outcomes showed improvement (mortality, p = 0.034; length of stay, p = 0.003) or remained stable (30-day readmission rates, p = 0.909). Outcome improvements were even more pronounced in patients who received blood transfusions, with decreased mortality rate (55.2 to 33.0, p < 0.001), length of stay (mean, 10.1 to 6.2 days, p < 0.001), and 30-day readmission rate (136.9 to 85.0, p < 0.001). The mean number of units transfused per patient also declined (3.6 to 2.7, p < 0.001). Acquisition costs of RBC units per 1000 patient discharges decreased from $283,130 in 2009 to $205,050 in 2013 with total estimated savings of $6.4 million and likely far greater impact on total transfusion-related costs.Improved blood utilization is associated with improved clinical patient outcomes.

    View details for DOI 10.1111/trf.12723

    View details for PubMedID 24995770

  • Readmissions After Treatment of Distal Radius Fractures JOURNAL OF HAND SURGERY-AMERICAN VOLUME Curtin, C. M., Hernandez-Boussard, T. 2014; 39 (10): 1926-1932

    View details for DOI 10.1016/j.jhsa.2014.07.041

    View details for Web of Science ID 000342733500006

  • Restrictive blood transfusion practices are associated with improved patient outcomes TRANSFUSION Goodnough, L. T., Maggio, P., Hadhazy, E., Shieh, L., Hernandez-Boussard, T., Khari, P., Shah, N. 2014; 54 (10): 2753-2759

    View details for DOI 10.1111/trf.12723

    View details for Web of Science ID 000343821100023

  • Readmissions after treatment of distal radius fractures. journal of hand surgery Curtin, C. M., Hernandez-Boussard, T. 2014; 39 (10): 1926-1932

    Abstract

    To assess the rates and associated diagnoses of readmissions for patients having received an intervention for treatment of distal radius fracture.We analyzed patient discharges from 2005-2011 for California, Florida, and New York. We used Agency for Healthcare Research and Quality data sets: (1) State Inpatient Database, (2) State Ambulatory Surgery Database, and (3) State Emergency Department Database. We examined inpatient, outpatient, and emergency room treatment locations. We identified patients by diagnosis code for distal radius fracture (813.41). Patients were stratified based on procedure codes for open reduction, closed reduction, and external fixation. The cohort was followed for 30 days to examine all-cause 30-day inpatient admissions and emergency department visits.We identified 35,241 discharges with a primary diagnosis of distal radius facture. Of those, 18,388 patients underwent a procedure for their fracture, and 1,679 (9%) were readmitted within 30 days of discharge. Readmission rates varied by procedure type: internal fixation 8%, closed reduction 14%, and external fixation 11%. The most common diagnosis codes associated with readmission were general distal radius fracture codes (11%) and pain diagnoses (10%). Open procedures had higher odds of having a readmission associated with pain compared with closed treatment and external fixation.Readmissions after treatment of distal radius fracture care are common. Our results show many distal radius fracture patients return to the health care system for pain-related issues. As more emphasis is placed on quality health care delivery, implementation of better pain management will be important to health care providers and patients.This study highlights that improved perioperative pain control may improve patient care and reduce readmissions.

    View details for DOI 10.1016/j.jhsa.2014.07.041

    View details for PubMedID 25257486

  • Interfacility transfer and mortality for patients with ruptured abdominal aortic aneurysm JOURNAL OF VASCULAR SURGERY Mell, M. W., Wang, N. E., Morrison, D. E., Hernandez-Boussard, T. 2014; 60 (3): 553-557

    Abstract

    Patients receiving interfacility transfer to a higher level of medical care for ruptured abdominal aortic aneurysms (rAAAs) are an important minority that are not well characterized and are typically omitted from outcomes and quality indicator studies. Our objective was to compare patients transferred for treatment of rAAAs with those treated without transfer, with particular emphasis on mortality and resource utilization.We linked longitudinal data from 2005 to 2010 Healthcare Cost and Utilization Project (HCUP) State Inpatient Databases and Emergency Department Databases from California, Florida, and New York. Patients were identified using International Classification of Diseases-Ninth Revision-Clinical Modification codes. Our main outcome variables were mortality, length of stay, and cost. Data included discharge information on the transfer-out and transfer-in hospital. We used univariate and multivariate analysis to identify variables independently associated with transfer and in-hospital mortality.Of 4439 rAAA patients identified with intent to treat, 847 (19.1%) were transferred before receiving operative repair. Of those transferred, 141 (17%) died without undergoing AAA repair. By multivariate analysis, increasing age in years (odds ratio [OR] 0.98; 95% confidence interval [CI], 0.97-0.99; P < .001), private insurance vs Medicare (OR, 0.62; 95% CI, 0.47-0.80; P < .001), and increasing comorbidities as measured by the Elixhauser Comorbidity Index (OR, 0.90; 95% CI, 0.86-0.95; P < .001) were negatively associated with transfer. Weekend presentation (OR, 1.23; 95% CI, 1.02-1.47; P = .03) was positively associated with transfer. Transfer was associated with a lower operative mortality (adjusted OR, 0.81; 95% CI, 0.68-0.97; P < .02) but an increased overall mortality when including transferred patients who died without surgery (OR, 1.30; 95% CI, 1.05-1.60; P = .01). Among the transferred patients, there was no significant difference in travel distance between those who survived and those who died (median, 28.7 vs 25.8 miles; P = .07). Length of stay (median, 10 vs 9 days; P = .008), and hospital costs ($161,000 vs $146,000; P = .02) were higher for those transferred.The survival advantage for patients transferred who received treatment was eclipsed by increased mortality of the transfer process. Including 17% of transferred patients who died without receiving definitive repair, mortality was increased for patients transferred for rAAA repair compared with those not transferred after adjusting for demographic, clinical, and hospital factors. Transferred patients used significantly more hospital resources. Improving systems and guidelines for interfacility transfer may further improve the outcomes for these patients and decrease associated hospital resource utilization.

    View details for DOI 10.1016/j.jvs.2014.02.061

    View details for Web of Science ID 000341629700001

  • National Review of Factors Influencing Disparities and Types of Major Lower Extremity Amputations ANNALS OF VASCULAR SURGERY Zayed, M., Bech, F., Hernandez-Boussard, T. 2014; 28 (5): 1157-1165

    Abstract

    Despite advancements in the diagnosis and treatment of peripheral vascular disease, major lower extremity amputations are still performed at high rates with non-negligible economic burdens. Peri-operative morbidity and mortality is greater for patients who receive an above knee amputation (AKA) compared to patients who receive a below knee amputation (BKA). We sought to further evaluate what variables affect whether a patient receives a BKA versus an AKA using the Nationwide Inpatient Sample (NIS).From 2005 to 2008, all adult AKA and BKA procedures were identified in the NIS. Patients with trauma and oncologic diagnoses were excluded from the analysis. Rates of AKA and BKA were evaluated according to patient demographics, co-morbidities, extent of pre-amputation vascular intervention, hospital setting/type, and geographic region. Multivariate logistic regression and 2-way ANOVA analyses was used to determine statistical significance.A total of 228,624 patients met inclusion criteria (126,076 BKA, 102,548 AKA). Patients who received an AKA were more likely to be female (p<0.0001), older (p<0.0001), have non-private insurance (p<0.0001), and have a higher Elixhauser Co-morbidity Index (p<0.0001). Patients who received a BKA were more likely to have hypertension, diabetes, and a spinal cord injury (p<0.0001). Less limb salvage vascular interventions were attempted in low-volume hospitals and in patients who subsequently received AKA (p<0.0001), while more limb salvage vascular interventions were performed at high-volume centers where more BKA procedures were performed (p<0.0001). The majority of major amputations were performed in southern states (46.4%), and more BKA procedures were performed in urban and teaching hospitals (p<0.0001).Using the NIS database we found important differences between patients who receive a BKA versus an AKA. These differences are broadly observed between patient demographics, race, and co-morbidities, as well as insurance type, geographic region, and hospital type. Our findings highlight the need for more aggressive surveillance and preventative care of at risk populations.

    View details for DOI 10.1016/j.avsg.2013.11.008

    View details for Web of Science ID 000338090700011

    View details for PubMedID 24365081

  • Cleft palate surgery: an evaluation of length of stay, complications, and costs by hospital type. Cleft palate-craniofacial journal Nguyen, C., Hernandez-Boussard, T., Davies, S. M., Bhattacharya, J., Khosla, R. K., Curtin, C. M. 2014; 51 (4): 412-419

    Abstract

    Objective : The purpose of this study was to assess length of stay (LOS), complication rates, costs, and charges of cleft palate repair by various hospital types. We hypothesized that pediatric hospitals would have shorter LOS, fewer complications, and lower costs and charges. Methods : Patients were identified by ICD-9-CM code for cleft palate repair (27.62) using databases from the Agency for Health Research and Quality Healthcare Cost and Utilization Project Kids' Inpatient Database from 1997, 2000, 2003, and 2006. Patient characteristics (age, race, gender, insurer, comorbidities) and facility resources (hospital beds, cleft palate surgery volume, nurse-to-bed ratio, pediatric intensive care unit [PICU], PICU intensivist, burn unit) were examined. Hospitals types included pediatric hospitals, general hospitals, and nonaccredited children's hospital. For each hospital type, mean LOS, extended LOS (LOS > 2), and complications were assessed. Results : A total of 14,153 patients had cleft repair with a mean LOS of 2 days (SD, 0.04), mortality 0.01%, transfusion 0.3%, and complication <3%. Pediatric hospitals had fewer patients with extended hospital stays. Patients with an LOS >2 days were associated with fourfold higher complications. Comorbidities increased the relative rate of LOS >2 days by 90%. Pediatric hospitals had the highest comorbidities, yet 35% decreased the relative rate of LOS >2 days. Median total charges of $10,835 increased to $15,104 with LOS >2 days; median total costs of $4367 increased to $6148 with a LOS >2 days. Conclusion : Pediatric hospitals had higher comorbidities yet shorter LOS. Pediatric resources significantly decreased the relative rate of LOS >2 days. Median costs and charges increased by 41% with LOS >2 days. Further research is needed to understand additional aspects of pediatric hospitals associated with lower LOS.

    View details for DOI 10.1597/12-150

    View details for PubMedID 24063682

  • PHYSICIAN IDENTIFICATION AND PATIENT SATISFACTION IN THE EMERGENCY DEPARTMENT: ARE THEY RELATED? JOURNAL OF EMERGENCY MEDICINE Mercer, M. P., Hernandez-Boussard, T., Mahadevan, S. V., Strehlow, M. C. 2014; 46 (5): 711-718

    Abstract

    Patient satisfaction has become a quality indicator tracked closely by hospitals and emergency departments (EDs). Unfortunately, the primary factors driving patient satisfaction remain poorly studied. It has been suggested that correct physician identification impacts patient satisfaction in hospitalized patients, however, the limited studies that exist have demonstrated mixed results.In this study, we sought to identify factors associated with improved satisfaction among ED patients, and specifically, to test whether improving physician identification by patients would lead to increased satisfaction.We performed a pre- and postintervention, survey-based study of patients at the end of their ED visits. We compared patient satisfaction scores as well as patients' abilities to correctly identify their physicians over two separate 1-week periods: prior to and after introducing a multimedia presentation of the attending physicians into the waiting room.A total of 486 patients (25% of all ED visits) were enrolled in the study. In the combined study population, overall patient satisfaction was higher among patients who correctly identified their physicians than among those who could not identify their physicians (combined mean satisfaction score of 8.1 vs. 7.2; odds ratio [OR] 1.07). Overall satisfaction was also higher among parents or guardians of pediatric patients than among adult patients (satisfaction score of 8.4 vs. 7.4; OR 1.07), and among patients who experienced a shorter door-to-doctor time (satisfaction score of 8.2 for shorter waiting time vs. 5.6 for longer waiting time; OR 1.15). Ambulance patients showed decreased satisfaction over some satisfaction parameters, including physician courtesy and knowledge. No direct relationship was demonstrated between the study intervention (multimedia presentation) and improved patient satisfaction or physician identification.Improved patient satisfaction was found to be positively correlated with correct physician identification, shorter waiting times, and among the pediatric patient population. Further studies are needed to determine interventions that improve patients' abilities to identify their physicians and lower waiting times.

    View details for DOI 10.1016/j.jemermed.2013.08.036

    View details for Web of Science ID 000334791000028

    View details for PubMedID 24462030

  • Factors Associated With the Disposition of Severely Injured Patients Initially Seen at Non-Trauma Center Emergency Departments Disparities by Insurance Status JAMA SURGERY Delgado, M. K., Yokell, M. A., Staudenmayer, K. L., Spain, D. A., Hernandez-Boussard, T., Wang, N. E. 2014; 149 (5): 422-430

    View details for DOI 10.1001/jamasurg.2013.4398

    View details for Web of Science ID 000337908600005

  • The Association of Nurse-to-Patient Ratio with Mortality and Preventable Complications Following Aortic Valve Replacement JOURNAL OF CARDIAC SURGERY Arkin, N., Lee, P. H., McDonald, K., Hernandez-Boussard, T. 2014; 29 (2): 141-148

    Abstract

    To examine hospital resources associated with patient outcomes for aortic valve replacement (AVR), including inpatient adverse events and mortality.We used the Nationwide Inpatient Sample to identify AVR procedures from 1998 to 2010 and the American Hospital Association Annual Survey to augment hospital characteristics. Primary outcomes included mortality and the development of adverse events, identified using standardized patient safety indicators (PSI). Patient and hospital characteristics associated with PSI development were evaluated using univariate and multivariate analyses.An estimated 410,157 AVRs at 5009 hospitals were performed in the US between 1998 and 2010. The number of procedures grew annually by 4.72% (p = 0.0003) in high volume hospitals, 4.48% in medium volume hospitals (p < 0.0001), and 2.03% in low volume hospitals (p = 0.154). Mortality was highest in low volume hospitals, 4.70%, decreased from 4.14% to 3.73% in medium and high volume hospitals, respectively (p = 0.0002). Rates of PSIs did not vary significantly across volume terciles (p = 0.254). Multivariate logistic regression analysis showed low volume hospitals had increased risk of mortality as compared with high volume hospitals (odds ratio [OR]: 1.42; 95% confidence interval [CI]: 1.01 to 2.00), while hospital volume was not associated with adverse events. PSI development was associated with small hospitals as compared with large (OR: 1.63, 95% CI: 1.16 to 2.28) and inversely associated with higher nurse-to-patient ratio (OR: 0.94, 95% CI: 0.90 to 0.99).The volume-outcomes relationship was associated with mortality outcomes but not postoperative complications. We identified structural differences in hospital size, nurses-to-patient ratio, and nursing skill level indicative of high quality outcomes.

    View details for DOI 10.1111/jocs.12284

    View details for Web of Science ID 000332156200003

  • Interhospital Facility Transfers in the United States: A Nationwide Outcomes Study. Journal of patient safety Hernandez-Boussard, T., Davies, S., McDonald, K., Wang, N. E. 2014

    Abstract

    Patient transfers between hospitals are becoming more common in the United States. Disease-specific studies have reported varying outcomes associated with transfer status. However, even as national quality improvement efforts and regulations are being actively adopted, forcing hospitals to become financially accountable for the quality of care provided, surprisingly little is known about transfer patients or their outcomes at a population level. This population-wide study provides timely analyses of the characteristics of this particularly vulnerable and sizable inpatient population. We identified and compared characteristics and outcomes of transfer and nontransfer patients.With the use of the 2009 Nationwide Inpatient Sample, a nationally representative sample of U.S. hospitalizations, we examined patient characteristics, in-hospital adverse events, and discharge disposition for transfer versus nontransfer patients in this observational study.We identified 1,397,712 transfer patients and 31,692,211 nontransfer patients. Age, sex, race, and payer were significantly associated with odds of transfer (P < 0.05). Transfer patients had higher risk-adjusted inpatient mortality (4.6 versus 2.1, P < 0.01), longer length of stay (13.3 versus 4.5, P < 0.01), and fewer routine disposition discharges (53.6 versus 68.7, P < 0.01). In-hospital adverse events were significantly higher in transfer patients compared with nontransfer patients (P < 0.05).Our results suggest that transfer patients have inferior outcomes compared with nontransfer patients. Although they are clinically complex patients and assessing accountability as between the transferring and receiving hospitals is methodologically difficult, transfer patients must nonetheless be included in quality benchmark data to assess the potential impact this population has on hospital outcome profiles. With hospital accountability and value-based payments constituting an integral part of health care reform, documenting the quality of care delivered to transfer patients is essential before accurate quality assessment improvement efforts can begin in this patient population.

    View details for DOI 10.1097/PTS.0000000000000148

    View details for PubMedID 25397857

  • Lower Skin Cancer Risk in Women with Higher Body Mass Index: The Women's Health Initiative Observational Study CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Tang, J. Y., Henderson, M. T., Hernandez-Boussard, T., Kubo, J., Desai, M., Sims, S. T., Aroda, V., Thomas, F., McTiernan, A., Stefanick, M. L. 2013; 22 (12): 2412-2415

    Abstract

    The unclear relationship of obesity to incident melanoma and nonmelanoma skin cancer (NMSC) risks was evaluated in the large, geographically diverse longitudinal, prospective Women's Health Initiative (WHI) observational study. Risks of melanoma and NMSC in normal weight women were compared with risks in overweight [body mass index (BMI) = 25-29.0 kg/m(2)] and obese (BMI ≥ 30 kg/m(2)) women, using Cox proportional hazards models for melanoma and logistic regression for NMSC. Over a mean 9.4 years of follow-up, there were 386 melanoma and 9,870 NSMC cases. Risk of melanoma did not differ across weight categories (P = 0.86), whereas in fully adjusted models, NMSC risk was lower in overweight [OR, 0.93; 95% confidence interval (CI), 0.89-0.99] and obese (OR, 0.85; 95% CI, 0.80-0.91) women (P < 0.001). Excess body weight was not associated with melanoma risk in postmenopausal women but was inversely associated with NMSC risk, possibly due to lower sun exposure in overweight and obese women. This supports previous work demonstrating the relationship between excess body weight and skin cancer risk. Cancer Epidemiol Biomarkers Prev; 22(12); 2412-5. ©2013 AACR.

    View details for DOI 10.1158/1055-9965.EPI-13-0647

    View details for Web of Science ID 000329975700027

    View details for PubMedID 24042260

  • Breast Reconstruction National Trends and Healthcare Implications BREAST JOURNAL Hernandez-Boussard, T., Zeidler, K., Barzin, A., Lee, G., Curtin, C. 2013; 19 (5): 463-469

    Abstract

    Breast reconstruction improves quality-of-life of breast cancer patients. Different reconstructive options exist, yet commentary in the plastic surgery literature suggests that financial constraints are limiting access to autologous reconstruction (AR). This study follows national trends in breast reconstruction and identifies factors associated with reconstructive choices. Data were obtained from the Nationwide Inpatient Sample from 1998 to 2008. Patients were categorized as having either implant or ARs. Bivariate and multivariate regression analysis identified variables associated with receiving implants versus AR. Physician fee schedules were analyzed using national average Medicare physician reimbursement rates. From 1998 to 2008, 324,134 breast reconstructions were performed. Reconstructions increased 4% per year. The proportion of implant reconstructions increased 11% per year, whereasARs decreased 5% per year (p < 0.05). Our model showed that the odds of having implant-based versus AR were significantly associated with age, disease severity, payer type, hospital teaching status, and year of surgery. Year of surgery was the strongest predictor of implant reconstruction; patients receiving breast reconstructive surgery in 2009 were three times more likely to have implant breast reconstructive surgery compared with similar patients in 2002. Medicare reimbursement steadily declined for AR over a similar time frame. From 1998 to 2008, autologous breast reconstruction has significantly declined, parallel to a decrease in physician reimbursement. Our data found no significant change in patient characteristics supporting the lack of choice of AR. Further research is warranted to better understand this shift to implant reconstruction and to ensure future access of these complex reconstructive procedures.

