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https://www.readbyqxmd.com/read/27899675/jet2-viewer-a-database-of-predicted-multiple-possibly-overlapping-protein-protein-interaction-sites-for-pdb-structures
#1
Hughes Ripoche, Elodie Laine, Nicoletta Ceres, Alessandra Carbone
The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET(2) at large-scale on more than 20 000 chains. JET(2) strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET(2) analyses...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27893191/young-investigator-challenge-molecular-testing-in-noninvasive-follicular-thyroid-neoplasm-with-papillary-like-nuclear-features
#2
Xiaoyin Sara Jiang, Grant P Harrison, Michael B Datto
BACKGROUND: Molecular testing provides an important ancillary study for thyroid nodules with indeterminate cytology. The nomenclature shift to "noninvasive follicular thyroid neoplasm with papillary-like nuclear features" (NIFTP) will impact the performance of molecular tests. For the current study, the authors reviewed the performance of the Afirma gene-expression classifier (GEC) and the University of Pittsburgh Medical Center (UPMC) targeted mutation panel tests in thyroid nodules that were subsequently diagnosed as NIFTP on surgical resection...
November 28, 2016: Cancer
https://www.readbyqxmd.com/read/27889492/surgical-complications-following-early-genitourinary-reconstructive-surgery-for-congenital-adrenal-hyperplasia-interim-analysis-at-6-years
#3
Pankaj Dangle, Andy Lee, Rajeev Chaudhry, Francis X Schneck
OBJECTIVE: To review the intermediate to long-term surgical complications following feminizing reconstructive surgery for patients with congenital adrenal hyperplasia (CAH), at a single tertiary center. Genitourinary reconstructive surgery is pivotal for favorable cosmetic and functional outcome for patients with CAH. MATERIAL AND METHODS: We conducted a retrospective review identifying 26 patients from April 2003 to April 2015 who underwent genitourinary reconstructive surgeries...
November 23, 2016: Urology
https://www.readbyqxmd.com/read/27880082/perceived-performance-and-impact-of-a-non-physician-led-interprofessional-team-in-a-trauma-clinic-setting
#4
Julia Driessen, Johanna E Bellon, Joel Stevans, Raquel M Forsythe, Benjamin R Reynolds, A Everette James
Faced with the challenge of meeting the wide degree of post-discharge needs in their trauma population, the University of Pittsburgh Medical Center (UPMC) developed a non-physician-led interprofessional team to provide follow-up care at its UPMC Falk Trauma Clinic. We assessed this model of care using a survey to gauge team member perceptions of this model, and used clinic visit documentation to apply a novel approach to assessing how this model improves the care received by clinic patients. The high level of perceived team performance and cohesion suggests that this model has been successful thus far from a provider perspective...
November 23, 2016: Journal of Interprofessional Care
https://www.readbyqxmd.com/read/27845339/a-combination-of-muc5ac-and-ca19-9-improves-the-diagnosis-of-pancreatic-cancer-a-multicenter-study
#5
Sukhwinder Kaur, Lynette M Smith, Asish Patel, Melanie Menning, Duncan C Watley, Saad S Malik, Shiv Ram Krishn, Kavita Mallya, Abhijit Aithal, Aaron R Sasson, Sonny L Johansson, Maneesh Jain, Shailender Singh, Sushovan Guha, Chandrakanth Are, Massimo Raimondo, Michael A Hollingsworth, Randall E Brand, Surinder K Batra
OBJECTIVES: Pancreatic cancer (PC) is a lethal malignancy that lacks specific diagnostic markers. The present study explores the diagnostic potential of the most differentially overexpressed secretory mucin MUC5AC alone and in combination with CA19-9 using multi-center training and validation sets. METHODS: The expression of MUC5AC in benign pancreatic pathologies, PC precursor lesions, primary PC tissues and metastatic lesions was evaluated by immunohistochemistry...
