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https://www.readbyqxmd.com/read/29141660/xcell-digitally-portraying-the-tissue-cellular-heterogeneity-landscape
#1
Dvir Aran, Zicheng Hu, Atul J Butte
Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene signature-based method, and use it to infer 64 immune and stromal cell types. We harmonized 1822 pure human cell type transcriptomes from various sources and employed a curve fitting approach for linear comparison of cell types and introduced a novel spillover compensation technique for separating them...
November 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/29129350/evaluation-of-ecg-algorithms-designed-to-improve-detect-of-transient-myocardial-ischemia-to-minimize-false-alarms-in-patients-with-suspected-acute-coronary-syndrome
#2
Michele M Pelter, Yuan Xu, Richard Fidler, Ran Xiao, David W Mortara, Hu Xiao
BACKGROUND: Patients hospitalized for suspected acute coronary syndrome (ACS) are at risk for transient myocardial ischemia. During the "rule-out" phase, continuous ECG ST-segment monitoring can identify transient myocardial ischemia, even when asymptomatic. However, current ST-segment monitoring software is vastly underutilized due to false positive alarms, with resultant alarm fatigue. Current ST algorithms may contribute to alarm fatigue because; (1) they are not designed with a delay (minutes), rather alarm to brief spikes (i...
October 24, 2017: Journal of Electrocardiology
https://www.readbyqxmd.com/read/29116980/rethinking-the-educator-portfolio-an-innovative-criteria-based-model
#3
Kanade Shinkai, Chen Amy Chen, Brian S Schwartz, Helen Loeser, Cynthia Ashe, David M Irby
PROBLEM: Academic medical centers struggle to achieve parity in advancement and promotions between educators and discovery-oriented researchers in part because of narrow definitions of scholarship, lack of clear criteria for measuring excellence, and barriers to making educational contributions available for peer review. Despite recent progress in expanding scholarship definitions and identifying excellence criteria, these advances are not integrated into educator portfolio (EP) templates or curriculum vitae platforms...
November 7, 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/29106441/orchid-a-novel-management-annotation-and-machine-learning-framework-for-analyzing-cancer-mutations
#4
Clinton L Cario, John S Witte
Motivation: As whole-genome tumor sequence and biological annotation datasets grow in size, number, and content, there is an increasing basic science and clinical need for efficient and accurate data management and analysis software. With the emergence of increasingly sophisticated data stores, execution environments, and machine learning algorithms, there is also a need for the integration of functionality across frameworks. Results: We present orchid, a python based software package for the management, annotation, and machine learning of cancer mutations...
November 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29088948/safety-and-effectiveness-of-early-chemical-deep-venous-thrombosis-prophylaxis-after-spinal-cord-injury-pilot-prospective-data
#5
Anthony M DiGiorgio, Rachel Tsolinas, Mohanad Alazzeh, Jenny Haefeli, Jason F Talbott, Adam R Ferguson, Jacqueline C Bresnahan, Michael S Beattie, Geoffrey T Manley, William D Whetstone, Praveen V Mummaneni, Sanjay S Dhall
OBJECTIVE Spinal cord injuries (SCIs) occur in approximately 17,000 people in the US each year. The average length of hospital stay is 11 days, and deep venous thrombosis (DVT) rates as high as 65% are reported in these patients. There is no consensus on the appropriate timing of chemical DVT prophylaxis for this critically injured patient cohort. The object of this study was to determine if low-molecular-weight heparin (LMWH) was safe and effective if given within 24 hours of SCI. METHODS The Transforming Research and Clinical Knowledge in SCIs study is a prospective observational study conducted by the UCSF Brain and Spinal Injury Center...
November 2017: Neurosurgical Focus
https://www.readbyqxmd.com/read/29059638/high-quality-rendering-of-protein-dynamics-in-space-filling-mode
#6
Nick Matthews, Robert Easdon, Akio Kitao, Steven Hayward, Stephen Laycock
Producing high quality depictions of molecular structures has been an area of academic interest for years, with visualisation tools such as UCSF Chimera, Yasara and PyMol providing a huge number of different rendering modes and lighting effects. However, no visualisation program supports per-pixel lighting effects with shadows whilst rendering a molecular trajectory in space filling mode. In this paper, a new approach to rendering high quality visualisations of molecular trajectories is presented. To enhance depth, ambient occlusion is included within the render...
September 29, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28989060/metroticket-2-0-model-for-analysis-of-competing-risks-of-death-following-liver-transplantation-for-hepatocellular-carcinoma
#7
Vincenzo Mazzaferro, Carlo Sposito, Jian Zhou, Antonio D Pinna, Luciano De Carlis, Jia Fan, Matteo Cescon, Stefano Di Sandro, He Yi-Feng, Andrea Lauterio, Marco Bongini, Alessandro Cucchetti
BACKGROUND & AIMS: Outcomes of liver transplantation for hepatocellular carcinoma (HCC) are determined by cancer-related and non-related events. Treatments for hepatitis C virus (HCV) infection have reduced non-cancer events among patients receiving liver transplants, so reducing HCC-related death might be an actionable endpoint. We performed a competing risk analysis to evaluate factors associated with survival of patients with HCC, and developed a prognostic model based on features of HCC patients before liver transplantation...