    View details for DOI 10.1111/tbj.12148

    View details for Web of Science ID 000329284500002

  • A National Study on Craniosynostosis Surgical Repair CLEFT PALATE-CRANIOFACIAL JOURNAL Christine Nguyen, C., Hernandez-Boussard, T., Khosla, R. K., Curtin, C. M. 2013; 50 (5): 555-560

    View details for DOI 10.1597/11-324

    View details for Web of Science ID 000327536100011

  • No Difference in Mortality After Inter-Facility Transfer for Patients with Ruptured Abdominal Aortic Aneurysm JOURNAL OF VASCULAR SURGERY Mell, M. W., Wang, N. E., Morrison, D. E., Hernandez-Boussard, T. 2013; 58 (2): 562-562

    View details for Web of Science ID 000322759500074

  • Overlapping meta-analyses on the same topic: survey of published studies BMJ-BRITISH MEDICAL JOURNAL Siontis, K. C., Hernandez-Boussard, T., Ioannidis, J. P. 2013; 347

    View details for DOI 10.1136/bmj.f4501

    View details for Web of Science ID 000322247400002

  • Poor compliance with breast cancer treatment guidelines in men undergoing breast-conserving surgery BREAST CANCER RESEARCH AND TREATMENT Cloyd, J. M., Hernandez-Boussard, T., Wapnir, I. L. 2013; 139 (1): 177-182

    Abstract

    Lumpectomy is performed in a small but growing proportion of men with breast cancer. It is unknown whether men undergoing breast-conserving surgery (BCS) receive care compliant with breast cancer treatment guidelines. Patients with breast cancer in the surveillance, epidemiology, and end results (SEER) database who underwent lumpectomy between 1983 and 2009 were identified. Gender differences in the receipt of lymph node staging and adjuvant radiation therapy were assessed. Multivariate logistic regression was utilized to evaluate the independent association of gender on these outcomes. The influence of gender on breast cancer-specific survival (BCSS) was analyzed. 382,030 of 824,408 (46.3 %) women compared to 712 of 6,039 (11.8 %) men with breast cancer underwent lumpectomy. Men were older, more likely to be black, less likely to have stage I disease and more likely to have stage IV disease. Only 59.2 % of men had lymph nodes sampled at the time of surgery compared to 81.6 % of women (p < 0.0001). In addition, only 35.4 % of men received adjuvant breast radiation therapy compared to 69.8 % of women (p < 0.0001). After controlling for age, race, stage, grade, and year of diagnosis, female gender was significantly associated with receiving adjuvant radiation therapy (OR 2.9, 95 % CI 2.4-3.4) and lymph node staging (OR 1.6, 95 % CI 1.3-1.90). Five- and ten-year BCSS were 88.0 and 83.5 % for men compared to 93.2 and 88.2 % for women (p < 0.001). Men with breast cancer are less likely to receive lymph node staging or adjuvant radiation therapy following BCS compared to women.

    View details for DOI 10.1007/s10549-013-2517-y

    View details for Web of Science ID 000318524600018

  • Outcomes of Partial Mastectomy in Male Breast Cancer Patients: Analysis of SEER, 1983-2009 ANNALS OF SURGICAL ONCOLOGY Cloyd, J. M., Hernandez-Boussard, T., Wapnir, I. L. 2013; 20 (5): 1545-1550

    Abstract

    Although mastectomy is considered the gold standard for male breast cancer (MBC), the utilization of lumpectomy and its impact on outcomes in MBC patients has not been previously studied.The Surveillance, Epidemiology and End Results (SEER) database was used to identify all MBC patients who underwent either mastectomy or less than mastectomy (i.e., lumpectomy) between 1983 and 2009.A total of 4707 (86.8 %) men underwent mastectomy and 718 (13.2 %) underwent lumpectomy. A greater proportion of patients underwent lumpectomy later in the study period (1983 to 1986, 10.6 %, vs. 2007 to 2009, 15.1 %). A greater percentage of lumpectomy patients were 80 years or older (21.3 % vs. 16.3 %), had stage IV disease (7.3 % vs. 3.1 %), and received no lymph node sampling (34.3 % vs. 6.9 %). Only 35.4 % of patients underwent adjuvant radiotherapy after lumpectomy. Ten-year breast cancer-specific survival and overall survival were 82.8 % and 46.9 %, respectively, in lumpectomy patients vs. 77.3 % and 46.4 %, respectively, in mastectomy patients. On Cox proportional hazards regression, lumpectomy was not independently associated with worse breast cancer-specific survival (odds ratio 1.09, 95 % confidence interval 0.87-1.37) or overall survival (odds ratio 1.12, 95 % confidence interval 0.98-1.27) after controlling for age, race, stage, and grade, as well as whether radiotherapy was received.Lumpectomy is performed in a small but growing proportion of MBC patients. These patients are not only older and more likely to have advanced disease at the time of diagnosis, but they also are less likely to receive standard of care therapy, such as lymph node sampling and adjuvant radiotherapy. Despite these observations, breast cancer-specific survival is unaffected by the type of surgery.

    View details for DOI 10.1245/s10434-013-2918-5

    View details for Web of Science ID 000317308200021

  • Nonmelanoma Skin Cancer Visits and Procedure Patterns in a Nationally Representative Sample: National Ambulatory Medical Care Survey 1995-2007 DERMATOLOGIC SURGERY Wysong, A., Linos, E., Hernandez-Boussard, T., Arron, S. T., Gladstone, H., Tang, J. Y. 2013; 39 (4): 596-602

    Abstract

    The rising incidence of nonmelanoma skin cancer (NMSC) is well documented, but data are limited on the number of visits and treatment patterns of NMSC in the outpatient setting.To evaluate practice and treatment patterns of NMSC in the United States over the last decade and to characterize differences according to sex, age, race, insurance type, and physician specialty.Adults with an International Classification of Diseases, Ninth Revision, diagnosis of NMSC were included in this cross-sectional survey study of the National Ambulatory Medical Care Survey between 1995 and 2007. Primary outcomes included population-adjusted NMSC visit rates and odds ratios of receiving a procedure for NMSC using logistic regression.Rates of NMSC visits increased between 1995 and 2007. The number of visits was significantly higher in men, particularly those aged 65 and older. Fifty-nine percent of NMSC visits were associated with a procedure, and the individuals associated with that visit were more likely to be male, to be seen by a dermatologist, and to have private-pay insurance.Nonmelanoma skin cancer visit rates increased from 1995 to 2007 and were higher in men than women. Visits to a dermatologist are more likely to be associated with a procedure for NMSC, and there may be discrepancies in treatment patterns based on insurance type and sex.

    View details for DOI 10.1111/dsu.12092

    View details for Web of Science ID 000317018200010

  • Overlapping meta-analyses on the same topic: survey of published studies. BMJ (Clinical research ed.) Siontis, K. C., Hernandez-Boussard, T., Ioannidis, J. P. 2013; 347: f4501-?

    Abstract

    To assess how common it is to have multiple overlapping meta-analyses of randomized trials published on the same topic.Survey of published meta-analyses.PubMed.Meta-analyses published in 2010 were identified, and 5% of them were randomly selected. We further selected those that included randomized trials and examined effectiveness of any medical intervention. For eligible meta-analyses, we searched for other meta-analyses on the same topic (covering the same comparisons, indications/settings, and outcomes or overlapping subsets of them) published until February 2013.Of 73 eligible meta-analyses published in 2010, 49 (67%) had at least one other overlapping meta-analysis (median two meta-analyses per topic, interquartile range 1-4, maximum 13). In 17 topics at least one author was involved in at least two of the overlapping meta-analyses. No characteristics of the index meta-analyses were associated with the potential for overlapping meta-analyses. Among pairs of overlapping meta-analyses in 20 randomly selected topics, 13 of the more recent meta-analyses did not include any additional outcomes. In three of the four topics with eight or more published meta-analyses, many meta-analyses examined only a subset of the eligible interventions or indications/settings covered by the index meta-analysis. Conversely, for statins in the prevention of atrial fibrillation after cardiac surgery, 11 meta-analyses were published with similar eligibility criteria for interventions and setting: there was still variability on which studies were included, but the results were always similar or even identical across meta-analyses.While some independent replication of meta-analyses by different teams is possibly useful, the overall picture suggests that there is a waste of efforts with many topics covered by multiple overlapping meta-analyses.

    View details for DOI 10.1136/bmj.f4501

    View details for PubMedID 23873947

  • Differences in readmissions after open repair versus endovascular aneurysm repair JOURNAL OF VASCULAR SURGERY Casey, K., Hernandez-Boussard, T., Mell, M. W., Lee, J. T. 2013; 57 (1): 89-95

    Abstract

    Reintervention rates after repair of abdominal aortic aneurysm (AAA) are higher for endovascular repair (EVAR) than for open repair, mostly due to treatment for endoleaks, whereas open surgical operations for bowel obstruction and abdominal hernias are higher after open repair. However, readmission rates after EVAR or open repair for nonoperative conditions and complications that do not require an intervention are not well documented. We sought to determine reasons for all-cause readmissions within the first year after open repair and EVAR.Patients who underwent elective AAA repair in California during a 6-year period were identified from the Health Care and Utilization Project State Inpatient Database. All patients who had a readmission in California ≤1 year of their index procedure were included for evaluation. Readmission rates and primary and secondary diagnoses associated with each readmission were analyzed and recorded.From 2003 to 2008, there were 15,736 operations for elective AAA repair, comprising 9356 EVARs (60%) and 6380 open repairs (40%). At 1 year postoperatively, the readmission rate was 52.1% after open repair and 55.4% after EVAR (P=.0003). The three most common principle diagnoses associated with readmission after any type of AAA repair were failure to thrive, cardiac issues, and infection. When stratified by repair type, patients who underwent open repair were more likely to be readmitted with primary diagnoses associated with failure to thrive, cardiac complications, and infection compared with EVAR (all P<.001). Those who underwent EVAR were more likely, however, to be readmitted with primary diagnoses of device-related complications (P=.05), cardiac complications, and infection.Total readmission rates within 1 year after elective AAA repair are greater after EVAR than after open repair. Reasons for readmission vary between the two cohorts but are related to the magnitude of open surgery after open repair, device issues after EVAR, and the usual cardiac and infectious complications after either intervention. Systems-based analysis of these causes of readmission can potentially improve patient expectations and care after elective aneurysm repair.

    View details for DOI 10.1016/j.jvs.2012.07.005

    View details for Web of Science ID 000312833800016

  • The Epidemiology of Idiopathic Acute Pancreatitis, Analysis of the Nationwide Inpatient Sample From 1998 to 2007 PANCREAS Chen, Y., Zak, Y., Hernandez-Boussard, T., Park, W., Visser, B. C. 2013; 42 (1): 1-5

    Abstract

    The study aimed to better define the epidemiology of idiopathic acute pancreatitis (IAP).We identified admissions with primary diagnosis of acute pancreatitis (AP) in Nationwide Inpatient Sample between 1998 and 2007. Idiopathic AP was defined as all cases after excluding International Classification of Diseases, Ninth Revision, codes for other causes of AP (including biliary, alcoholic, trauma, iatrogenic, hyperparathyroidism, hyperlipidemia, etc).Among the primary admissions for AP, 26.9% had biliary pancreatitis, 25.1% alcoholic, and 36.5% idiopathic. Idiopathic AP had estimated 81,8025 admissions with a mean hospitalization of 5.6 days. Patients with IAP accounted for almost half of the fatalities among the cases of AP (48.2%) and had a higher mortality rate than both patients with biliary pancreatitis and patients with alcoholic pancreatitis (1.9%, 1.5%, and 1.0%, respectively, P < 0.01). Forty-six percent of patients with biliary pancreatitis underwent cholecystectomy during the index hospitalization, compared with 0.42% of patients with IAP. Patients with IAP had a demographic distribution similar to that of patients with biliary AP (female predominant and older), which was distinct from patients with alcoholic pancreatitis (male predominant and younger). There was a gradual but steady decrease in the incidence of IAP, from 41% in 1998 to 30% in 2007.Despite improving diagnostics, IAP remains a common clinical problem with a significant mortality. Standardization of the clinical management of these patients warrants further investigation.

    View details for DOI 10.1097/MPA.0b013e3182572d3a

    View details for Web of Science ID 000312560200001

  • Normal Alcohol Metabolism after Gastric Banding and Sleeve Gastrectomy: A Case-Cross-Over Trial JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS Changchien, E. M., Woodard, G. A., Hernandez-Boussard, T., Morton, J. M. 2012; 215 (4): 475-479

    Abstract

    Severe obesity remains the leading public health concern of the industrialized world, with bariatric surgery as the only current effective enduring treatment. In addition to gastric bypass, gastric banding and sleeve gastrectomy have emerged as viable treatment options for the severely obese. Occasionally, poor postoperative psychological adjustment has been reported. It has been previously demonstrated that breath alcohol content (BAC) levels and time to sober were increased in postoperative gastric bypass patients. The aim of this study was to examine whether alcohol metabolism in patients undergoing restrictive-type bariatric procedures is also altered.Nine patients undergoing laparoscopic adjustable gastric banding (LAGB) and 7 patients undergoing laparoscopic sleeve gastrectomy (LSG) were recruited. Preoperatively, 3-month and 6-month BAC and time to sober were measured after administration of 5 ounces of red wine. In addition, participants were asked to complete a questionnaire of drinking habits.The 16 total participants achieved a mean 44.7% 6-month excess weight loss. There were no significant changes in peak BAC or time to sober from preoperative levels (0.033%, 67.8 min, respectively) to 3 months (0.032%, 77.1 min, respectively, p = 0.421) or 6 months (0.035%, 81.2 min, respectively, p = 0.198).Patients undergoing LAGB and LSG do not share the same altered alcohol metabolism as seen in gastric bypass patients. However, all bariatric surgery patients should be counseled regarding alcohol use.

    View details for DOI 10.1016/j.jamcollsurg.2012.06.008

    View details for Web of Science ID 000308910300003

    View details for PubMedID 22770864

  • Predictors of emergency department death for patients presenting with ruptured abdominal aortic aneurysms JOURNAL OF VASCULAR SURGERY Mell, M. W., Callcut, R. A., Bech, F., Delgado, M. K., Staudenmayer, K., Spain, D. A., Hernandez-Boussard, T. 2012; 56 (3): 651-655

    Abstract

    Ruptured abdominal aortic aneurysm (rAAA) is a critically time-sensitive condition with outcomes dependent on rapid diagnosis and definitive treatment. Emergency department (ED) death reflects the hemodynamic stability of the patient upon arrival and the ability to mobilize resources before hemodynamic stability is lost. The goals of this study were to determine the incidence and predictors of ED death for patients presenting to EDs with rAAAs.Data for patients presenting with International Classification of Disease, 9th Revision, Clinical Modification codes for rAAA from 2006 to 2008 were extracted from discharge data using the Nationwide Emergency Department Sample (NEDS), Healthcare Cost and Utilization Project, and Agency for Healthcare Research and Quality. The NEDS is the largest stratified weighted sample of US hospital-based ED visits with links to inpatient files. We compared those transferred to those admitted and treated. Sample weights were applied to produce nationally representative estimates. Patient and hospital factors associated with transfer were identified using multivariate logistic regression. These factors were then analyzed for a relationship with ED deaths.A total of 18,363 patients were evaluated for rAAAs. Of these, 7% (1201) died in the ED, 6% (1160) were admitted and died without a procedure, 42% (7731) were admitted and died after repair, and 41% (7479) were admitted, treated, and survived. Transfers accounted for 4% (793) of all ED visits for rAAAs. ED death was more likely for patients seen in nonmetropolitan hospitals (12.7%) vs metropolitan nonteaching (7.0%) or metropolitan teaching hospitals (4.5%; P < .0001). Compared with other regions, the West had a higher ED mortality rate (9.6% vs 5.1%-6.9%; P = .0038). On multivariate analysis, ED death was associated with hospital groups exhibiting both high and low transfer rates.ED death remains a significant cause for mortality for rAAAs and varies by hospital type, rural/urban location, and geographic region. Both delays in ED arrival and delays in providing definitive care may contribute to increased ED death rates, suggesting that improved regional systems of care may improve survival after rAAA.

    View details for DOI 10.1016/j.jvs.2012.02.025

    View details for Web of Science ID 000308085500010

    View details for PubMedID 22560234

  • Pathologic Response to Preoperative Chemotherapy in Colorectal Liver Metastases: Fibrosis, not Necrosis, Predicts Outcome ANNALS OF SURGICAL ONCOLOGY Poultsides, G. A., Bao, F., Servais, E. L., Hernandez-Boussard, T., DeMatteo, R. P., Allen, P. J., Fong, Y., Kemeny, N. E., Saltz, L. B., Klimstra, D. S., Jarnagin, W. R., Shia, J., D'Angelica, M. I. 2012; 19 (9): 2797-2804

    Abstract

    Pathologic response to preoperative chemotherapy for colorectal liver metastases (CLM) is associated with survival after hepatectomy. Histologically, dominant response patterns include fibrosis, necrosis and/or acellular mucin, but some of these changes can appear without previous chemotherapy and their individual correlation with outcome is unknown.Pathology slides from patients who underwent CLM resection (irrespective of preoperative chemotherapy status) were rereviewed by a blinded pathologist. Pathologic response was recorded as the summation of percentage necrosis, fibrosis and acellular mucin. Associations between pathologic response, its components, preoperative chemotherapy, and survival were analyzed.Pathology slides were rereviewed in 366 patients undergoing CLM resection from 2003 to 2007. Preoperative chemotherapy was administered in 249 (68 %) patients, who, when compared to no preoperative chemotherapy patients, had higher rates of overall pathologic response (57 vs. 46 %, P < .01), fibrosis (21 vs. 12 %, P < .01) and acellular mucin (6 vs. 3 %, P = .05) but similar rates of necrosis (30 vs. 31 %, P = .30). In patients receiving preoperative chemotherapy, overall pathologic response ? 75 % (5 year, 83 vs. 47 %, P < .01) and fibrosis ? 40 % (5 year, 87 vs. 51 %, P < .01) independently correlated with disease-specific survival after hepatectomy. Preoperative hepatic artery infusion chemotherapy (P = .04) and bevacizumab (P = .05) were marginally associated with overall pathologic response and fibrosis, respectively.Fibrosis is the predominant chemotherapy-related pathologic alteration driving the association of treatment response with survival after CLM resection. Necrosis in CLM is not related to chemotherapy or outcome.