November 15, 2016: American Journal of Gastroenterology
https://www.readbyqxmd.com/read/27783544/evaluating-the-impact-of-sample-medication-on-subsequent-patient-adherence
#6
Janice L Pringle, Arnie Aldridge, Shannon M Kearney, Kim Grasso, John Radack, Susan Hogue, Chronis Manolis
BACKGROUND: Medication nonadherence is problematic throughout health care practice. Patient nonadherence is a result of several factors, such as financial issues, confusion about the medication, or concerns about possible side effects. Efforts to improve adherence have been implemented, but new strategies are needed to ensure that patients fill their medication prescriptions and adhere to their prescribed use. OBJECTIVE: To investigate whether providing patients with a free 30-day supply of medication at the point of care via a dispensing kiosk-a secure, computerized cabinet placed in the prescriber's office-that provides sample medication and educational materials had a measurable impact on adherence and health care cost...
November 2016: Journal of Managed Care & Specialty Pharmacy
https://www.readbyqxmd.com/read/27780583/development-of-an-evidence-based-decision-pathway-for-vestibular-schwannoma-treatment-options
#7
Faina Linkov, Benita Valappil, Jacob McAfee, Sharon L Goughnour, Douglas M Hildrew, Andrew A McCall, Igor Linkov, Barry Hirsch, Carl Snyderman
OBJECTIVE: To integrate multiple sources of clinical information with patient feedback to build evidence-based decision support model to facilitate treatment selection for patients suffering from vestibular schwannomas (VS). METHODS: This was a mixed methods study utilizing focus group and survey methodology to solicit feedback on factors important for making treatment decisions among patients. Two 90-minute focus groups were conducted by an experienced facilitator...
September 30, 2016: American Journal of Otolaryngology
https://www.readbyqxmd.com/read/27675951/outcomes-of-stage-ii-endometrial-cancer-upmc-cancer-center-experience
#8
H Berhane, B S Gill, M Bernard, A Olawaiye, S Paniti, J L Kelley, S Beriwal
No abstract text is available yet for this article.
October 1, 2016: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/27619390/development-of-an-inflammatory-bowel-disease-research-registry-derived-from-observational-electronic-health-record-data-for-comprehensive-clinical-phenotyping
#9
Alyce J M Anderson, Benjamin Click, Claudia Ramos-Rivers, Dmitriy Babichenko, Ioannis E Koutroubakis, Douglas J Hartman, Jana G Hashash, Marc Schwartz, Jason Swoger, Arthur M Barrie, Michael A Dunn, Miguel Regueiro, David G Binion
BACKGROUND: Inflammatory bowel disease (IBD) is a heterogeneous collection of chronic inflammatory disorders of the digestive tract. Clinical, genetic, and pathological heterogeneity makes it increasingly difficult to translate efficacy studies into real-world practice. Our objective was to develop a comprehensive natural history registry derived from multi-year observational data to facilitate effectiveness and clinical phenotypic research in IBD. METHODS: A longitudinal, consented registry with prospectively collected data was developed at UPMC...
November 2016: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/27557451/the-diagnostic-accuracy-of-somatosensory-evoked-potentials-in-evaluating-new-neurological-deficits-after-posterior-cervical-fusions
#10
Parthasarathy D Thirumala, Samyuktha R Melachuri, Jaspreet Kaur, David Ninaci, Manasa K Melachuri, Miguel E Habeych, Donald J Crammond, Jeffrey R Balzer
STUDY DESIGN: This study examined the diagnostic accuracy of significant changes of somatosensory evoked potentials (SSEPs) to evaluate and predict post-operative neurological deficits after posterior cervical fusions (PCF). 846 eligible patients underwent PCF at the University of Pittsburgh Medical Center (UPMC), from 2010 to 2012. OBJECTIVE: to assess the specificity and sensitivity of intraoperative monitoring in predicting post-operative neurological deficits during PCF...
August 24, 2016: Spine
https://www.readbyqxmd.com/read/27472895/improvement-in-protein-domain-identification-is-reached-by-breaking-consensus-with-the-agreement-of-many-profiles-and-domain-co-occurrence
#11
Juliana Bernardes, Gerson Zaverucha, Catherine Vaquero, Alessandra Carbone
Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences. However, when relevant signals become too weak to be identified by a global consensus, attempts for annotation fail. Here we address the fundamental question of domain identification for highly divergent proteins. By using high performance computing, we demonstrate that the limits of state-of-the-art annotation methods can be bypassed. We design a new strategy based on the observation that many structural and functional protein constraints are not globally conserved through all species but might be locally conserved in separate clades...
July 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27450967/endoscopic-sphincterotomy-es-may-not-alter-the-natural-history-of-idiopathic-recurrent-acute-pancreatitis-irap
#12
Rohit Das, Bridger Clarke, Gong Tang, Georgios I Papachristou, David C Whitcomb, Adam Slivka, Dhiraj Yadav
BACKGROUND: The role of endoscopic sphincterotomy (ES) in idiopathic recurrent acute pancreatitis (IRAP) is unclear. We hypothesized that ES will alter the natural history of IRAP. METHODS: We retrospectively studied the course of 50 IRAP patients from the NAPS2 study from UPMC based on whether they underwent ES or were managed medically. Data included age at first AP, rate of attacks, and history of severe AP. Primary outcomes were any subsequent AP and rate of attacks; secondary outcome was chronic pancreatitis (CP) diagnosis during follow-up...
September 2016: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
https://www.readbyqxmd.com/read/27257702/severe-complicated-clostridium-difficile-infection-can-the-upmc-proposed-scoring-system-predict-the-need-for-surgery
#13
Michelle Julien, Jeffrey L Wild, Joseph Blansfield, Mohsen Shabahang, Kristen Halm, Paul Meade, James Dove, Marcus Fluck, Marie Hunsinger, Diane Leonard
INTRODUCTION: Clostridium difficile infection (CDI) is one of the most common health care-associated infections, and it continues to have significant morbidity and mortality. The onset of fulminant colitis often requires total abdominal colectomy with ileostomy, which has a mortality rate of 35% to 57%. University of Pittsburgh Medical Center (UPMC) developed a scoring system for severity and recommended surgical consultation for severe complicated disease. The aim of this study was to evaluate if the UPMC-proposed scoring system for severe complicated CDI can predict the need for surgical intervention...
August 2016: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/27221995/pathways-clinical-decision-support-for-appropriate-use-of-key-biomarkers
#14
Peter G Ellis, Adam M Brufsky, Sushil Beriwal, Kathleen G Lokay, Hans O Benson, Stephanie B McCutcheon, Melinda Krebs
PURPOSE: Breast cancer diagnostics have the ability to predict disease recurrence and the benefit of chemotherapy. This study measures the use of a diagnostic assay, Oncotype DX, when embedded in a breast cancer decision support algorithm and, on the basis of the assay results, the use of chemotherapy in the adjuvant setting. METHODS: UPMC CancerCenter retrospectively reviewed patients with estrogen receptor-positive, human epidermal growth factor receptor 2 (HER2)Neu-negative disease with zero to three positive nodes navigated in the Via Pathways decision support portal during a 12-month period...
June 2016: Journal of Oncology Practice
https://www.readbyqxmd.com/read/27176160/changes-in-hysterectomy-trends-and-patient-outcomes-following-the-implementation-of-a-clinical-pathway-7
#15
Suketu M Mansuria, John Comerci, Robert Edwards, Amin Sanei Moghaddam, Tianzhou Ma, Faina Linkov
INTRODUCTION: The goal of this project is to describe the development and implementation of an evidence-based hysterectomy clinical pathway to reduce unnecessary variations in care and to promote improved patient outcomes at a reduced cost. This study characterized the longitudinal impact of hysterectomy pathway implementation on the number of total abdominal hysterectomy (TAH) procedures performed between fiscal years (FY) 2012 to 2014. METHODS: All noncancerous hysterectomy surgeries performed at University of Pittsburgh Medical Center (UPMC) hospitals from FY 2012 to FY 2014 were identified through various systems including Medipac and EpicCare...