    View details for DOI 10.1245/s10434-012-2335-1

    View details for Web of Science ID 000308357100005

    View details for PubMedID 22476753

  • Long-term results after accessory renal artery coverage during endovascular aortic aneurysm repair Greenberg, J. I., Dorsey, C., Dalman, R. L., Lee, J. T., Harris, E. J., Hernandez-Boussard, T., Mell, M. W. MOSBY-ELSEVIER. 2012: 291-297

    Abstract

    Current information regarding coverage of accessory renal arteries (ARAs) during endovascular aneurysm repair (EVAR) is based on small case series with limited follow-up. This study evaluates the outcomes of ARA coverage in a large contemporary cohort.Consecutive EVAR data from January 2004 to August 2010 were collected in a prospective database at a University Hospital. Patient and aneurysm-related characteristics, imaging studies, and ARA coverage versus preservation were analyzed. Volumetric analysis of three-dimensional reconstruction computed tomography scans was used to assess renal infarction volume extent. Long-term renal function and overall technical success of aneurysm exclusion were compared.A cohort of 426 EVARs was identified. ARAs were present in 69 patients with a mean follow-up of 27 months (range, 1 to 60 months). Forty-five ARAs were covered in 40 patients; 29 patients had intentional ARA preservation. Patient and anatomic characteristics were similar between groups except that ARA coverage patients had shorter aneurysm necks (P = .03). Renal infarctions occurred in 84% of kidneys with covered ARAs. There was no significant deterioration in long-term glomerular filtration rate when compared with patients in the control group. No difference in the rate of endoleak, secondary procedures, or the requirement for antihypertensive medications was found.This study is the largest to date with the longest follow-up relating to ARA coverage. Contrary to previous reports, renal infarction after ARA coverage is common. Nevertheless, coverage is well tolerated based upon preservation of renal function without additional morbidity. These results support the long-term safety of ARA coverage for EVAR when necessary.

    View details for DOI 10.1016/j.jvs.2012.01.049

    View details for Web of Science ID 000307160400002

    View details for PubMedID 22480767

  • Obesity Disparities in Preventive Care: Findings From the National Ambulatory Medical Care Survey, 2005-2007 OBESITY Hernandez-Boussard, T., Ahmed, S. M., Morton, J. M. 2012; 20 (8): 1639-1644

    Abstract

    Obesity and its consequences are a major health concern. There are conflicting reports regarding utilization of preventive health-care services among obese patients. Our objective was to determine whether obese patients receive the same preventive care as normal weight patients. Weighted patient clinic visit data from the National Ambulatory Medical Care Survey (NAMCS) were analyzed for all adult patient visits with height/weight data (N = 866,415,856) from 2005 to 2007. Preventive care practice patterns were compared among different weight groups of normal, obese, and morbidly obese. Obese patients received the least number of preventive exams with a clear gradient present by weight. Obese patients were significantly less likely to receive cancer screening including breast examination (normal weight, reference, obese, odds ratio (OR), 0.8), mammogram (obese OR, 0.7), pap smear (obese OR, 0.7), pelvic exam (obese OR, 0.8), and rectal exam (obese OR, 0.7). The obese population also received less tobacco (obese OR, 0.7) and injury prevention education (obese OR, 0.7), yet significantly more diet, exercise, and weight reduction education. Significant differences in clinic practice patterns relative to normal weight patients were also evident with more physician referral (obese OR, 1.2) and less likely to see physician at the index clinic visit (obese OR, 0.8) and less likely to receive psychotherapy referral (obese OR, 0.6). Significant gaps in preventive care exist for the obese including cancer screening, tobacco cessation and injury prevention counseling, and psychological referral. Although obese patients received more weight-related education, this emphasis may have the consequence of de-emphasizing other needed preventive health measures.

    View details for DOI 10.1038/oby.2011.258

    View details for Web of Science ID 000306920900013

    View details for PubMedID 21818146

  • Laparoscopic vs Open Gastric Bypass Surgery Differences in Patient Demographics, Safety, and Outcomes ARCHIVES OF SURGERY Banka, G., Woodard, G., Hernandez-Boussard, T., Morton, J. M. 2012; 147 (6): 550-556

    Abstract

    To determine national outcome differences between laparoscopic Roux-en-Y gastric bypass (LRYGB) and open Roux-en-Y gastric bypass (ORYGB).Retrospective cohort study.The Nationwide Inpatient Sample.Patients undergoing ORYGB and LRYGB.Outcome measures were number of procedures performed, patient and hospital characteristics, patient complications, mortality, length of stay, resource use, and Agency for Healthcare Research and Quality Patient Safety Indicators. Both demographic and outcomes variables were compared by either t test or ?2 analysis, with regression analysis adjusting for confounding variables.The ORYGB and LRYGB cohorts consisted of 41 094 and 115 177 cases, respectively. From 2005 to 2007, LRYGB was more commonly performed than ORYGB (72% vs 28%; P < .001) and at high-volume hospitals (69% vs 61%; P < .001). A higher percentage of ORYGB compared with LRYGB patients were Medicare (9.3% vs 7.1%) and Medicaid (10.4% vs 5.9%; P < .01) beneficiaries. More ORYGB patients compared with LRYGB patients were discharged with nonroutine dispositions (7.7% vs 2.4%; P = .005), died (0.2% vs 0.1%; P < .001), and had 1 or more complications (18.7% vs 12.3%; P < .001). All Patient Safety Indicator rates were higher for ORYGB. Patients who had ORYGB compared with LRYGB also had longer median lengths of stay (3.5 vs 2.4 days; P < .001) and higher total charges ($35 018 vs $32 671; P < .001). Patients who had LRYGB had a lower odds ratio than patients who had ORYGB for both mortality (odds ratio, 0.54; P < .001) and having 1 or more complications (odds ratio, 0.66; P < .001) even after adjusting for confounding variables.In this population-based study, LRYGB provided greater safety than ORYGB even after adjusting for patient-level socioeconomic and comorbidity differences.

    View details for Web of Science ID 000305428500014

    View details for PubMedID 22786543

  • Effect of Roux-en-Y gastric bypass on testosterone and prostate-specific antigen BRITISH JOURNAL OF SURGERY Woodard, G., Ahmed, S., Podelski, V., Hernandez-Boussard, T., Presti, J., Morton, J. M. 2012; 99 (5): 693-698

    Abstract

    Obese men have lower serum levels of testosterone, dehydroepiandrosterone (DHEA) and prostate-specific antigen (PSA), but an increased risk of dying from prostate cancer. The aim of this study was to examine the effect of surgically induced weight loss on serum testosterone, DHEA and PSA levels in obese men.Consecutive men undergoing Roux-en-Y gastric bypass (RYGB) participated in a prospective, longitudinal study. Main outcomes were changes were body mass index (BMI), percentage excess weight loss, serum levels of testosterone, DHEA and PSA, PSA mass and plasma volume, measured before operation and 3, 6 and 12 months later.In 64 patients, mean BMI fell from 48.2 kg/m(2) before operation to 39.2, 35.6 and 32.4 kg/m(2) at 3, 6 and 12 months after RYGB. Testosterone levels rose significantly from 259 ng/dl to 386, 452 and 520 ng/dl respectively. Serum PSA levels increased significantly from 0.51 ng/ml to 0.67 ng/ml at 12 months. There were no significant changes in DHEA or PSA mass.RYGB normalizes the serum testosterone level. PSA levels increase with weight loss and may be inversely correlated with changes in plasma volume, indicating that PSA levels may be artificially low in obese men owing to haemodilution.

    View details for DOI 10.1002/bjs.8693

    View details for Web of Science ID 000303150700016

    View details for PubMedID 22302466

  • Determinants of Adverse Events in Vascular Surgery JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS Hernandez-Boussard, T., McDonald, K. M., Morton, J. M., Dalman, R. L., Bech, F. R. 2012; 214 (5): 788-797

    Abstract

    Patient safety is a national priority. Patient Safety Indicators (PSIs) monitor potential adverse events during hospital stays. Surgical specialty PSI benchmarks do not exist, and are needed to account for differences in the range of procedures performed, reasons for the procedure, and differences in patient characteristics. A comprehensive profile of adverse events in vascular surgery was created.The Nationwide Inpatient Sample was queried for 8 vascular procedures using ICD-9-CM codes from 2005 to 2009. Factors associated with PSI development were evaluated in univariate and multivariate analyses.A total of 1,412,703 patients underwent a vascular procedure and a PSI developed in 5.2%. PSIs were more frequent in female, nonwhite patients with public payers (p < 0.01). Patients at mid and low-volume hospitals had greater odds of developing a PSI (odds ratio [OR] = 1.17; 95% CI, 1.10-1.23 and OR = 1.69; 95% CI, 1.53-1.87). Amputations had highest PSI risk-adjusted rate and carotid endarterectomy and endovascular abdominal aortic aneurysm repair had lower risk-adjusted rate (p < 0.0001). PSI risk-adjusted rate increased linearly by severity of patient indication: claudicants (OR = 0.40; 95% CI, 0.35-0.46), rest pain patients (OR = 0.78; 95% CI, 0.69-0.90), ulcer (OR = 1.20; 95% CI, 1.07-1.34), and gangrene patients (OR = 1.85; 95% CI, 1.66-2.06).Patient safety events in vascular surgery were high and varied by procedure, with amputations and open abdominal aortic aneurysm repair having considerably more potential adverse events. PSIs were associated with black race, public payer, and procedure indication. It is important to note the overall higher rates of PSIs occurring in vascular patients and to adjust benchmarks for this surgical specialty appropriately.

    View details for DOI 10.1016/j.jamcollsurg.2012.01.045

    View details for Web of Science ID 000303724200009

    View details for PubMedID 22425449

  • Relationship between Patient Safety and Hospital Surgical Volume HEALTH SERVICES RESEARCH Hernandez-Boussard, T., Downey, J. R., McDonald, K., Morton, J. M. 2012; 47 (2): 756-769

    Abstract

    To examine the relationship between hospital volume and in-hospital adverse events.Patient safety indicator (PSI) was used to identify hospital-acquired adverse events in the Nationwide Inpatient Sample database in abdominal aortic aneurysm, coronary artery bypass graft, and Roux-en-Y gastric bypass from 2005 to 2008.In this observational study, volume thresholds were defined by mean year-specific terciles. PSI risk-adjusted rates were analyzed by volume tercile for each procedure.Overall, hospital volume was inversely related to preventable adverse events. High-volume hospitals had significantly lower risk-adjusted PSI rates compared to lower volume hospitals (p < .05).These data support the relationship between hospital volume and quality health care delivery in select surgical cases. This study highlights differences between hospital volume and risk-adjusted PSI rates for three common surgical procedures and highlights areas of focus for future studies to identify pathways to reduce hospital-acquired events.

    View details for DOI 10.1111/j.1475-6773.2011.01310.x

    View details for Web of Science ID 000301229300012

    View details for PubMedID 22091561

  • "Phantom" Publications Among Plastic Surgery Residency Applicants ANNALS OF PLASTIC SURGERY Chung, C. K., Hernandez-Boussard, T., Lee, G. K. 2012; 68 (4): 391-395

    Abstract

    Previous studies in other medical specialties have shown a significant percentage of publications represented in residency applications are not actually published. A comprehensive evaluation of applicants to plastic surgery residency over an extended period has not been previously reported in the literature. The purpose of our study was to determine the incidence of misrepresented or "phantom" publications in plastic surgery residency applicants and to identify possible predisposing characteristics.We used the Electronic Residency Application Services database to our plastic surgery residency program during a 4-year period from 2006 to 2009. Applicant demographic information and listed citations were extracted. Peer-reviewed journal article citations were verified using robust methods including PubMed, Institute for Scientific Information (ISI) Web of Knowledge, and Google. Unverifiable articles were categorized as phantom publications and then evaluated with respect to applicant demographic information and characteristics.During the 4-year study period, there were 804 applications (average, 201 applicants per year). There was a total of 4725 publications listed; of which, 1975 had been categorized as peer-reviewed journal articles. Two hundred seventy-six (14%) of peer-reviewed publications could not be verified and were categorized as phantom publications. There was an overall significant positive trend in percentage of phantom publications during the 4 application years (P = 0.005). A positive predictive factor for having phantom publications was being a foreign medical graduate (P = 0.02). A negative predictive factor for phantom publications was being a female applicant (P = 0.03). There also appeared to be a positive correlation with the number of publications listed and likelihood of phantom publications.Among plastic surgery residency applicants, we found a significant percentage of unverifiable publications. There are several possible explanations for our findings, which include the fact that plastic surgery is a highly sought-after specialty and applicants may feel the need to appear competitive to residency programs. Publications are an important aspect of the residency selection process and factors into applicant ranking, but our study suggests publications listed in plastic surgery residency applications may not necessarily be an accurate representation of actual published articles. Program directors and faculty are advised to scrutinize listed publications carefully when evaluating applicants.

    View details for DOI 10.1097/SAP.0b013e31823d2c4e

    View details for Web of Science ID 000301800600015

    View details for PubMedID 22421486

  • Is Patient Safety Improving? National Trends in Patient Safety Indicators: 1998-2007 HEALTH SERVICES RESEARCH Downey, J. R., Hernandez-Boussard, T., Banka, G., Morton, J. M. 2012; 47 (1): 414-430

    Abstract

    Emphasis has been placed on quality and patient safety in medicine; however, little is known about whether quality over time has actually improved in areas such as patient safety indicators (PSIs).To determine whether national trends for hospital PSIs have improved from 1998 to 2007.Using PSI criteria from the Agency for Healthcare Research and Quality, PSIs were identified in the Nationwide Inpatient Sample (NIS) for all eligible inpatient admissions between 1998 and 2007. Joinpoint regression was used to estimate annual percentage changes (APCs) for PSIs.Annual percent change for PSIs.From 1998 to 2007, 7.6 million PSI events occurred for over 69 million hospitalizations. A total of 14 PSIs showed statistically significant trends. Seven PSIs had increasing APC: postoperative pulmonary embolism or deep vein thrombosis (8.94), postoperative physiological or metabolic derangement (7.67), postoperative sepsis (7.17), selected infections due to medical care (4.05), decubitus ulcer (3.05), accidental puncture or laceration (2.64), and postoperative respiratory failure (1.46). Seven PSIs showed decreasing APCs: birth trauma injury to neonate (-17.79), failure to rescue (-6.05), postoperative hip fracture (-5.86), obstetric trauma-vaginal without instrument (-5.69), obstetric trauma-vaginal with instrument (-4.11), iatrogenic pneumothorax (-2.5), and postoperative wound dehiscence (-1.8).This is the first study to establish national trends of PSIs during the past decade indicating areas for potential quality improvement prioritization. While many factors influence these trends, the results indicate opportunities for either emulation or elimination of current patient safety trends.

    View details for DOI 10.1111/j.1475-6773.2011.01361.x

    View details for Web of Science ID 000299041600007

    View details for PubMedID 22150789

  • A National Study on Craniosynostosis Surgical Repair. The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association Nguyen, C., Hernandez-Boussard, T., Khosla, R. K., Curtin, C. M. 2012

    Abstract

    Objective :? Our study aimed to use national data to assess the perioperative outcomes of craniosynostosis surgical repair. Design :? Data were obtained from the Agency for Healthcare Research and Quality Healthcare Cost and Utilization Project Kids Inpatient Database from 1997, 2000, 2003, and 2006. Setting :? Community hospitals in the United States. Patients :? The cohort was identified using the ICD-9-CM procedure codes for craniosynostosis surgical repair (2.01, 2.03, 2.04, 2.06). Main Outcome Measures(s) :? We determined patient and hospital characteristics. We clustered patients by age group (<7 months, 7 to 12 months, 1 to 3 years) and assessed mortality, comorbidities, mean length of stay (LOS), and total charge. We performed logistic regression with our dependent variable being longer average hospital stay: LOS >4.2 days. Results :? We found 3426 patients. Average age at the time of surgery was 181 days (SD 84). Average length of stay was 4.2 days. The majority of the patients were boys (66%), white (71%), and insured (93%). Nearly all patients underwent surgery in a teaching hospital (98%) in urban centers (99%). Approximately 10% of patients experienced an acute complication, most commonly hemorrhages or hematomas and airway or respiratory failure. Patients ages 1 to 3 years had the highest rates of comorbidities and a longer LOS. Mortality rate was <1%. Conclusions :? Craniosynostosis surgery is safe with low rates of mortality and acute complications. LOS >4.2 appears to be associated more with comorbidities than with complications. Higher rates of comorbidities and LOS >4.2 days for patients age 1 to 3 years warrant addition research to assess potential barriers to care.

    View details for PubMedID 23030675

  • Halo Effect for Bariatric Surgery: Collateral Weight Loss in Patients' Family Members (vol 146, pg 1185, 2011) ARCHIVES OF SURGERY Woodard, G. A., Encarnacion, B., Peraza, J., Hernandez-Boussard, T., Morton, J. 2011; 146 (12): 1410-1410

    View details for Web of Science ID 000298256900020

  • Halo Effect for Bariatric Surgery Collateral Weight Loss in Patients' Family Members ARCHIVES OF SURGERY Woodard, G. A., Encarnacion, B., Peraza, J., Hernandez-Boussard, T., Morton, J. 2011; 146 (10): 1185-1190

    Abstract

    Bariatric surgery is an effective treatment for morbid obesity, which is increasingly recognized as a familial disease. Healthy behavior transmission may be enhanced by family relationships.To determine changes in weight and healthy behavior in patients who underwent Roux-en-Y gastric bypass surgery and their family members.Prospective, longitudinal, and multidimensional health assessment before and 1 year after index Roux-en-Y gastric bypass surgery.An academic bariatric center of excellence, from January 1, 2007, through December 31, 2009.Eighty-five participants (35 patients, 35 adult family members, and 15 children <18 years old).Roux-en-Y gastric bypass surgery and associated dietary and lifestyle counseling.Weight and expected body mass index (calculated as weight in kilograms divided by height in meters squared). Secondary outcomes were waist circumference, quality of life (36-Item Short Form or Pediatric Quality of Life Inventory), healthy behaviors, eating behaviors, and activity levels.Participants were grouped by relationship to patient for analysis with paired 2-sample t tests. Before the operation, 60% of adult family members and 73% of children of patients undergoing Roux-en-Y gastric bypass surgery were obese. At 12 months after the operation, significant weight loss was observed in obese adult family members (from 234 to 226 lb; P = .01). There was a trend for obese children to have a lower body mass index than expected for their growth curve (31.2 expected vs 29.6 observed; P = .07). Family members increased their daily activity levels (adults, from 8 to 17 metabolic equivalent task-hours, P = .005; and children, from 13 to 22, P = .04). Adult family members also had improved eating habits with less uncontrollable eating (from 35 to 28; P = .01), emotional eating (from 36 to 28; P = .04), and alcohol consumption (from 11 drinks per month to 1 drink per month; P = .009).Gastric bypass surgery may render an additional benefit of weight loss and improved healthy behavior for bariatric patients' family members.

    View details for Web of Science ID 000295942300018

    View details for PubMedID 22006878

  • Another Use of the Mobile Device: Warm-up for Laparoscopic Surgery JOURNAL OF SURGICAL RESEARCH Plerhoples, T. A., Zak, Y., Hernandez-Boussard, T., Lau, J. 2011; 170 (2): 185-188

    Abstract

    An important facet of laparoscopic surgery is its psychomotor component. As this aspect of surgery gains attention, lessons from other psychomotor-intense fields such as athletics have led to an investigation of the benefits of "warming up" prior to entering the operating room. Practical implementation of established methods of warm-up is hampered by a reliance on special equipment and instrumentations that are not readily available. In light of emerging evidence of translatability between video-game play and operative performance, we sought to find if laparoscopic task performance improved after warming up on a mobile device balance game.Laparoscopic novices were randomized into either the intervention group (n = 20) or the control group (n = 20). The intervention group played a mobile device balance game for 10 min while the control group did no warm-up whatsoever. Assessment was performed using two tasks on the ProMIS laparoscopic simulation system: "object positioning" (where small beads are transferred between four cups) and "tissue manipulation" (where pieces of plastic are stretched over pegs). Metrics measured were time to task completion, path length, smoothness, hand dominance, and errors.The intervention group made fewer errors: object positioning task 0.20 versus 0.70, P = 0.01, tissue manipulation task 0.15 versus 0.55, P = 0.05, total errors 0.35 versus 1.25, P = 0.002. The two groups performed similarly on the other metrics.Warm-up using a mobile device balance game decreases errors on basic tasks performed on a laparoscopic surgery simulator, suggesting a practical way to warm-up prior to cases in the operating room.

    View details for DOI 10.1016/j.jss.2011.03.015

    View details for Web of Science ID 000295128600013

    View details for PubMedID 21529831

  • Readmissions after Abdominal Aortic Aneurysm Repair: Differences between Open Repair and Endovascular Aneurysm Repair Casey, K. M., Hernandez-Boussard, T., Al-Khatib, W. K., Mell, M. W., Lee, J. T. MOSBY-ELSEVIER. 2011: 590-590

    View details for Web of Science ID 000293814400073

  • Under-Utilization of Transfer for Ruptured Abdominal Aortic Aneurysm (rAAA) in the Western United States JOURNAL OF VASCULAR SURGERY Mell, M. W., Callcut, R. A., Bech, F., Delgado, K., Staudenmayer, K., Spain, D. A., Hernandez-Boussard, T. 2011; 54 (2): 590-591

    View details for Web of Science ID 000293814400076

  • Doxorubicin pathways: pharmacodynamics and adverse effects PHARMACOGENETICS AND GENOMICS Thorn, C. F., Oshiro, C., Marsh, S., Hernandez-Boussard, T., McLeod, H., Klein, T. E., Altman, R. B. 2011; 21 (7): 440-446

    View details for DOI 10.1097/FPC.0b013e32833ffb56

    View details for Web of Science ID 000291633300011

    View details for PubMedID 21048526

  • B-type natriuretic peptide increases after gastric bypass surgery and correlates with weight loss Changchien, E. M., Ahmed, S., Betti, F., Higa, J., Kiely, K., Hernandez-Boussard, T., Morton, J. SPRINGER. 2011: 2338-2343

    Abstract

    Coronary artery disease is the primary cause of death in the United States, with obesity as a leading preventable risk factor. Previous studies have established the beneficial effect of Roux-en-Y gastric bypass on both weight and cardiac risk factors. Further assessment of cardiac function may be accomplished using B-type natriuretic peptide (BNP), which has demonstrated clinical utility in diagnosing congestive heart failure. This study aimed to assess changes in BNP after intentional weight loss through gastric bypass surgery.Plasma volume, weight, and BNP were measured preoperatively and at 3, 6, and 12 months postoperatively for 101 consecutive patients undergoing laparoscopic gastric bypass surgery by a single surgeon in an academic medical setting. Outcomes were compared by matched t-test. Multivariable linear regression and Pearson's correlation were used to examine predictors of pro-B-type natriuretic peptide (NT-proBNP) concentration.The concentration of BNP increased significantly from a mean preoperative level of 50.5 ng/l to postoperative levels of 73.9 ng/l at 3 months (P=0.013), 74.3 ng/l at 6 months (P<0.001), and 156.3 ng/l at 12 months (P<0.001). In addition, excess weight loss was the only statistically significant predictor of increased BNP concentration (odds ratio, 1.483; P<0.05).Gastric bypass leads to significant excess weight loss and surprisingly increased BNP concentrations. Correlation of BNP increase with weight loss suggests an additional novel mechanism for surgically induced weight loss.

    View details for DOI 10.1007/s00464-010-1565-1

    View details for Web of Science ID 000291690100039

    View details for PubMedID 21424205

  • Surgery for Thoracic Outlet Syndrome: A Nationwide Perspective Lee, J. T., Dua, M. M., Chandra, V., Hernandez-Boussard, T. M., Illig, K. A. MOSBY-ELSEVIER. 2011: 100S-101S

    View details for Web of Science ID 000291410700194

  • Adverse Events Following Digital Replantation in the Elderly JOURNAL OF HAND SURGERY-AMERICAN VOLUME Barzin, A., Hernandez-Boussard, T., Lee, G. K., Curtin, C. 2011; 36A (5): 870-874

    Abstract

    The decision to proceed with digital replantation in the elderly can be challenging. In addition to success of the replanted part, perioperative morbidity and mortality must be considered. The purpose of this study was to compare adverse events in patients less than 65 years of age compared with those 65 years and older after digital replantation. We hypothesize that there is an increased incidence of mortality and sentinel adverse events in patients aged 65 and older.We obtained data from the Nationwide Inpatient Sample over a 10-year period from 1998 to 2007. Replantation was identified using International Classification of Diseases-9 procedure codes for finger and thumb reattachment (84.21 and 84.22). Adverse events were identified using Patient Safety Indicators (PSI) to identify adverse events occurring during hospitalization. We used the Charlson index to study medical comorbidities and bivariate statistics.During the study period 15,413 finger and thumb replantations were performed in the United States, with 616 performed on patients age 65 and older. The overall in-hospital mortality was 0.04% with no statistical difference when factoring age. For the entire group, the percentage of PSI was 0.6%, the most common being postoperative deep venous thrombosis and pulmonary embolus. Overall, there was no difference in PSI between the 2 groups. The older group had a higher rate of transfusion, 4% versus 8% (p < .05) and were more likely to have a nonroutine disposition (ie, nursing home) (p < .001). We found no correlation between the Charlson index and PSI.This study found no difference in sentinel perioperative complications or mortality when comparing replantation patients under 65 years of age and those age 65 and older. Age alone should not be an absolute contraindication to finger replantation. Instead, the patient's functional demands, type of injury, general state of health, and rehabilitative potential should drive the decision of whether to proceed with replantation.

    View details for DOI 10.1016/j.jhsa.2011.01.031

    View details for Web of Science ID 000290185700017

  • Risk factors predictive of carotid artery stenting-associated subclinical microemboli. The International journal of angiology : official publication of the International College of Angiology, Inc Zhou, W., Zareie, R., Tedesco, M., Gholibeikian, S., Lane, B., Hernandez-Boussard, T., Rosen, A. 2011; 20 (1): 25-32

    Abstract

    Subclinical microemboli documented on diffusion-weighted magnetic resonance imaging (DWI) are common following carotid artery stenting (CAS) procedures despite absence of neurological symptoms. This study was to evaluate risk factors predictive of microemboli in patients undergoing protected CAS with a distal embolic protection device. All CAS patients who received pre- and postprocedural magnetic resonance imaging (MRI) evaluations for carotid interventions at a single academic institution from July 2004 to December 2008 were examined. Microemboli were defined by new hyperintensities on postoperative DWI with corresponding decreased diffusion. Risk factors including patient demographics, medical comorbidities, clinical symptoms, lesion morphologies, and perioperative information were examined, and logistic regression analyses were utilized to determine predictors of CAS-related microemboli. A total of 204 patients underwent carotid interventions (76 CAS and 128 carotid endarterectomies) during the study period; 167 of them, including 67 CAS patients, received both preoperative and postoperative MRIs. Among those who underwent protected CAS, the incidence of microemboli was 46.3% despite a relative low incidence of associated neurological symptoms (2.9%). Univariate and multivariate regression analyses showed that date of procedure (odds ratio [OR] 30.6 and p?=?0.019) and preoperative transient ischemic attack symptoms (OR 9.24 and p?=?0.009) were independent predictors of developing postoperative changes on DWI in the ipsilateral hemisphere, and age >76 years was predictive of having new lesions on DWI in the contralateral hemisphere (OR 6.11 and p?=?0.026). Our study underscores that certain risk factors are significantly associated with CAS-related microemboli and that physician experience and patient selection are essential in improving outcome of CAS procedures.

    View details for DOI 10.1055/s-0031-1272546

    View details for PubMedID 22532767

  • Impaired Alcohol Metabolism after Gastric Bypass Surgery: A Case-Crossover Trial JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS Woodard, G. A., Downey, J., Hernandez-Boussard, T., Morton, J. M. 2011; 212 (2): 209-214

    Abstract

    Severe obesity remains the leading public health crisis of the industrialized world, with bariatric surgery the only effective and enduring treatment. Poor psychological adjustment has been occasionally reported postoperatively. In addition, evidence suggests that patients can metabolize alcohol differently after gastric bypass.Preoperatively and at 3 and 6 months postoperatively, 19 Roux-en-Y gastric bypass (RYGB) patients' breath alcohol content (BAC) was measured every 5 minutes after drinking 5 oz red wine to determine peak BAC and time until sober in a case-crossover design preoperatively and at 6 months postoperatively.Patients reported symptoms experienced when intoxicated and answered a questionnaire of drinking habits. The peak BAC in patients after RYGB was considerably higher at 3 months (0.059%) and 6 months (0.088%) postoperatively than matched preoperative levels (0.024%). Patients also took considerably more time to return to sober at 3 months (61 minutes) and 6 months (88 minutes) than preoperatively (49 minutes). Postoperative intoxication was associated with lower levels of diaphoresis, flushing, and hyperactivity and higher levels of dizziness, warmth, and double vision. Postoperative patients reported drinking considerably less alcohol, fewer preferred beer, and more preferred wine than before surgery.This is the first study to match preoperative and postoperative alcohol metabolism in gastric bypass patients. Post-RYGB patients have much higher peak BAC after ingesting alcohol and require more time to become sober. Patients who drink alcohol after gastric bypass surgery should exercise caution.

    View details for DOI 10.1016/j.jamcollsurg.2010.09.020

    View details for Web of Science ID 000287466200010

    View details for PubMedID 21183366

  • Declining Incidence of Neonatal Endophthalmitis in the United States AMERICAN JOURNAL OF OPHTHALMOLOGY Moshfeghi, A. A., Charalel, R. A., Hernandez-Boussard, T., Morton, J. M., Moshfeghi, D. M. 2011; 151 (1): 59-65

    Abstract

    To determine the incidence of neonatal endogenous endophthalmitis in the United States between 1998 and 2006 and to identify associated risk factors.Retrospective cohort study.We used the Nationwide Inpatient Sample database, a 20% representative sample of all hospital discharges in the United States, to help refine our understanding of this condition. International Classification of Diseases, ninth edition, codes for endophthalmitis, sepsis, and suspected endophthalmitis risk factors in hospitalized infants and neonates were searched in the database and were tracked over time. The main outcome measure was incidence of neonatal endophthalmitis over the study period.Of 3.64 million live births in 1998, 317 newborns were identified with endophthalmitis (8.71 cases per 100 000 live births). Of 4.14 million live births in 2006, only 183 newborns were identified with endophthalmitis (4.42 cases per 100 000 live births) by comparison. The incidence of endophthalmitis decreased at a rate of 6% per year (P = .01130) between 1998 and 2006. Neonates with endophthalmitis were more likely to have systemic bacteremia (odds ratio, 21.114; P < .0001), Candidemia (odds ratio, 2.356; P < .0001), a birth weight of less than 1500 g (odds ratio, 1.215; P < .0001), and retinopathy of prematurity (odds ratio, 2.052; P < .0001).We objectively validated the commonly held belief that Candidemia, bacteremia, retinopathy of prematurity, and low birth weight are significant risk factors for endophthalmitis development in infants, which seems to have had a decreasing incidence in recent years.

    View details for DOI 10.1016/j.ajo.2010.07.008

    View details for Web of Science ID 000286081200011

    View details for PubMedID 20970776

  • Do Preventive Care Disparities Exist For the Obese? OBESITY Morton, J., Hernandez-Boussard, T. 2010; 18: S196-S196

    View details for Web of Science ID 000283811500684

  • Post-traumatic stress disorder (PTSD) is not a contraindication to gastric bypass in veterans with morbid obesity SURGICAL ENDOSCOPY AND OTHER INTERVENTIONAL TECHNIQUES Ikossi, D. G., Maldonado, J. R., Hernandez-Boussard, T., Eisenberg, D. 2010; 24 (8): 1892-1897

    Abstract

    The veteran population is routinely screened for post-traumatic stress disorder (PTSD). The prevalence of obesity in this population continues to increase. We examined whether weight loss outcomes in veterans with PTSD is comparable to results in veterans who do not suffer from PTSD, after gastric bypass. We also examined the effect of bariatric surgery on PTSD symptoms.This retrospective review of prospective data compares veterans with and without PTSD who underwent laparoscopic gastric bypass. Differences between the means of age, initial BMI, and percent excess weight loss were compared between the groups using a Student's t test. Pearson's chi(2) was used to evaluate the relationship between a diagnosis of PTSD, major depressive disorder (MDD), and other Axis I psychiatric disorders. A similar analysis was done to assess for a relationship between PTSD and obesity-related comorbidities, including diabetes mellitus (DM), hypertension (HTN), hyperlipidemia, and GERD.We identified 24 patients who had gastric bypass and a diagnosis of PTSD before surgery and compared them to those without PTSD. Both groups had a similar mean age and initial BMI. There was no significant difference between the percent excess weight lost after 1 year follow-up between the PTSD group (66%) and the non-PTSD group (72%) (p = 0.102). In assessing comorbid conditions, we found a significant association between the diagnosis of PTSD and MDD (p = 0.002), PTSD and other Axis I disorders (p = 0.004), and PTSD and GERD (p = 0.002). However, we saw no significant association between PTSD and DM (p = 0.977), HTN (p = 0.332), and obstructive sleep apnea (OSA) (p = 0.676). The severity of PTSD symptoms fluctuated in the postoperative period.Veterans with PTSD have comparable weight loss to those without PTSD after gastric bypass. In addition, surgery does not seem to have an adverse effect on PTSD symptoms, although PTSD symptomatology tends to fluctuate over time. Further study in this patient population is warranted.

    View details for DOI 10.1007/s00464-009-0866-8

    View details for Web of Science ID 000279488400015

    View details for PubMedID 20063014

  • A comparison of laparoscopic and robotic assisted suturing performance by experts and novices SURGERY Chandra, V., Nehra, D., Parent, R., Woo, R., Reyes, R., Hernandez-Boussard, T., Dutta, S. 2010; 147 (6): 830-839

    Abstract

    Surgical robotics has been promoted as an enabling technology. This study tests the hypothesis that use of the robotic surgical system can significantly improve technical ability by comparing the performance of both experts and novices on a complex laparoscopic task and a robotically assisted task.Laparoscopic experts (LE) with substantial laparoscopic and robotic experience (n = 9) and laparoscopic novices (LN) (n = 20) without any robotic experience performed sequentially 10 trials of a suturing task using either robotic or standard laparoscopic instrumentation fitted to the ProMIS surgical simulator. Objective performance metrics provided by ProMIS (total task time, instrument pathlength, and smoothness) and an assessment of learning curves were analyzed.Compared with LNs, the LEs demonstrated significantly better performance on all assessment measures. Within the LE group, there was no difference in smoothness (328 +/- 159 vs 355 +/- 174; P = .09) between robot-assisted and standard laparoscopic tasks. An improvement was noted in total task time (113 +/- 41 vs 132 +/- 55 sec; P < .05) and instrument pathlengths (371 +/- 163 vs 645 +/- 269 cm; P < .05) when using the robot. This advantage in terms of total task time, however, was lost among the LEs by the last 3 trials (114 +/- 40 vs 118 +/- 49 s; P = .84), while instrument pathlength remained better consistently throughout all the trials. For the LNs, performance was significantly better in the robotic trials on all 3 measures throughout all the trials.The ProMIS surgical simulator was able to distinguish between skill levels (expert versus novice) on robotic suturing tasks, suggesting that the ProMIS is a valid tool for measuring skill in robot-assisted surgery. For all the ProMIS metrics, novices demonstrated consistently better performance on a suturing task using robotics as compared to a standard laparoscopic setup. This effect was less evident for experts who demonstrated improvements only in their economy of movement (pathlength), but not in the speed or smoothness of performance. Robotics eliminated the early learning curve for novices, which was present when they used standard laparoscopic tools. Overall, this study suggests that, when performing complex tasks such as knot tying, surgical robotics is most useful for inexperienced laparoscopists who experience an early and persistent enabling effect. For experts, robotics is most useful for improving economy of motion, which may have implications for the highly complex procedures in limited workspaces (eg, prostatectomy).

    View details for DOI 10.1016/j.surg.2009.11.002

    View details for Web of Science ID 000278532300011

    View details for PubMedID 20045162

  • Early, Intermediate, and Late Effects of a Surgical Skills "Boot Camp" on an Objective Structured Assessment of Technical Skills: A Randomized Controlled Study Parent, R. J., Plerhoples, T. A., Long, E. E., Zimmer, D. M., Teshome, M., Mohr, C. J., Ly, D. P., Hernandez-Boussard, T., Curet, M. J., Dutta, S. ELSEVIER SCIENCE INC. 2010: 984-989

    Abstract

    Surgical interns enter residency with variable technical abilities and many feel unprepared to perform necessary procedures. We hypothesized that interns exposed to a preinternship intensive surgical skills curriculum would demonstrate improved competency over unexposed colleagues on a test of surgical skills and that this effect would persist throughout internship.We designed a 3-day intensive skills "boot camp" with simulation-based training on 10 topics. Interns were randomized to an intervention group (boot camp) or a control group (no boot camp). All interns completed a survey including demographic information, previous experience, and comfort with basic surgical skills. Both groups completed a clinical skills assessment focused on 4 topics: chest tube insertion, central line placement, wound closure, and the Fundamentals of Laparoscopic Surgery peg transfer task. We assessed both groups immediately (month 0), early postcurriculum (month 1), and late postcurriculum (month 6).Fifteen participants were in the intervention group and 13 were in the control group. Before boot camp, mean comfort levels were similar for the groups. All participants had minimal prior experience. Competency for chest tube insertion and central line placement were considerably higher for the boot camp group at months 0 and 1, although much of this difference disappeared by month 6. There was no substantial difference between the 2 groups in the Fundamentals of Laparoscopic Surgery peg transfer and wound closure skills.A surgical skills boot camp accelerates the learning curve for interns in basic surgical skills as measured by a technical skills examination for some skills, although these improvements diminished over time. This can augment traditional training and translate into fewer patient errors.