May 2016: Obstetrics and Gynecology
https://www.readbyqxmd.com/read/27142839/assessing-career-outcomes-of-a-resident-academic-administrator-clinician-educator-track-a-seven-year-follow-up
#16
Anne E Penner, Wynne Lundblad, Pierre N Azzam, Priya Gopalan, Sansea L Jacobson, Michael J Travis
OBJECTIVE: This study reports the academic outcomes, including scholarly productivity, of the graduates of one residency training track for future clinician educators and academic administrators. Since its implementation in 2008, the Academic Administrator, Clinician Educator (AACE) track at Western Psychiatric Institute and Clinic - UPMC has grown in popularity with reports of participants achieving post-graduate academic success; however, there has been no prior assessment of outcomes...
May 3, 2016: Academic Psychiatry
https://www.readbyqxmd.com/read/26955500/how-can-we-improve-science-technology-engineering-and-math-education-to-encourage-careers-in-biomedical-and-pathology-informatics
#17
Rahul Uppal, Gunasheil Mandava, Katrina M Romagnoli, Andrew J King, Amie J Draper, Adam L Handen, Arielle M Fisher, Michael J Becich, Joyeeta Dutta-Moscato
The Computer Science, Biology, and Biomedical Informatics (CoSBBI) program was initiated in 2011 to expose the critical role of informatics in biomedicine to talented high school students.[1] By involving them in Science, Technology, Engineering, and Math (STEM) training at the high school level and providing mentorship and research opportunities throughout the formative years of their education, CoSBBI creates a research infrastructure designed to develop young informaticians. Our central premise is that the trajectory necessary to be an expert in the emerging fields of biomedical informatics and pathology informatics requires accelerated learning at an early age...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/26903336/developing-a-new-definition-and-assessing-new-clinical-criteria-for-septic-shock-for-the-third-international-consensus-definitions-for-sepsis-and-septic-shock-sepsis-3
#18
REVIEW
Manu Shankar-Hari, Gary S Phillips, Mitchell L Levy, Christopher W Seymour, Vincent X Liu, Clifford S Deutschman, Derek C Angus, Gordon D Rubenfeld, Mervyn Singer
IMPORTANCE: Septic shock currently refers to a state of acute circulatory failure associated with infection. Emerging biological insights and reported variation in epidemiology challenge the validity of this definition. OBJECTIVE: To develop a new definition and clinical criteria for identifying septic shock in adults. DESIGN, SETTING, AND PARTICIPANTS: The Society of Critical Care Medicine and the European Society of Intensive Care Medicine convened a task force (19 participants) to revise current sepsis/septic shock definitions...
February 23, 2016: JAMA: the Journal of the American Medical Association
https://www.readbyqxmd.com/read/26866645/does-a-weekly-didactic-conference-improve-resident-performance-on-the-pediatric-domain-of-the-orthopaedic-in-training-examination
#19
Corinna C Franklin, Patrick P Bosch, Jan S Grudziak, Ozgur Dede, Rey N Ramirez, Steven A Mendelson, W Timothy Ward, Maria Brooks, Tanya Kenkre, John D Lubahn, Vincent F Deeney, James W Roach
BACKGROUND: Performance on the Orthopaedic In-training Examination (OITE) has been correlated with performance on the written portion of the American Board of Orthopaedic Surgery examination. Herein we sought to discover whether adding a regular pediatric didactic lecture improved residents' performance on the OITE's pediatric domain. METHODS: In 2012, a didactic lecture series was started in the University of Pittsburgh Medical Center (UPMC) Hamot Orthopaedic Residency Program (Hamot)...
February 10, 2016: Journal of Pediatric Orthopedics
https://www.readbyqxmd.com/read/26823083/dissecting-protein-architecture-with-communication-blocks-and-communicating-segment-pairs
#20
Yasaman Karami, Elodie Laine, Alessandra Carbone
BACKGROUND: Proteins adapt to environmental conditions by changing their shape and motions. Characterising protein conformational dynamics is increasingly recognised as necessary to understand how proteins function. Given a conformational ensemble, computational tools are needed to extract in a systematic way pertinent and comprehensive biological information. RESULTS: Here, we present a method, Communication Mapping (COMMA), to decipher the dynamical architecture of a protein...
2016: BMC Bioinformatics
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