    View details for DOI 10.1016/j.jamcollsurg.2010.03.006

    View details for Web of Science ID 000278649100013

    View details for PubMedID 20510808

  • One Year Improvements in Cardiovascular Risk Factors: a Comparative Trial of Laparoscopic Roux-en-Y Gastric Bypass vs. Adjustable Gastric Banding OBESITY SURGERY Woodard, G. A., Peraza, J., Bravo, S., Toplosky, L., Hernandez-Boussard, T., Morton, J. M. 2010; 20 (5): 578-582

    Abstract

    Coronary artery disease (CAD) is the leading cause of death in the industrialized world with obesity as a leading preventable risk factor. Roux-en-Y gastric bypass (RYGB) and laparoscopic adjustable gastric banding (LAGB) have been shown to improve certain biochemical cardiovascular risk factors (BCRFs) at 1 year post-op, however no study has directly compared the 12-month BCRF improvements of RYGB vs. LAGB.At a single academic institution (2004-2009), we measured BCRF in 838 consecutive bariatric patients (765 RYGB, 73 LAGB) pre-operatively and at 12 months post-operatively. BCRF included total cholesterol (TC), low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides (Trig), Trig/HDL ratio, lipoprotein(a) (Lp(a)), homocysteine (HmC), high sensitivity C-reactive protein (hs-CRP), fasting insulin (FI), and hemoglobin A1C (Hgb A1C). Pre-op and 12-month post-op values were compared by a paired t test of equal variance.At 12 months post-op, RYGB patients had lost 77% of their excess weight and had significant improvements in TC, LDL, HDL, Trig, Trig/HDL, HmC, hs-CRP, FI, and Hgb A1C. LAGB patients lost 47.6% of their excess weight and had significant improvements in Trig, Trig/HDL, HmC, hs-CRP, and Hgb A1C. Having RYGB instead of LAGB was predictive of significantly greater improvements in TC at 12 months post-operatively.In this study, both RYGB and LAGB demonstrated significant weight loss and improvements in BCRF at 12 months post-op. RYGB produced significant improvements in a greater number of BCRFs and in some instances the 12-month post-op BCRF values were significantly lower risk in RYGB vs. LAGB patients.

    View details for DOI 10.1007/s11695-010-0088-0

    View details for Web of Science ID 000276470700007

    View details for PubMedID 20186576

  • Genomic and functional analysis identifies CRKL as an oncogene amplified in lung cancer ONCOGENE Kim, Y. H., Kwei, K. A., Girard, L., Salari, K., Kao, J., Pacyna-Gengelbach, M., Wang, P., Hernandez-Boussard, T., Gazdar, A. F., Petersen, I., Minna, J. D., Pollack, J. R. 2010; 29 (10): 1421-1430

    Abstract

    DNA amplifications, leading to the overexpression of oncogenes, are a cardinal feature of lung cancer and directly contribute to its pathogenesis. To uncover such novel alterations, we performed an array-based comparative genomic hybridization survey of 128 non-small-cell lung cancer cell lines and tumors. Prominent among our findings, we identified recurrent high-level amplification at cytoband 22q11.21 in 3% of lung cancer specimens, with another 11% of specimens exhibiting low-level gain spanning that locus. The 22q11.21 amplicon core contained eight named genes, only four of which were overexpressed (by transcript profiling) when amplified. Among these, CRKL encodes an adapter protein functioning in signal transduction, best known as a substrate of the BCR-ABL kinase in chronic myelogenous leukemia. RNA-interference-mediated knockdown of CRKL in lung cancer cell lines with (but not without) amplification led to significantly decreased cell proliferation, cell-cycle progression, cell survival, and cell motility and invasion. In addition, overexpression of CRKL in immortalized human bronchial epithelial cells led to enhanced growth factor-independent cell growth. Our findings indicate that amplification and resultant overexpression of CRKL contribute to diverse oncogenic phenotypes in lung cancer, with implications for targeted therapy, and highlight a role of adapter proteins as primary genetic drivers of tumorigenesis.

    View details for DOI 10.1038/onc.2009.437

    View details for Web of Science ID 000275392400002

    View details for PubMedID 19966867

  • A Second Look at the Fresh Frozen Plasma: Packed Red Blood Cell Ratio in Massive Transfusion Protocols Reply JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS Riskin, D. J., Hernandez-Boussard, T., Brundage, S. I. 2010; 210 (1): 117-118

    View details for Web of Science ID 000279279800020

  • Long-term radiographic outcomes of microemboli following carotid interventions JOURNAL OF VASCULAR SURGERY Zhou, W., Dinishak, D., Lane, B., Hernandez-Boussard, T., Bech, F., Rosen, A. 2009; 50 (6): 1314-1319

    Abstract

    Subclinical microemboli on diffusion-weighted magnetic resonance imaging (DWI) have been identified immediately following carotid revascularization procedures, but the clinical significance and long-term effects are largely unknown. The purpose of this study was to evaluate long-term radiographic outcomes of these DWI lesions.Patients who underwent perioperative magnetic resonance imaging (MRI) evaluations for carotid interventions at a single institution from July 2004 to December 2008 were evaluated, particularly those who had additional follow-up MRI. DWI with apparent diffusion coefficient (ADC), fluid-attenuated inversion recovery (FLAIR), and T2-weighted MRI images were compared to determine long-term effect of microemboli.One-hundred sixty-eight consecutive patients (68 carotid artery stenting [CAS] and 100 carotid endarterectomy [CEA]) who received perioperative MRI were included. All CAS were performed with an embolic protection device. The incidence of microemboli was significantly higher in the CAS group than the CEA group (46.3% and 12%, respectively, P < .05) despite a relative low incidence of procedure-associated neurologic symptoms in both groups (2.9% vs 2%). Thirty patients (16 CAS and 14 CEA) who had follow-up MRI were further analyzed and a total of 50 postoperative DWI lesions (mean size 46.57 mm(2); range 16 to 128 mm(2)) were identified among them. During a mean MRI follow-up of 10 months (range, 2 to 23 months), residual MRI abnormalities were only identified in DWI lesions larger than 60 mm(2) on postoperative MRI and on postoperative FLAIR images (n = 5, P < .001). The CEA group had fewer but larger ipsilateral distributed emboli (total 12 lesions, mean 79 mm(2)) compared with the CAS group (total 38 lesions, mean 27.5 mm(2), P < .05).The majority of microemboli do not have long-term radiographic sequelae. Size and hyperintensity on postoperative FLAIR are predictive of residual brain structure abnormality, and further neurocognitive evaluations are warranted.

    View details for DOI 10.1016/j.jvs.2009.07.105

    View details for Web of Science ID 000272860900010

    View details for PubMedID 19837533

  • The Halo Effect of Bariatric Surgery: Weight Loss in Patients Family Members OBESITY Morton, J., Woodard, G., Encarnacion, B., Downey, J., Peraza, J., Hernandez-Boussard, T. 2009; 17: S68-S69

    View details for Web of Science ID 000271237800075

  • Incidence of Retinopathy of Prematurity in the United States: 1997 through 2005 AMERICAN JOURNAL OF OPHTHALMOLOGY Lad, E. M., Hernandez-Boussard, T., Morton, J. M., Moshfeghi, D. M. 2009; 148 (3): 451-458

    Abstract

    To determine the incidence of retinopathy of prematurity (ROP) based on a national database and to identify baseline characteristics, demographic information, comorbidities, and surgical interventions.Retrospective study based on the National Inpatient Sample from 1997 through 2005.The National Inpatient Sample was queried for all newborn infants with and without ROP. Multivariate logistic regression was used to predict risk factors for ROP.Thirty-four million live births were recorded during the study period. The total ROP incidence was 0.17% overall and 15.58% for premature infants with length of stay of more than 28 days. Our results conclusively demonstrated the importance of low birth weight as a risk for ROP development in infants with length of stay of more than 28 days, as well as association with respiratory conditions, fetal hemorrhage, intraventricular hemorrhage, and blood transfer. An interesting finding was the protective effect conferred by hypoxia, necrotizing enterocolitis, and hemolytic disease of the newborn. Infants with ROP had a higher incidence of undergoing laser photocoagulation therapy, pars plana vitrectomy, and scleral buckle surgery.The current study represents a large, retrospective analysis of newborns with ROP. The multivariate analysis emphasizes the role of birth weight in extended-stay infants, as well as respiratory conditions, fetal hemorrhage, intraventricular hemorrhage, and blood transfer.

    View details for DOI 10.1016/j.ajo.2009.04.018

    View details for Web of Science ID 000269755400020

    View details for PubMedID 19541285

  • Massive Transfusion Protocols: The Role of Aggressive Resuscitation Versus Product Ratio in Mortality Reduction JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS Riskin, D. J., Tsai, T. C., Riskin, L., Hernandez-Boussard, T., Purtill, M., Maggio, P. M., Spain, D. A., Brundage, S. I. 2009; 209 (2): 198-205

    Abstract

    Exsanguinating hemorrhage necessitating massive blood product transfusion is associated with high mortality rates. Recent data suggest that altering the fresh frozen plasma to packed red blood cell ratio (FFP:PRBC) results in significant mortality reductions. Our purpose was to evaluate mortality and blood product use in the context of a newly initiated massive transfusion protocol (MTP).In July 2005, our American College of Surgeons-verified Level I trauma center implemented an MTP supporting a 1:1.5 FFP:PRBC ratio, improved communications, and enhanced systems flow to optimize rapid blood product availability. During the 4 years surrounding protocol implementation, we reviewed data on trauma patients directly admitted through the emergency department and requiring 10 or more units PRBCs during the first 24 hours.For the 2 years before and subsequent to MTP initiation, there were 4,223 and 4,414 trauma activations, of which 40 and 37 patients, respectively, met study criteria. The FFP:PRBC ratios were identical, at 1:1.8 and 1:1.8 (p = 0.97). Despite no change in FFP:PRBC ratio, mortality decreased from 45% to 19% (p = 0.02). Other significant findings included decreased mean time to first product: cross-matched RBCs (115 to 71 minutes; p = 0.02), FFP (254 to 169 minutes; p = 0.04), and platelets (418 to 241 minutes; p = 0.01).MTP implementation is associated with mortality reductions that have been ascribed principally to increased plasma use and decreased FFP:PRBC ratios. Our study found a significant reduction in mortality despite unchanged FFP:PRBC ratios and equivalent overall mean numbers of transfusions. Our data underscore the importance of expeditious product availability and emphasize that massive transfusion is a complex process in which product ratio and time to transfusion represent only the beginning of understanding.

    View details for DOI 10.1016/j.jamcollsurg.2009.04.016

    View details for Web of Science ID 000268747300006

    View details for PubMedID 19632596

  • Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery PLOS ONE Kao, J., Salari, K., Bocanegra, M., Choi, Y., Girard, L., Gandhi, J., Kwei, K. A., Hernandez-Boussard, T., Wang, P., Gazdar, A. F., Minna, J. D., Pollack, J. R. 2009; 4 (7)

    Abstract

    Breast cancer cell lines have been used widely to investigate breast cancer pathobiology and new therapies. Breast cancer is a molecularly heterogeneous disease, and it is important to understand how well and which cell lines best model that diversity. In particular, microarray studies have identified molecular subtypes-luminal A, luminal B, ERBB2-associated, basal-like and normal-like-with characteristic gene-expression patterns and underlying DNA copy number alterations (CNAs). Here, we studied a collection of breast cancer cell lines to catalog molecular profiles and to assess their relation to breast cancer subtypes.Whole-genome DNA microarrays were used to profile gene expression and CNAs in a collection of 52 widely-used breast cancer cell lines, and comparisons were made to existing profiles of primary breast tumors. Hierarchical clustering was used to identify gene-expression subtypes, and Gene Set Enrichment Analysis (GSEA) to discover biological features of those subtypes. Genomic and transcriptional profiles were integrated to discover within high-amplitude CNAs candidate cancer genes with coordinately altered gene copy number and expression.Transcriptional profiling of breast cancer cell lines identified one luminal and two basal-like (A and B) subtypes. Luminal lines displayed an estrogen receptor (ER) signature and resembled luminal-A/B tumors, basal-A lines were associated with ETS-pathway and BRCA1 signatures and resembled basal-like tumors, and basal-B lines displayed mesenchymal and stem/progenitor-cell characteristics. Compared to tumors, cell lines exhibited similar patterns of CNA, but an overall higher complexity of CNA (genetically simple luminal-A tumors were not represented), and only partial conservation of subtype-specific CNAs. We identified 80 high-level DNA amplifications and 13 multi-copy deletions, and the resident genes with concomitantly altered gene-expression, highlighting known and novel candidate breast cancer genes.Overall, breast cancer cell lines were genetically more complex than tumors, but retained expression patterns with relevance to the luminal-basal subtype distinction. The compendium of molecular profiles defines cell lines suitable for investigations of subtype-specific pathobiology, cancer stem cell biology, biomarkers and therapies, and provides a resource for discovery of new breast cancer genes.

    View details for DOI 10.1371/journal.pone.0006146

    View details for Web of Science ID 000267806300015

    View details for PubMedID 19582160

  • Probiotics Improve Outcomes After Roux-en-Y Gastric Bypass Surgery: A Prospective Randomized Trial JOURNAL OF GASTROINTESTINAL SURGERY Woodard, G. A., Encarnacion, B., Downey, J. R., Peraza, J., Chong, K., Hernandez-Boussard, T., Morton, J. M. 2009; 13 (7): 1198-1204

    Abstract

    Roux-en-Y gastric bypass (RNYGB) surgery offers an effective and enduring treatment for morbid obesity. Gastric bypass may alter gastrointestinal (GI) flora possibly resulting in bacterial overgrowth and dysmotility. Our hypothesis was that daily use of probiotics would improve GI outcomes after RNYGB.Forty-four patients undergoing RNYGB were randomized to either a probiotic or control group; 2.4 billion colonies of Lactobacillus were administered daily postoperatively to the probiotic group. The outcomes of H(2) levels indicative of bacterial overgrowth, GI-related quality of life (GIQoL), serologies, and weight loss were measured preoperatively and at 3 and 6 months postoperatively. Categorical variables were analyzed by chi(2) test and continuous variables were analyzed by t test with a p < 0.05 for significance.At 6 months, a statistically significant reduction in bacterial overgrowth was achieved in the probiotic group with a preoperative to postoperative change of sum H(2) part per million (probiotics = -32.13, controls = 0.80). Surprisingly, the probiotic group attained significantly greater percent excess weight loss than that of control group at 6 weeks (controls = 25.5%, probiotic = 29.9%) and 3 months (38.55%, 47.68%). This trend also continued but was not significant at 6 months (60.78%, 67.15%). The probiotic group had significantly higher postoperative vitamin B12 levels than the control group. Both probiotic and control groups significantly improved their GIQoL.In this novel study, probiotic administration improves bacterial overgrowth, vitamin B12 availability, and weight loss after RNYGB. These data may provide further evidence that altering the GI microbiota can influence weight loss.

    View details for DOI 10.1007/s11605-009-0891-x

    View details for Web of Science ID 000266821800008

    View details for PubMedID 19381735

  • Platinum pathway PHARMACOGENETICS AND GENOMICS Marsh, S., McLeod, H., Dolan, E., Shukla, S. J., Rabik, C. A., Gong, L., Hernandez-Boussard, T., Lou, X. J., Klein, T. E., Altman, R. B. 2009; 19 (7): 563-564

    View details for DOI 10.1097/FPC.0b013e32832e0ed7

    View details for Web of Science ID 000267619000011

    View details for PubMedID 19525887

  • Commitment to COT Verification Improves Patient Outcomes and Financial Performance JOURNAL OF TRAUMA-INJURY INFECTION AND CRITICAL CARE Maggio, P. M., Brundage, S. I., Hernandez-Boussard, T., Spain, D. A. 2009; 67 (1): 190-195

    Abstract

    After an unsuccessful American College of Surgery Committee on Trauma visit, our level I trauma center initiated an improvement program that included (1) hiring new personnel (trauma director and surgeons, nurse coordinator, orthopedic trauma surgeon, and registry staff), (2) correcting deficiencies in trauma quality assurance and process improvement programs, and (3) development of an outreach program. Subsequently, our trauma center had two successful verifications. We examined the longitudinal effects of these efforts on volume, patient outcomes and finances.The Trauma Registry was used to derive data for all trauma patients evaluated in the emergency department from 2001 to 2007. Clinical data analyzed included number of admissions, interfacility transfers, injury severity scores (ISS), length of stay, and mortality for 2001 to 2007. Financial performance was assessed for fiscal years 2001 to 2007. Data were divided into patients discharged from the emergency department and those admitted to the hospital.Admissions increased 30%, representing a 7.6% annual increase (p = 0.004), mostly due to a nearly fivefold increase in interfacility transfers. Severe trauma patients (ISS >24) increased 106% and mortality rate for ISS >24 decreased by 47% to almost half the average of the National Trauma Database. There was a 78% increase in revenue and a sustained increase in hospital profitability.A major hospital commitment to Committee on Trauma verification had several salient outcomes; increased admissions, interfacility transfers, and acuity. Despite more seriously injured patients, there has been a major, sustained reduction in mortality and a trend toward decreased intensive care unit length of stay. This resulted in a substantial increase in contribution to margin (CTM), net profit, and revenues. With a high level of commitment and favorable payer mix, trauma center verification improves outcomes for both patients and the hospital.

    View details for DOI 10.1097/TA.0b013e3181a51b2f

    View details for Web of Science ID 000267953100035

    View details for PubMedID 19590334

  • Preoperative Thrombus Volume Predicts Sac Regression After Endovascular Aneurysm Repair JOURNAL OF ENDOVASCULAR THERAPY Yeung, J. J., Hernandez-Boussard, T. M., Song, T. K., Dalman, R. L., Lee, J. T. 2009; 16 (3): 380-388

    Abstract

    To examine whether preoperative aneurysm thrombus volume correlated with abdominal aortic aneurysm (AAA) sac regression following endovascular aneurysm repair (EVAR).Clinical records and computed tomographic angiograms (CTAs) from patients undergoing EVAR from 2003 to 2008 were reviewed. Inclusion criteria for this study were available preoperative CTA images, >or=12-month follow-up with surveillance imaging, lack of re-intervention at 12 months, and treatment with commercially available devices. Patients with ruptured AAAs, those requiring an aortomonoiliac stent-graft, and clinical trial cases were excluded. Based on these criteria, satisfactory images and clinical follow-up were available in 100 patients (90 men; mean age 76.8 years, range 55-95). Preoperative CTAs were categorized as demonstrating "minimal," "moderate," or "severe" aneurysm thrombus load by 2 independent examiners blinded to clinical outcome. Percentage of the aortic cross-sectional area occluded by clot (% clot area) was calculated as [(total area) - (luminal area)]/(total area). Multivariate logistic regression analysis was performed to determine predictors of sac shrinkage at long-term follow-up.AAA thrombus was classified as minimal in 24%, moderate in 23%, and severe in 53%. Thrombus area averaged 11%+/-13%, 41%+/-14%, and 72+/-12% in each group, respectively. By multivariate analysis, minimal thrombus (OR = 1.47) and greater AAA diameter (OR = 1.3) were independent predictors of sac regression at 1, 6, and 12 months (all p<0.05). Presence of neck plaque and endoleak were also independent predictors of sac expansion (p<0.05). Patients with severe preoperative thrombus were less likely to demonstrate sac regression even in the absence of endoleak. Thrombus judgment (subjective) and percent clot area (objective) were strongly correlated (R = 0.82, p<0.05). Interobserver agreement on thrombus judgment was 86%.Thrombus burden on preoperative CTA is a strong independent predictor of sac regression following EVAR. If validated by prospective studies, relative thrombus burden should be incorporated into postoperative surveillance algorithms to define procedural success and optimize the timing and cost-effectiveness of cross-sectional imaging.

    View details for Web of Science ID 000268117500019

    View details for PubMedID 19642793

  • Bariatric Surgery Improves Musculoskeletal Quality of Life Independent of Weight Loss and Procedure Type GASTROENTEROLOGY Bravo, S., Woodard, G., Hernandez-Boussard, T., Morton, J. 2009; 136 (5): A903-A903

    View details for Web of Science ID 000275277204506

  • Does Insurance Status Affect Gastric Bypass Surgery Outcomes? GASTROENTEROLOGY Woodard, G., Hernandez-Boussard, T., Morton, J. 2009; 136 (5): A902-A902

    View details for Web of Science ID 000275277204504

  • Relationship Between Hospital Volume, System Clinical Resources, and Mortality in Pancreatic Resection JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS Joseph, B., Morton, J. M., Hernandez-Boussard, T., Rubinfeld, I., Faraj, C., Velanovich, V. 2009; 208 (4): 520-527

    Abstract

    The relationship between hospital volume and perioperative mortality in pancreaticoduodenectomy has been well established. We studied whether associations exist between hospital volume and hospital clinical resources and between both of these factors to mortality to help explain this relationship.This two-part study reviewed publicly available hospital information from the Leapfrog Group, HealthGrades, and hospital Web sites. Hospitals were evaluated for Leapfrog ICU staffing criteria and Safe Practice Score; HealthGrades five-star rating for complex gastrointestinal procedures and operations; and presence of a general surgery residency, gastroenterology fellowship, and interventional radiology. Evaluation used trend analysis and multiple logistic regression analysis. The second part determined the mortality rate for pancreaticoduodenectomy using inpatient mortality data from the National Inpatient Sample and Leapfrog. Hospitals were categorized by low volume (< or = 10/year), high volume (> or = 11/year), strong clinical support (presence of all support factors), and weak clinical support (absence of any factor). Data were correlated by number of pancreatic resections per hospital, hospital system clinical resources, and operative mortality.As hospital volume increased, statistically significant increases occurred in the frequency of hospitals meeting Leapfrog ICU staffing criteria (p < 0.0001), Leapfrog Safe Practice Score (p = 0.0004), HealthGrades 5-star rating (p < 0.00001), general surgery residency (p < 0.00001), gastroenterology fellowship (p < 0.00001), and interventional radiology services (p < 0.00001). No significant relationships were found between resection volume and any one of the clinical support factors and perioperative death. Presence of strong clinical support was associated with lower mortality (odds ratio = 0.32; p = 0.001).System clinical resources were more influential in operative mortality for pancreatic resection. This might help explain why high-volume hospitals, low-volume surgeons in high-volume institutions, and some lower-volume hospitals with excellent clinical resources have lower perioperative mortality rates for pancreatic resection.

    View details for DOI 10.1016/j.jamcollsurg.2009.01.019

    View details for Web of Science ID 000270996800005

    View details for PubMedID 19476785

  • Fate of the external carotid artery following carotid interventions. The International journal of angiology : official publication of the International College of Angiology, Inc Casey, K., Zhou, W., Tedesco, M. M., Al-Khatib, W. K., Hernandez-Boussard, T., Bech, F. 2009; 18 (4): 173-176

    Abstract

    The external carotid artery (ECA) is an important collateral pathway for cerebral blood flow. Carotid artery stenting (CAS) typically crosses the ECA, while carotid endarterectomy (CEA) includes deliberate ECA plaque removal. The purpose of the present study was to compare the long-term patency of the ECA following CAS and CEA as determined by carotid duplex ultrasound.Duplex ultrasounds and hospital records were reviewed for consecutive patients undergoing CAS between February 2002 and April 2008, and were compared with those undergoing CEA in the same time period. Preoperative and postoperative ECA peak systolic velocities were normalized to the common carotid artery (CCA) as ECA/CCA ratios. A significant (80% or greater) ECA stenosis was defined as an ECA/CCA ratio of 4.0. A change of ratio by more than 1 was defined as significant. Data were analyzed using Student's t test and ?(2) analysis.A total of 86 CAS procedures in 83 patients were performed (81 men, mean age 69.9 years). Among them, 38.4% of patients had previous CEA, 9.6% of whom had contralateral internal carotid artery occlusion. Sixty-seven CAS and 65 CEA patients with complete duplex data in the same time period were included in the analyses. There was no difference in the incidence of severe ECA stenosis on preoperative ultrasound evaluations. During a mean follow-up of 34 months (range four to 78 months), three postprocedure ECA occlusions were found in the CAS group. The likelihood of severe stenosis or occlusion following CAS was 28.3%, compared with 11% following CEA (P<0.025). However, 62% of CEA patients and 57% of CAS patients had no significant change in ECA status. Reduction in the patient's degree of ECA stenosis was observed in 9.4% of CAS versus 26.6% of CEA patients. Overall, immediate postoperative ratios of both groups were slightly improved, but there was a trend of more disease progression in the CAS group during follow-up.CAS is associated with a higher incidence of post-procedure ECA stenosis. Despite the absence of neurological symptoms, a trend toward late disease progression of ECA following CAS warrants long-term evaluation.

    View details for PubMedID 22477547

  • Validation of a Prehospital Trauma Triage Tool: A 10-Year Perspective JOURNAL OF TRAUMA-INJURY INFECTION AND CRITICAL CARE Purtill, M., Benedict, K., Hernandez-Boussard, T., Brundage, S. I., Kritayakirana, K., Sherck, J. P., Garland, A., Spain, D. A. 2008; 65 (6): 1253-1257

    Abstract

    Triage of the trauma patient in the field is a complex and challenging issue, especially deciding when to use aeromedical transport. The American College of Surgeons Committee on Trauma recently defined an acceptable under-triage rate [seriously injured patient not taken to a trauma center (TC)] as 5%, whereas over-triage rates may be as high as 25% to 50%. Effective utilization of prehospital helicopter transport requires both accurate assessment of patients and effective communication. The rural county adjacent to our developed trauma system uses standardized triage criteria to identify patients for direct transport to our TCs. We hypothesized these criteria accurately identify major trauma victims (MTV) and further that communication could be simplified to expedite transport.Prehospital personnel use a MAP (mechanism, anatomy, and physiology) scoring system to triage trauma patients. Patients with > or = 2 "hits" are defined as MTV. In 2004, the triage policy was changed so that MTV would be transported directly to a TC without base hospital consultation (previously required). The Emergency Medical Services (EMS) Medical Director reviewed cases transported to the TC to determine the appropriateness of triage decisions (over- and under-triage using the American College of Surgeons Committee on Trauma definitions). Data were compared before and after this policy change.For 2004 to 2006, we evaluated 676 air transports to TC and compared them to 468 in the prior 56 months. The overall transport rate increased slightly 7% to 10%. During the study period the over-triage rate was 31% compared with 21%, before the policy change. The MAP triage tool yielded a 93.8% sensitivity and a 99.5% specificity. Therefore, it determined the need for air-medical transport out of a rural environment into an established trauma system with > 90% accuracy.Prehospital personnel can accurately use a trauma triage tool to identify MTV. Eliminating base station contact, a potential for introducing communication error, did increase over-triage but still well within accepted limits. The system change also resulted in the transport of a greater proportion of minor trauma patients who later proved to have major injuries.

    View details for DOI 10.1097/TA.0b013e31818bbfc2

    View details for Web of Science ID 000261706000010

    View details for PubMedID 19077609

  • Mechanical Bowel Preparation in Intestinal Surgery: A Meta-Analysis and Review of the Literature JOURNAL OF GASTROINTESTINAL SURGERY Pineda, C. E., Shelton, A. A., Hernandez-Boussard, T., Morton, J. M., Welton, M. L. 2008; 12 (11): 2037-2044

    Abstract

    Despite several meta-analyses and randomized controlled trials showing no benefit to patients, mechanical bowel preparation (MBP) remains the standard of practice for patients undergoing elective colorectal surgery.We performed a systematic review of the literature of trials that prospectively compared MBP with no MBP for patients undergoing elective colorectal resection. We searched MEDLINE, LILACS, and SCISEARCH, abstracts of pertinent scientific meetings and reference lists for each article found. Experts in the field were queried as to knowledge of additional reports. Outcomes abstracted were anastomotic leaks and wound infections. Meta-analysis was performed using Peto Odds ratio.Of 4,601 patients (13 trials), 2,304 received MBP (Group 1) and 2,297 did not (Group 2). Anastomotic leaks occurred in 97(4.2%) patients in Group 1 and in 81(3.5%) patients in Group 2 (Peto OR = 1.214, CI 95%:0.899-1.64, P = 0.206). Wound infections occurred in 227(9.9%) patients in Group 1 and in 201(8.8%) patients in Group 2 (Peto OR = 1.156, CI 95%:0.946-1.413, P = 0.155).This meta-analysis demonstrates that MBP provides no benefit to patients undergoing elective colorectal surgery, thus, supporting elimination of routine MBP in elective colorectal surgery.In conclusion, MBP is of no benefit to patients undergoing elective colorectal resection and need not be recommended to meet "standard of care."

    View details for DOI 10.1007/s11605-008-0594-8

    View details for Web of Science ID 000260282200037

    View details for PubMedID 18622653

  • Disparity in Utilization, Demographics and Outcomes for Bariatric Surgeries OBESITY Morton, J., Woodard, G., Downey, J., Hernandez-Boussard, T. 2008; 16: S297-S297

    View details for Web of Science ID 000259796601370

  • Gastric Bypass Surgery Improves Markers of Aging OBESITY Downey, J., Woodard, G., Hernandez-Boussard, T., Morton, J. 2008; 16: S144-S144

    View details for Web of Science ID 000259796600335

  • Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer ONCOGENE Kwei, K. A., Kim, Y. H., Girard, L., Kao, J., Pacyna-Gengelbach, M., Salari, K., Lee, J., Choi, Y., Sato, M., Wang, P., Hernandez-Boussard, T., Gazdar, A. F., Petersen, I., Minna, J. D., Pollack, J. R. 2008; 27 (25): 3635-3640

    Abstract

    Lung cancer is a leading cause of cancer death, where the amplification of oncogenes contributes to tumorigenesis. Genomic profiling of 128 lung cancer cell lines and tumors revealed frequent focal DNA amplification at cytoband 14q13.3, a locus not amplified in other tumor types. The smallest region of recurrent amplification spanned the homeobox transcription factor TITF1 (thyroid transcription factor 1; also called NKX2-1), previously linked to normal lung development and function. When amplified, TITF1 exhibited increased expression at both the RNA and protein levels. Small interfering RNA (siRNA)-mediated knockdown of TITF1 in lung cancer cell lines with amplification led to reduced cell proliferation, manifested by both decreased cell-cycle progression and increased apoptosis. Our findings indicate that TITF1 amplification and overexpression contribute to lung cancer cell proliferation rates and survival and implicate TITF1 as a lineage-specific oncogene in lung cancer.

    View details for DOI 10.1038/sj.onc.1211012

    View details for Web of Science ID 000256468500015

    View details for PubMedID 18212743

  • Genomic profiling identifies GATA6 as a candidate oncogene amplified in pancreatobiliary cancer PLOS GENETICS Kwei, K. A., Bashyam, M. D., Kao, J., Ratheesh, R., Reddy, E. C., Kim, Y. H., Montgomery, K., Giacomini, C. P., Choi, Y., Chatterjee, S., Karikari, C. A., Salari, K., Wang, P., Hernandez-Boussard, T., Swarnalata, G., van de Rijn, M., Maitra, A., Pollack, J. R. 2008; 4 (5)

    Abstract

    Pancreatobiliary cancers have among the highest mortality rates of any cancer type. Discovering the full spectrum of molecular genetic alterations may suggest new avenues for therapy. To catalogue genomic alterations, we carried out array-based genomic profiling of 31 exocrine pancreatic cancers and 6 distal bile duct cancers, expanded as xenografts to enrich the tumor cell fraction. We identified numerous focal DNA amplifications and deletions, including in 19% of pancreatobiliary cases gain at cytoband 18q11.2, a locus uncommonly amplified in other tumor types. The smallest shared amplification at 18q11.2 included GATA6, a transcriptional regulator previously linked to normal pancreas development. When amplified, GATA6 was overexpressed at both the mRNA and protein levels, and strong immunostaining was observed in 25 of 54 (46%) primary pancreatic cancers compared to 0 of 33 normal pancreas specimens surveyed. GATA6 expression in xenografts was associated with specific microarray gene-expression patterns, enriched for GATA binding sites and mitochondrial oxidative phosphorylation activity. siRNA mediated knockdown of GATA6 in pancreatic cancer cell lines with amplification led to reduced cell proliferation, cell cycle progression, and colony formation. Our findings indicate that GATA6 amplification and overexpression contribute to the oncogenic phenotypes of pancreatic cancer cells, and identify GATA6 as a candidate lineage-specific oncogene in pancreatobiliary cancer, with implications for novel treatment strategies.

    View details for DOI 10.1371/journal.pgen.1000081

    View details for Web of Science ID 000256869100012

    View details for PubMedID 18535672

  • Signal detection: A new statistical method to predict NASH in gastric bypass patients GASTROENTEROLOGY Morton, J. M., Woodard, G. A., Hernandez-Boussard, T. 2008; 134 (4): A855-A855

    View details for Web of Science ID 000255101506282

  • Meta-analysis of mechanical bowel preparation for elective colon and rectal resection GASTROENTEROLOGY Pineda, C. E., Shelton, A. A., Hernandez-Boussard, T., Morton, J. M., Welton, M. L. 2008; 134 (4): A860-A860

    View details for Web of Science ID 000255101506308

  • The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge NUCLEIC ACIDS RESEARCH Hernandez-Boussard, T., Whirl-Carrillo, M., Hebert, J. M., Gong, L., Owen, R., Gong, M., Gor, W., Liu, F., Truong, C., Whaley, R., Woon, M., Zhou, T., Altman, R. B., Klein, T. E. 2008; 36: D913-D918

    Abstract

    PharmGKB is a knowledge base that captures the relationships between drugs, diseases/phenotypes and genes involved in pharmacokinetics (PK) and pharmacodynamics (PD). This information includes literature annotations, primary data sets, PK and PD pathways, and expert-generated summaries of PK/PD relationships between drugs, diseases/phenotypes and genes. PharmGKB's website is designed to effectively disseminate knowledge to meet the needs of our users. PharmGKB currently has literature annotations documenting the relationship of over 500 drugs, 450 diseases and 600 variant genes. In order to meet the needs of whole genome studies, PharmGKB has added new functionalities, including browsing the variant display by chromosome and cytogenetic locations, allowing the user to view variants not located within a gene. We have developed new infrastructure for handling whole genome data, including increased methods for quality control and tools for comparison across other data sources, such as dbSNP, JSNP and HapMap data. PharmGKB has also added functionality to accept, store, display and query high throughput SNP array data. These changes allow us to capture more structured information on phenotypes for better cataloging and comparison of data. PharmGKB is available at www.pharmgkb.org.

    View details for DOI 10.1093/nar/gkm1009

    View details for Web of Science ID 000252545400160

    View details for PubMedID 18032438

  • Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis CANCER RESEARCH Lapointe, J., Li, C., Giacomini, C. P., Salari, K., Huang, S., Wang, P., Ferrari, M., Hernandez-Boussard, T., Brooks, J. D., Pollack, J. R. 2007; 67 (18): 8504-8510

    Abstract

    Prostate cancer is clinically heterogeneous, ranging from indolent to lethal disease. Expression profiling previously defined three subtypes of prostate cancer, one (subtype-1) linked to clinically favorable behavior, and the others (subtypes-2 and -3) linked with a more aggressive form of the disease. To explore disease heterogeneity at the genomic level, we carried out array-based comparative genomic hybridization (array CGH) on 64 prostate tumor specimens, including 55 primary tumors and 9 pelvic lymph node metastases. Unsupervised cluster analysis of DNA copy number alterations (CNA) identified recurrent aberrations, including a 6q15-deletion group associated with subtype-1 gene expression patterns and decreased tumor recurrence. Supervised analysis further disclosed distinct patterns of CNA among gene-expression subtypes, where subtype-1 tumors exhibited characteristic deletions at 5q21 and 6q15, and subtype-2 cases harbored deletions at 8p21 (NKX3-1) and 21q22 (resulting in TMPRSS2-ERG fusion). Lymph node metastases, predominantly subtype-3, displayed overall higher frequencies of CNA, and in particular gains at 8q24 (MYC) and 16p13, and loss at 10q23 (PTEN) and 16q23. Our findings reveal that prostate cancers develop via a limited number of alternative preferred genetic pathways. The resultant molecular genetic subtypes provide a new framework for investigating prostate cancer biology and explain in part the clinical heterogeneity of the disease.

    View details for DOI 10.1158/0008-5472.CAN-07-0673

    View details for Web of Science ID 000249679500013

    View details for PubMedID 17875689

  • The Stanford Microarray Database: implementation of new analysis tools and open source release of software NUCLEIC ACIDS RESEARCH Demeter, J., Beauheim, C., Gollub, J., Hernandez-Boussard, T., Jin, H., Maier, D., Matese, J. C., Nitzberg, M., Wymore, F., Zachariah, Z. K., Brown, P. O., Sherlock, G., Ball, C. A. 2007; 35: D766-D770

    Abstract

    The Stanford Microarray Database (SMD; http://smd.stanford.edu/) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD. In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release.

    View details for DOI 10.1093/nar/gkl1019

    View details for Web of Science ID 000243494600151

    View details for PubMedID 17182626

  • Integrating large-scale genotype and phenotype data OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY Hernandez-Boussard, T., Woon, M., Klein, T. E., Altman, R. B. 2006; 10 (4): 545-554

    Abstract

    With the completion of the Human Genome Project, a new emphasis is focusing on the sequence variation and the resulting phenotype. The number of data available from genomic studies addressing this relationship is rapidly growing. In order to analyze these data as a whole, they need to be integrated, aggregated and annotated in a timely manner. The Pharmacogenetics and Pharmacogenomics Knowledge Base PharmGKB; () assembles and disseminates these data and their associated metadata that are needed for unambiguous identification and replication. Assembling these data in a timely manner is challenging, and the scalability of these data produce major challenges for a knowledge base such as PharmGKB. However, it is only through rapid global meta-annotation of these data that we will understand the relationship between specific genotype(s) and the related phenotype. PharmGKB has confronted these challenges, and these experiences and solutions can benefit all genome communities.

    View details for Web of Science ID 000243893500009

    View details for PubMedID 17233563

  • Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer GENES CHROMOSOMES & CANCER Bergamaschi, A., Kim, Y. H., Wang, P., Sorlie, T., Hernandez-Boussard, T., Lonning, P. E., Tibshirani, R., Borresen-Dale, A., Pollack, J. R. 2006; 45 (11): 1033-1040

    Abstract

    Breast cancer is a leading cause of cancer-death among women, where the clinicopathological features of tumors are used to prognosticate and guide therapy. DNA copy number alterations (CNAs), which occur frequently in breast cancer and define key pathogenetic events, are also potentially useful prognostic or predictive factors. Here, we report a genome-wide array-based comparative genomic hybridization (array CGH) survey of CNAs in 89 breast tumors from a patient cohort with locally advanced disease. Statistical analysis links distinct cytoband loci harboring CNAs to specific clinicopathological parameters, including tumor grade, estrogen receptor status, presence of TP53 mutation, and overall survival. Notably, distinct spectra of CNAs also underlie the different subtypes of breast cancer recently defined by expression-profiling, implying these subtypes develop along distinct genetic pathways. In addition, higher numbers of gains/losses are associated with the "basal-like" tumor subtype, while high-level DNA amplification is more frequent in "luminal-B" subtype tumors, suggesting also that distinct mechanisms of genomic instability might underlie their pathogenesis. The identified CNAs may provide a basis for improved patient prognostication, as well as a starting point to define important genes to further our understanding of the pathobiology of breast cancer. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat

    View details for DOI 10.1002/gcc.20366

    View details for Web of Science ID 000240601400005

    View details for PubMedID 16897746

  • Development of FuGO: An ontology for Functional Genomics Investigations OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY Whetzel, P. L., Brinkman, R. R., Causton, H. C., Fan, L., Field, D., Fostel, J., Fragoso, G., Gray, T., Heiskanen, M., Hernandez-Boussard, T., Morrison, N., Parkinson, H., Rocca-Serra, P., Sansone, S., Schober, D., Smith, B., Stevens, R., Stoeckert, C. J., Taylor, C., White, J., Wood, A. 2006; 10 (2): 199-204

    Abstract

    The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the "semantic glue" to provide a common understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans.

    View details for Web of Science ID 000240210900016

    View details for PubMedID 16901226

  • Pharmacogenomics: The relevance of emerging genotyping technologies. MLO: medical laboratory observer Hernandez-Boussard, T., Klein, T. E., Altman, R. B. 2006; 38 (3): 24-?

    View details for PubMedID 16610446

  • Combined microarray analysis of small cell lung cancer reveals altered apoptotic balance and distinct expression signatures of MYC family gene amplification ONCOGENE Kim, Y. H., Girard, L., Giacomini, C. P., Wang, P., Hernandez-Boussard, T., Tibshirani, R., Minna, J. D., Pollack, J. R. 2006; 25 (1): 130-138

    Abstract

    DNA amplifications and deletions frequently contribute to the development and progression of lung cancer. To identify such novel alterations in small cell lung cancer (SCLC), we performed comparative genomic hybridization on a set of 24 SCLC cell lines, using cDNA microarrays representing approximately 22,000 human genes (providing an average mapping resolution of <70 kb). We identified localized DNA amplifications corresponding to oncogenes known to be amplified in SCLC, including MYC (8q24), MYCN (2p24) and MYCL1 (1p34). Additional highly localized DNA amplifications suggested candidate oncogenes not previously identified as amplified in SCLC, including the antiapoptotic genes TNFRSF4 (1p36), DAD1 (14q11), BCL2L1 (20q11) and BCL2L2 (14q11). Likewise, newly discovered PCR-validated homozygous deletions suggested candidate tumor-suppressor genes, including the proapoptotic genes MAPK10 (4q21) and TNFRSF6 (10q23). To characterize the effect of DNA amplification on gene expression patterns, we performed expression profiling using the same microarray platform. Among our findings, we identified sets of genes whose expression correlated with MYC, MYCN or MYCL1 amplification, with surprisingly little overlap among gene sets. While both MYC and MYCN amplification were associated with increased and decreased expression of known MYC upregulated and downregulated targets, respectively, MYCL1 amplification was associated only with the latter. Our findings support a role of altered apoptotic balance in the pathogenesis of SCLC, and suggest that MYC family genes might affect oncogenesis through distinct sets of targets, in particular implicating the importance of transcriptional repression.

    View details for DOI 10.1038/sj.onc.1208997

    View details for Web of Science ID 000234406400014

    View details for PubMedID 16116477

  • Transcriptional analysis of the molecular basis of human kidney aging using cDNA microarray profiling KIDNEY INTERNATIONAL Melk, A., Mansfield, E. S., Hsieh, S. C., Hernandez-Boussard, T., Grimm, P., Rayner, D. C., Halloran, P. F., Sarwal, M. M. 2005; 68 (6): 2667-2679

    Abstract

    The molecular basis of renal aging is not completely understood.We used global gene expression monitoring by cDNA microarrays to identify age associated genes in human kidney samples. Our samples included young (8 weeks-8 years, N= 4), adult (31-46 years, N= 7), and old kidneys (71-88 years, N= 9).Old kidneys had more glomerulosclerosis, tubular atrophy, interstitial fibrosis, and fibrous intimal thickening in small arteries. We identified approximately 500 genes that were differentially expressed among the three age groups. Old kidneys appeared to have increased extracellular matrix turnover and a nonspecific inflammatory response, combined with a reduction in processes dependent on energy metabolism and mitochondrial function. Quantitative supervised bioinformatics analyses of adult and old kidney expression data correlated the expression of 255 gene profiles with renal pathology scores. Microarray class prediction analysis (PAM) identified 50 unique genes that segregated old kidneys into two distinct clusters: those more similar within age class (OO, N= 5) versus old kidneys more similar to adult kidneys (OA, N= 4). The expression of six functionally significant genes was further validated by quantitative reverse transcription-polymerase chain reaction (RT-PCR) (FN1, MMP7, TNC, SERPIN3A, BPHL, CSPG2) in the experiment group and, subsequently, confirmed independently in 17 additional old and adult age-stratified test kidney samples. The p53 inducible gene, CSPG2, performed best in separating OO kidneys from adults and OA samples in this analysis.The method described in this study using independent validation samples can be envisioned to test utility of the identified genes in assessing age-related changes that contribute to decline in renal function.

    View details for Web of Science ID 000233204300022

    View details for PubMedID 16316342

  • Comparative genomic hybridization on mouse cDNA microarrays and its application to a murine lymphoma model ONCOGENE Sander, S., Bullinger, L., Karlsson, A., Giuriato, S., Hernandez-Boussard, T., Felsher, D. W., Pollack, J. R. 2005; 24 (40): 6101-6107

    Abstract

    Microarray-based formats offer a high-resolution alternative to conventional, chromosome-based comparative genomic hybridization (CGH) methods for assessing DNA copy number alteration (CNA) genome-wide in human cancer. For murine tumors, array CGH should provide even greater advantage, since murine chromosomes are more difficult to individually discern. We report here the adaptation and evaluation of a cDNA microarray-based CGH method for the routine characterization of CNAs in murine tumors, using mouse cDNA microarrays representing approximately 14,000 different genes, thereby providing an average mapping resolution of 109 kb. As a first application, we have characterized CNAs in a set of 10 primary and recurrent lymphomas derived from a Myc-induced murine lymphoma model. In primary lymphomas and more commonly in Myc-independent relapses, we identified a recurrent genomic DNA loss at chromosome 3G3-3H4, and recurrent amplifications at chromosome 3F2.1-3G3 and chromosome 15E1/E2-15F3, the boundaries of which we defined with high resolution. Further, by profiling gene expression using the same microarray platform, we identified within CNAs the relevant subset of candidate cancer genes displaying comparably altered expression, including Mcl1 (myeloid cell leukemia sequence 1), a highly expressed antiapoptotic gene residing within the chr 3 amplicon peak. CGH on mouse cDNA microarrays therefore represents a reliable method for the high-resolution characterization of CNAs in murine tumors, and a powerful approach for elucidating the molecular events in tumor development and progression in murine models.

    View details for DOI 10.1038/sj.onc.1208751

    View details for Web of Science ID 000231718100004

    View details for PubMedID 16007205

  • Array-based comparative genomic hybridization identifies localized DNA amplifications and homozygous deletions in pancreatic cancer NEOPLASIA Bashyam, M. D., Bair, R., Kim, Y. H., Wang, P., Hernandez-Boussard, T., Karikari, C. A., Tibshirani, R., Maitra, A., Pollack, J. R. 2005; 7 (6): 556-562

    Abstract

    Pancreatic cancer, the fourth leading cause of cancer death in the United States, is frequently associated with the amplification and deletion of specific oncogenes and tumor-suppressor genes (TSGs), respectively. To identify such novel alterations and to discover the underlying genes, we performed comparative genomic hybridization on a set of 22 human pancreatic cancer cell lines, using cDNA microarrays measuring approximately 26,000 human genes (thereby providing an average mapping resolution of <60 kb). To define the subset of amplified and deleted genes with correspondingly altered expression, we also profiled mRNA levels in parallel using the same cDNA microarray platform. In total, we identified 14 high-level amplifications (38-4934 kb in size) and 15 homozygous deletions (46-725 kb). We discovered novel localized amplicons, suggesting previously unrecognized candidate oncogenes at 6p21, 7q21 (SMURF1, TRRAP), 11q22 (BIRC2, BIRC3), 12p12, 14q24 (TGFB3), 17q12, and 19q13. Likewise, we identified novel polymerase chain reaction-validated homozygous deletions indicating new candidate TSGs at 6q25, 8p23, 8p22 (TUSC3), 9q33 (TNC, TNFSF15), 10q22, 10q24 (CHUK), 11p15 (DKK3), 16q23, 18q23, 21q22 (PRDM15, ANKRD3), and Xp11. Our findings suggest candidate genes and pathways, which may contribute to the development or progression of pancreatic cancer.

    View details for DOI 10.1593/neo.04586

    View details for Web of Science ID 000230209600002

    View details for PubMedID 16036106

  • Determination of stromal signatures in breast carcinoma PLOS BIOLOGY West, R. B., Nuyten, D. S., Subramanian, S., Nielsen, T. O., Corless, C. L., Rubin, B. P., Montgomery, K., Zhu, S., Patel, R., Hernandez-Boussard, T., Goldblum, J. R., Brown, P. O., van De Vijver, M., van de Rijn, M. 2005; 3 (6): 1101-1110

    Abstract

    Many soft tissue tumors recapitulate features of normal connective tissue. We hypothesize that different types of fibroblastic tumors are representative of different populations of fibroblastic cells or different activation states of these cells. We examined two tumors with fibroblastic features, solitary fibrous tumor (SFT) and desmoid-type fibromatosis (DTF), by DNA microarray analysis and found that they have very different expression profiles, including significant differences in their patterns of expression of extracellular matrix genes and growth factors. Using immunohistochemistry and in situ hybridization on a tissue microarray, we found that genes specific for these two tumors have mutually specific expression in the stroma of nonneoplastic tissues. We defined a set of 786 gene spots whose pattern of expression distinguishes SFT from DTF. In an analysis of DNA microarray gene expression data from 295 previously published breast carcinomas, we found that expression of this gene set defined two groups of breast carcinomas with significant differences in overall survival. One of the groups had a favorable outcome and was defined by the expression of DTF genes. The other group of tumors had a poor prognosis and showed variable expression of genes enriched for SFT type. Our findings suggest that the host stromal response varies significantly among carcinomas and that gene expression patterns characteristic of soft tissue tumors can be used to discover new markers for normal connective tissue cells.

    View details for DOI 10.1371/journal.pbio.0030187

    View details for Web of Science ID 000229992900019

    View details for PubMedID 15869330

  • Expression profiling of murine double-negative regulatory T cells suggest mechanisms for prolonged cardiac allograft survival JOURNAL OF IMMUNOLOGY Lee, B. P., Mansfield, E., Hsieh, S. C., Hernandez-Boussard, T., Chen, W. H., Thomson, C. W., Ford, M. S., Bosinger, S. E., Der, S., Zhang, Z. X., Zhang, M. X., Kelvin, D. J., Sarwal, M. M., Zhang, L. 2005; 174 (8): 4535-4544

    Abstract

    Recent studies have demonstrated that both mouse and human alpha beta TCR(+)CD3(+)NK1.1(-)CD4(-)CD8- double-negative regulatory T (DN Treg) cells can suppress Ag-specific immune responses mediated by CD8+ and CD4+ T cells. To identify molecules involved in DN Treg cell function, we generated a panel of murine DN Treg clones, which specifically kill activated syngeneic CD8+ T cells. Through serial cultivation of DN Treg clones, mutant clones arose that lost regulatory capacity in vitro and in vivo. Although all allogeneic cardiac grafts in animals preinfused with tolerant CD4/CD8 negative 12 DN Treg clones survived over 100 days, allograft survival is unchanged following infusion of mutant clones (19.5 +/- 11.1 days) compared with untreated controls (22.8 +/- 10.5 days; p < 0.001). Global gene expression differences between functional DN Treg cells and nonfunctional mutants were compared. We found 1099 differentially expressed genes (q < 0.025%), suggesting increased cell proliferation and survival, immune regulation, and chemotaxis, together with decreased expression of genes for Ag presentation, apoptosis, and protein phosphatases involved in signal transduction. Expression of 33 overexpressed and 24 underexpressed genes were confirmed using quantitative real-time PCR. Protein expression of several genes, including Fc epsilon RI gamma subunit and CXCR5, which are >50-fold higher, was also confirmed using FACS. These findings shed light on the mechanisms by which DN Treg cells down-regulate immune responses and prolong cardiac allograft survival.

    View details for Web of Science ID 000228234600014

    View details for PubMedID 15814674

  • The Stanford Microarray Database accommodates additional microarray platforms and data formats NUCLEIC ACIDS RESEARCH Ball, C. A., Awad, I. A., Demeter, J., Gollub, J., Hebert, J. M., Hernandez-Boussard, T., Jin, H., Matese, J. C., Nitzberg, M., Wymore, F., Zachariah, Z. K., Brown, P. O., Sherlock, G. 2005; 33: D580-D582

    Abstract

    The Stanford Microarray Database (SMD) (http://smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. In addition, SMD functions as a resource for the entire biological research community by providing unrestricted access to microarray data published by SMD users and by disseminating its source code. In addition to storing GenePix (Axon Instruments) and ScanAlyze output from spotted microarrays, SMD has recently added the ability to store, retrieve, display and analyze the complete raw data produced by several additional microarray platforms and image analysis software packages, so that we can also now accept data from Affymetrix GeneChips (MAS5/GCOS or dChip), Agilent Catalog or Custom arrays (using Agilent's Feature Extraction software) or data created by SpotReader (Niles Scientific). We have implemented software that allows us to accept MAGE-ML documents from array manufacturers and to submit MIAME-compliant data in MAGE-ML format directly to ArrayExpress and GEO, greatly increasing the ease with which data from SMD can be published adhering to accepted standards and also increasing the accessibility of published microarray data to the general public. We have introduced a new tool to facilitate data sharing among our users, so that datasets can be shared during, before or after the completion of data analysis. The latest version of the source code for the complete database package was released in November 2004 (http://smd.stanford.edu/download/), allowing researchers around the world to deploy their own installations of SMD.

    View details for Web of Science ID 000226524300119

    View details for PubMedID 15608265

  • Gene expression profiles and the TP53 mutation status are powerful prognostic markers of breast cancer Langerod, A., Zhao, H., Borgan, O., Nesland, J. M., Hernandez-Boussard, T., Bukholm, I. K., Karesen, R., Borresen-Dale, A. L., Jeffrey, S. S. BIOMED CENTRAL LTD. 2005: S52-S52

    View details for DOI 10.1186/bcr1174

    View details for Web of Science ID 000232330500127

  • Caryoscope: An Open Source Java application for viewing microarray data in a genomic context BMC BIOINFORMATICS Awad, I. A., Rees, C. A., Hernandez-Boussard, T., Ball, C. A., Sherlock, G. 2004; 5

    Abstract

    Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context.We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files), as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript.Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context.

    View details for DOI 10.1186/1471-2105-5-151

    View details for Web of Science ID 000225769900002

    View details for PubMedID 15488149

  • Gastrointestinal stromal tumors (GISTs) with KIT and PDGFRA mutations have distinct gene expression profiles ONCOGENE Subramanian, S., West, R. B., Corless, C. L., Ou, W. B., Rubin, B. P., Chu, K. M., Leung, S. Y., Yuen, S. T., Zhu, S., Hernandez-Boussard, T., Montgomery, K., Nielsen, T. O., Patel, R. M., Goldblum, J. R., Heinrich, M. C., Fletcher, J. A., van de Rijn, M. 2004; 23 (47): 7780-7790

    Abstract

    Most GISTs require oncogenic activation of the KIT or PDGFRA receptor tyrosine kinase proteins, and the genomic mechanisms of oncogene activation are heterogeneous. Notably, the kinase mutation type correlates with both tumor biology and imatinib response. For example, GISTs with KIT exon 11 mutations are typically gastric and have excellent imatinib response, whereas those with KIT exon 9 mutations generally arise in the small bowel and are less responsive to imatinib. To identify genes that might contribute to these biological differences, we carried out gene expression profiling of 26 GISTs with known KIT and PDGFRA mutational status. Expression differences were then evaluated further by RNA in situ hybridization, immunohistochemistry, and immunoblotting. Unsupervised hierarchical clustering grouped tumors with similar mutations together, but the distinction between the different groups was not absolute. Differentially expressed genes included ezrin, p70S6K, and PKCs, which are known to have key roles in KIT or PDGFRA signaling, and which might therefore contribute to the distinctive clinicopathological features in GISTs with different mutation types. These gene products could serve as highly selective therapeutic targets in GISTs containing the KIT or PDGFRA mutational types with which they are associated.

    View details for DOI 10.1038/sj.onc.1208056

    View details for Web of Science ID 000224331600004

    View details for PubMedID 15326474

  • Apo D in soft tissue tumors: a novel marker for dermatofibrosarcoma protuberans (vol 28, pg 1063, 2004) AMERICAN JOURNAL OF SURGICAL PATHOLOGY West, R. B., Harvell, J., Linn, S. C., Lui, C. L., Prapong, W., Hernandez-Boussard, T., Montgomery, K., Nielsen, T. O., Rubin, B. P., Patel, R., Goldblum, J. R., Brown, P. O., van de Rijn, M. 2004; 28 (10): 1400-1400

    View details for Web of Science ID 000224109400023

  • Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma CLINICAL CANCER RESEARCH Nielsen, T. O., Hsu, F. D., Jensen, K., Cheang, M., Karaca, G., Hu, Z. Y., Hernandez-Boussard, T., Livasy, C., Cowan, D., Dressler, L., Akslen, L. A., Ragaz, J., GOWN, A. M., Gilks, C. B., van de Rijn, M. V., Perou, C. M. 2004; 10 (16): 5367-5374

    Abstract

    Expression profiling studies classified breast carcinomas into estrogen receptor (ER)+/luminal, normal breast-like, HER2 overexpressing, and basal-like groups, with the latter two associated with poor outcomes. Currently, there exist clinical assays that identify ER+/luminal and HER2-overexpressing tumors, and we sought to develop a clinical assay for breast basal-like tumors.To identify an immunohistochemical profile for breast basal-like tumors, we collected a series of known basal-like tumors and tested them for protein patterns that are characteristic of this subtype. Next, we examined the significance of these protein patterns using tissue microarrays and evaluated the prognostic significance of these findings.Using a panel of 21 basal-like tumors, which was determined using gene expression profiles, we saw that this subtype was typically immunohistochemically negative for estrogen receptor and HER2 but positive for basal cytokeratins, HER1, and/or c-KIT. Using breast carcinoma tissue microarrays representing 930 patients with 17.4-year mean follow-up, basal cytokeratin expression was associated with low disease-specific survival. HER1 expression was observed in 54% of cases positive for basal cytokeratins (versus 11% of negative cases) and was associated with poor survival independent of nodal status and size. c-KIT expression was more common in basal-like tumors than in other breast cancers but did not influence prognosis.A panel of four antibodies (ER, HER1, HER2, and cytokeratin 5/6) can accurately identify basal-like tumors using standard available clinical tools and shows high specificity. These studies show that many basal-like tumors express HER1, which suggests candidate drugs for evaluation in these patients.

    View details for Web of Science ID 000223454600011

    View details for PubMedID 15328174

  • Apo D in soft tissue tumors - A novel marker for dermatofibrosarcoma protuberans AMERICAN JOURNAL OF SURGICAL PATHOLOGY West, R. B., Harvell, J., Linn, S. C., Lui, C. L., Prapong, W., Hernandez-Boussard, T., Montgomery, K., Nielsen, T. O., Rubin, B. P., Patel, R., Goldblum, J. R., Brown, P. O., van de Rijn, M. 2004; 28 (8): 1063-1069

    Abstract

    Using gene microarray expression profiling, we previously found that apolipoprotein D (Apo D) was highly expressed in dermatofibrosarcoma protuberans (DFSP). In this study, we confirm that Apo D is highly and relatively specifically expressed in DFSP using immunohistochemistry. A tissue microarray containing 421 soft tissue tumors was constructed and stained with antibodies against Apo D and CD34. Cytoplasmic immunostaining for Apo D was found in 9 of 10 typical DFSPs. In addition, 3 of 3 Bednar tumors and 2 of 3 giant cell fibroblastomas stained in conventional sections. In contrast, Apo D was immunoreactive in only a very small subset of a diverse collection of other soft tissue tumors, including Malignant Fibrous Histiocytoma (MFH), glomus tumor, neurofibroma, and malignant peripheral nerve sheath tumors. Immunostains for Apo D were negative in conventional sections of 16 fibrous histiocytomas, and an additional 12 variants of fibrous histiocytoma. Digital images of all immunohistochemical and hematoxylin and eosin tissue microarray stains are available at the accompanying website (http://microarray-pubs.stanford.edu/tma_portal/apod/). We conclude that Apo D is strongly expressed in DFSPs and neural lesions and may be useful in differentiating DFSP from fibrous histiocytoma.

    View details for Web of Science ID 000222891400012

    View details for PubMedID 15252314

  • Lineage-specific gene duplication and loss in human and great ape evolution PLOS BIOLOGY Fortna, A., Kim, Y., MacLaren, E., Marshall, K., Hahn, G., Meltesen, L., Brenton, M., Hink, R., Burgers, S., Hernandez-Boussard, T., Karimpour-Fard, A., Glueck, D., McGavran, L., Berry, R., Pollack, J., Sikela, J. M. 2004; 2 (7): 937-954

    View details for DOI 10.1371/journal.pbio.0020207

    View details for Web of Science ID 000222977900012

  • Lineage-specific gene duplication and loss in human and great ape evolution. PLoS biology Fortna, A., Kim, Y., MacLaren, E., Marshall, K., Hahn, G., Meltesen, L., Brenton, M., Hink, R., Burgers, S., Hernandez-Boussard, T., Karimpour-Fard, A., Glueck, D., McGavran, L., Berry, R., Pollack, J., Sikela, J. M. 2004; 2 (7): E207-?

    Abstract

    Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.

    View details for PubMedID 15252450

  • High-resolution array-based comparative genomic hybridization for distinguishing paraffin-embedded Spitz nevi and melanomas DIAGNOSTIC MOLECULAR PATHOLOGY Harvell, J. D., Kohler, S., Zhu, S., Hernandez-Boussard, T., Pollack, J. R., van de Rijn, M. 2004; 13 (1): 22-25

    Abstract

    Distinguishing between Spitz nevus and melanoma presents a challenging task for clinicians and pathologists. Most of these lesions are submitted entirely in formalin for histologic analysis by conventional hematoxylin and eosin-stained sections, and fresh-frozen material for ancillary studies is rarely collected. Molecular techniques, such as comparative genomic hybridization (CGH), can detect chromosomal alterations in tumor DNA that differ between these 2 lesions. This study investigated the ability of high-resolution array-based CGH to serve as a diagnostic test in distinguishing Spitz nevus and melanoma using DNA isolated from formalin-fixed and paraffin-embedded samples. Two of 3 Spitz nevi exhibited no significant chromosomal alterations, while the third showed gain of the short arm of chromosome 11p. The latter finding has previously been described as characteristic of a subset of Spitz nevi. The 2 melanomas showed multiple copy number alterations characteristic of melanoma such as 1q amplification and chromosome 9 deletion. This study has shown the utility of array-based CGH as a potential molecular test in distinguishing Spitz nevus from melanoma. The assay is capable of using archival paraffin-embedded, formalin-fixed material; is technically easier to perform as compared with conventional CGH; is more sensitive than conventional CGH in being able to detect focal alterations; and can detect copy number alterations even with relatively small amounts of lesional tissue as is typical of many skin tumors.

    View details for Web of Science ID 000189276600004

    View details for PubMedID 15163005

  • Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans AMERICAN JOURNAL OF PATHOLOGY Linn, S. C., West, R. B., Pollack, J. R., Zhu, S., Hernandez-Boussard, T., Nielsen, T. O., Rubin, B. P., Patel, R., Goldblum, J. R., Siegmund, D., Botstein, D., Brown, P. O., Gilks, C. B., van de Rijn, M. 2003; 163 (6): 2383-2395

    Abstract

    Dermatofibrosarcoma protuberans (DFSP) is an aggressive spindle cell neoplasm. It is associated with the chromosomal translocation, t(17:22), which fuses the COL1A1 and PDGFbeta genes. We determined the characteristic gene expression profile of DFSP and characterized DNA copy number changes in DFSP by array-based comparative genomic hybridization (array CGH). Fresh frozen and formalin-fixed, paraffin-embedded samples of DFSP were analyzed by array CGH (four cases) and DNA microarray analysis of global gene expression (nine cases). The nine DFSPs were readily distinguished from 27 other diverse soft tissue tumors based on their gene expression patterns. Genes characteristically expressed in the DFSPs included PDGF beta and its receptor, PDGFRB, APOD, MEOX1, PLA2R, and PRKCA. Array CGH of DNA extracted either from frozen tumor samples or from paraffin blocks yielded equivalent results. Large areas of chromosomes 17q and 22q, bounded by COL1A1 and PDGF beta, respectively, were amplified in DFSP. Expression of genes in the amplified regions was significantly elevated. Our data shows that: 1) DFSP has a distinctive gene expression profile; 2) array CGH can be applied successfully to frozen or formalin-fixed, paraffin-embedded tumor samples; 3) a characteristic amplification of sequences from chromosomes 17q and 22q, demarcated by the COL1A1 and PDGF beta genes, respectively, was associated with elevated expression of the amplified genes.

    View details for Web of Science ID 000186769800024

    View details for PubMedID 14633610

  • Gene expression patterns in ovarian carcinomas MOLECULAR BIOLOGY OF THE CELL Schaner, M. E., Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., Sikic, B. I. 2003; 14 (11): 4376-4386

    Abstract

    We used DNA microarrays to characterize the global gene expression patterns in surface epithelial cancers of the ovary. We identified groups of genes that distinguished the clear cell subtype from other ovarian carcinomas, grade I and II from grade III serous papillary carcinomas, and ovarian from breast carcinomas. Six clear cell carcinomas were distinguished from 36 other ovarian carcinomas (predominantly serous papillary) based on their gene expression patterns. The differences may yield insights into the worse prognosis and therapeutic resistance associated with clear cell carcinomas. A comparison of the gene expression patterns in the ovarian cancers to published data of gene expression in breast cancers revealed a large number of differentially expressed genes. We identified a group of 62 genes that correctly classified all 125 breast and ovarian cancer specimens. Among the best discriminators more highly expressed in the ovarian carcinomas were PAX8 (paired box gene 8), mesothelin, and ephrin-B1 (EFNB1). Although estrogen receptor was expressed in both the ovarian and breast cancers, genes that are coregulated with the estrogen receptor in breast cancers, including GATA-3, LIV-1, and X-box binding protein 1, did not show a similar pattern of coexpression in the ovarian cancers.

    View details for Web of Science ID 000186738300005

    View details for PubMedID 12960427

  • Identification of great ape and human lineage-specific genes using cDNA array-based CGH. Sikela, J., Marshall, K., Kim, Y., MacLaren, E., Hahn, G., Meltesen, L., Hink, R., Burgers, S., Hernandez-Boussard, T., Karimpour-Fard, A., Glueck, D., McGavrin, L., Berry, R., Pollack, J. CELL PRESS. 2003: 431-431

    View details for Web of Science ID 000185599701532

  • The Stanford Microarray Database: data access and quality assessment tools NUCLEIC ACIDS RESEARCH Gollub, J., Ball, C. A., Binkley, G., Demeter, J., Finkelstein, D. B., Hebert, J. M., Hernandez-Boussard, T., Jin, H., Kaloper, M., Matese, J. C., Schroeder, M., Brown, P. O., Botstein, D., Sherlock, G. 2003; 31 (1): 94-96

    Abstract

    The Stanford Microarray Database (SMD; http://genome-www.stanford.edu/microarray/) serves as a microarray research database for Stanford investigators and their collaborators. In addition, SMD functions as a resource for the entire scientific community, by making freely available all of its source code and providing full public access to data published by SMD users, along with many tools to explore and analyze those data. SMD currently provides public access to data from 3500 microarrays, including data from 85 publications, and this total is increasing rapidly. In this article, we describe some of SMD's newer tools for accessing public data, assessing data quality and for data analysis.

    View details for DOI 10.1093/nar/gkg078

    View details for Web of Science ID 000181079700020

    View details for PubMedID 12519956

  • SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data NUCLEIC ACIDS RESEARCH Diehn, M., Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., Cherry, J. M., Botstein, D., Brown, P. O., Alizadeh, A. A. 2003; 31 (1): 219-223

    Abstract

    The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that brings together information from a broad range of resources, and provides it in manner particularly useful for genome-scale analyses. SOURCE's GeneReports include aliases, chromosomal location, functional descriptions, GeneOntology annotations, gene expression data, and links to external databases. We curate published microarray gene expression datasets and allow users to rapidly identify sets of co-regulated genes across a variety of tissues and a large number of conditions using a simple and intuitive interface. SOURCE provides content both in gene and cDNA clone-centric pages, and thus simplifies analysis of datasets generated using cDNA microarrays. SOURCE is continuously updated and contains the most recent and accurate information available for human, mouse, and rat genes. By allowing dynamic linking to individual gene or clone reports, SOURCE facilitates browsing of large genomic datasets. Finally, SOURCEs batch interface allows rapid extraction of data for thousands of genes or clones at once and thus facilitates statistical analyses such as assessing the enrichment of functional attributes within clusters of genes. SOURCE is available at http://source.stanford.edu.

    View details for DOI 10.1093/nar/gkg014

    View details for Web of Science ID 000181079700050

    View details for PubMedID 12519986

  • Integrating mutation data and structural analysis of the TP53 tumor, suppressor protein HUMAN MUTATION Martin, A. C., Facchiano, A. M., Cuff, A. L., Hernandez-Boussard, T., Olivier, M., Hainaut, P., Thornton, J. M. 2002; 19 (2): 149-164

    Abstract

    TP53 encodes p53, which is a nuclear phosphoprotein with cancer-inhibiting properties. In response to DNA damage, p53 is activated and mediates a set of antiproliferative responses including cell-cycle arrest and apoptosis. Mutations in the TP53 gene are associated with more than 50% of human cancers, and 90% of these affect p53-DNA interactions, resulting in a partial or complete loss of transactivation functions. These mutations affect the structural integrity and/or p53-DNA interactions, leading to the partial or complete loss of the protein's function. We report here the results of a systematic automated analysis of the effects of p53 mutations on the structure of the core domain of the protein. We found that 304 of the 882 (34.4%) distinct mutations reported in the core domain can be explained in structural terms by their predicted effects on protein folding or on protein-DNA contacts. The proportion of "explained" mutations increased to 55.6% when substitutions of evolutionary conserved amino acids were included. The automated method of structural analysis developed here may be applied to other frequently mutated gene mutations such as dystrophin, BRCA1, and G6PD.

    View details for Web of Science ID 000173628700008

    View details for PubMedID 11793474

  • The Stanford Microarray Database NUCLEIC ACIDS RESEARCH Sherlock, G., Hernandez-Boussard, T., Kasarskis, A., Binkley, G., Matese, J. C., Dwight, S. S., Kaloper, M., Weng, S., Jin, H., Ball, C. A., Eisen, M. B., Spellman, P. T., Brown, P. O., Botstein, D., Cherry, J. M. 2001; 29 (1): 152-155

    Abstract

    The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two immediate goals for SMD are to serve as a storage site for microarray data from ongoing research at Stanford University, and to facilitate the public dissemination of that data once published, or released by the researcher. Of paramount importance is the connection of microarray data with the biological data that pertains to the DNA deposited on the microarray (genes, clones etc.). SMD makes use of many public resources to connect expression information to the relevant biology, including SGD [Ball,C.A., Dolinski,K., Dwight,S.S., Harris,M.A., Issel-Tarver,L., Kasarskis,A., Scafe,C.R., Sherlock,G., Binkley,G., Jin,H. et al. (2000) Nucleic Acids Res., 28, 77-80], YPD and WormPD [Costanzo,M.C., Hogan,J.D., Cusick,M.E., Davis,B.P., Fancher,A.M., Hodges,P.E., Kondu,P., Lengieza,C., Lew-Smith,J.E., Lingner,C. et al. (2000) Nucleic Acids Res., 28, 73-76], Unigene [Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Nucleic Acids Res., 28, 10-14], dbEST [Boguski,M.S., Lowe,T.M. and Tolstoshev,C.M. (1993) Nature Genet., 4, 332-333] and SWISS-PROT [Bairoch,A. and Apweiler,R. (2000) Nucleic Acids Res., 28, 45-48] and can be accessed at http://genome-www.stanford.edu/microarray.

    View details for Web of Science ID 000166360300039

    View details for PubMedID 11125075

  • Sources of bias in the detection and reporting of p53 mutations in human cancer: analysis of the IARC p53 mutation database Hernandez-Boussard, T., Montesano, R., Hainaut, P. ELSEVIER SCIENCE BV. 1999: 229-233

    Abstract

    p53 gene encodes a transcription factor with tumor suppressive properties and to date, somatic mutation of this gene is the most common genetic event in human cancer. A relational database has been developed to facilitate the retrieval and analysis of these mutations at the International Agency for Research on Cancer (IARC) and it currently contains information on over 8000 individual tumors and cell lines. Many factors may influence the detection and reporting of mutations, including selection of tumor samples, study design, choice of methods, and quality control. There is also concern that several biases may affect the way data appear in the literature. Minimizing these biases is an essential methodological issue in the development of mutation data-bases. In this paper, we review and discuss these main sources of bias and make recommendations to authors in order to minimize bias in mutation detection and reporting.

    View details for Web of Science ID 000078934400015

    View details for PubMedID 10084119

  • IARC p53 mutation database: A relational database to compile and analyze p53 mutations in human tumors and cell lines HUMAN MUTATION Hernandez-Boussard, T., Rodriguez-Tome, P., Montesano, R., Hainaut, P. 1999; 14 (1): 1-8

    Abstract

    The tumor suppressor p53 gene is the most frequently mutated gene in human cancer. To date, more than 10,000 mutations have been described in the literature, and these data are available in various electronic formats on the World Wide Web. Here we describe the structure and format of the different p53 datasets maintained and curated at the International Agency for Research on Cancer (IARC) in Lyon, France. These include p53 somatic mutations (more than 10,000 entries), p53 germline mutations (144 entries), and p53 polymorphisms (13 entries), with the somatic mutations organized into a relational database using AccessTM. The main features of these datasets are (1) controlled entry with standardized format and restricted vocabulary, (2) inclusion of annotations on individual characteristics and exposures, and (3) a classification of pathologies based on the International Classification of Diseases for Oncology (ICD-O). In addition, several interfaces have been developed to analyze the data in order to produce mutation spectra, codon analyses, or visualization of the mutation with the tertiary structure of the protein. All datasets and tools for analysis are available at http://www.iarc.fr/p53/homepage.

    View details for Web of Science ID 000081207100001

    View details for PubMedID 10447253

  • Analysis of somatic mutations of the p53 gene in human cancers: A tool to generate hypotheses about the natural history of cancer Hernandez-Boussard, T., Montesano, R., Hainaut, P. INT AGENCY RESEARCH CANCER. 1999: 43-53

    View details for Web of Science ID 000167234600003

    View details for PubMedID 10353383

  • A specific spectrum of p53 mutations in lung cancer from smokers: Review of mutations compiled in the IARC p53 database ENVIRONMENTAL HEALTH PERSPECTIVES Hernandez-Boussard, T. M., Hainaut, P. 1998; 106 (7): 385-391

    Abstract

    Mutations in the p53 gene are common in lung cancer. Using data from the the International Agency for Research on Cancer p53 mutation database (R1), we have analyzed the distribution and nature of p53 mutations in 876 lung tumors described in the literature. These analyses confirm that G to T transitions are the predominant type of p53 mutation in lung cancer from smokers. The most frequently mutated codons include 157, 158, 179, 248, 249, and 273, and several of them (157, 248, and 273) have been shown to correspond to sites of in vitro DNA adduct formation by metabolites of polycyclic aromatic hydrocarbons (PAHs) such as benzo(a)pyrene. Furthermore, most of the base changes at codons 248, 249, and 273 in lung cancer differ from those commonly observed at these codons in other cancers reported in the database. Thus, lung cancer from smokers shows a distinct, unique p53 mutation spectrum that is not observed in lung cancer from nonsmokers. These results further strengthen the association between active smoking, exposure to PAHs, and lung cancer. They also indicate that a different pattern of mutations occurs in nonsmokers, and this observation may help to identify other agents causally involved in lung cancer in nonsmokers.

    View details for Web of Science ID 000075380700018

    View details for PubMedID 9637795

  • IARC Database of p53 gene mutations in human tumors and cell lines: updated compilation, revised formats and new visualisation tools NUCLEIC ACIDS RESEARCH Hainaut, P., Hernandez, T., Robinson, A., Rodriguez-Tome, P., Flores, T., Hollstein, M., Harris, C. C., Montesano, R. 1998; 26 (1): 205-213

    Abstract

    Since 1989, about 570 different p53 mutations have been identified in more than 8000 human cancers. A database of these mutations was initiated by M. Hollstein and C. C. Harris in 1990. This database originally consisted of a list of somatic point mutations in the p 53 gene of human tumors and cell lines, compiled from the published literature and made available in a standard electronic form. The database is maintained at the International Agency for Research on Cancer (IARC) and updated versions are released twice a year (January and July). The current version (July 1997) contains records on 6800 published mutations and will surpass the 8000 mark in the January 1998 release. The database now contains information on somatic and germline mutations in a new format to facilitate data retrieval. In addition, new tools are constructed to improve data analysis, such as a Mutation Viewer Java applet developed at the European Bioinformatics Institute (EBI) to visualise the location and impact of mutations on p53 protein structure. The database is available in different electronic formats at IARC (http://www.iarc. fr/p53/homepage.htm ) or from the EBI server (http://www.ebi.ac.uk ). The IARC p53 website also provides reports on database analysis and links with other p53 sites as well as with related databases. In this report, we describe the criteria for inclusion of data, the revised format and the new visualisation tools. We also briefly discuss the relevance of p 53 mutations to clinical and biological questions.

    View details for Web of Science ID 000071778900049

    View details for PubMedID 9399837