October 5, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28984590/disinhibition-in-alzheimer-s-disease-is%C3%A2-associated-with-reduced-right-frontal-pole-cortical-thickness
#8
Elizabeth Finger, Jing Zhang, Bradford Dickerson, Yves Bureau, Mario Masellis
Neuropsychiatric symptoms in Alzheimer's disease are among the most disabling and difficult aspects for caregivers and treating health professionals to manage. Despite the high prevalence of these behaviors, little is known about the factors which lead some patients to develop florid behavioral symptoms while others may progress to severe dementia without such phenomenon. We examined whether regional brain volumes as measured by cortical thickness would predict the presence or absence of disinhibition in patients with Alzheimer's disease...
2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28973834/the-relationship-between-poverty-and-mortality-in-systemic-lupus-erythematosus
#9
Edward Yelin, Jinoos Yazdany, Laura Trupin
OBJECTIVES: A prior study established that concurrent poverty, persistent poverty, and exiting poverty were associated with the subsequent extent of damage accumulation in systemic lupus erythematosus (SLE). The present study examines whether concurrent poverty affects mortality after taking extent of damage accumulation into account. METHODS: Analyses were conducted on 807 persons with SLE participating in the UCSF Lupus Outcomes Study in 2009, stratified by whether they were in households ≤125% of the Federal Poverty Level in that year...
October 3, 2017: Arthritis Care & Research
https://www.readbyqxmd.com/read/28920518/the-indirect-costs-of-underfunding-foreign-partners-in-global-health-research-a-case-study
#10
Johanna T Crane, Irene Andia Biraro, Tamer M Fouad, Yap Boum, David R Bangsberg
This study of a global health research partnership assesses how U.S. fiscal administrative policies impact capacity building at foreign partner institutions. We conducted a case study of a research collaboration between Mbarara University of Science and Technology (MUST) in Mbarara, Uganda, and originally the University of California San Francisco (UCSF), but now Massachusetts General Hospital (MGH). Our case study is based on three of the authors' experiences directing and working with this partnership from its inception in 2003 through 2015...
September 16, 2017: Global Public Health
https://www.readbyqxmd.com/read/28894793/infiltrative-hepatocellular-carcinoma-with-portal-vein-tumor-thrombosis-treated-with-a-single-high-dose-y90-radioembolization-and-subsequent-liver-transplantation-without-a-recurrence
#11
Meaghan S Dendy, Juan C Camacho, Johannes M Ludwig, Alyssa M Krasinskas, Stuart J Knechtle, Hyun S Kim
BACKGROUND: Infiltrative hepatocellular carcinoma with macrovascular invasion is a relatively rare presentation and usually fatal disease. METHODS: Both patients exceeded Milan and University of California-San Francisco (UCSF) criteria, and per Barcelona Clinic Liver Cancer group guidelines, they were enrolled in a prospective open-label radioembolization phase II trial that gave them optimized lobar doses of Yttrium-90 as solely the first-line therapy without concomitant or additional pharmacological or locoregional therapies...
September 2017: Transplantation Direct
https://www.readbyqxmd.com/read/28827903/predictors-of-outcome-of-living-donor-liver-transplantation-for-hepatocellular-carcinoma
#12
Hazem Mohamed Zakaria, Ahmed N Sallam, Islam I Ayoub, Sherif M Saleh, Doha Maher, Hazem Omar, Mohamed Abou-Shady, Ibrahim A Salama, El-Sayed A Soliman, Khaled Abou El-Ella, Tarek M Ibrahim, Essam M Hammad
The aim of this work is to study the different factors that affect the outcome of living donor liver transplantation for patients with hepatocellular carcinoma (HCC). Between April 2003 to November 2014, 62 patients with liver cirrhosis and HCC underwent living donor liver transplantation (LDLT) in the National Liver Institute, Menoufia University, Egypt. The preoperative, operative, and postoperative data were analyzed. After studying the pathology of explanted liver; 44 (71 %) patients were within the Milan criteria, and 18 (29 %) patients were beyond Milan; 13 (21...
August 2017: Indian Journal of Surgery
https://www.readbyqxmd.com/read/28815132/precision-diagnosis-of-melanoma-and-other-skin-lesions-from-digital-images
#13
Abhishek Bhattacharya, Albert Young, Andrew Wong, Simone Stalling, Maria Wei, Dexter Hadley
Melanoma will affect an estimated 73,000 new cases this year and result in 9,000 deaths, yet precise diagnosis remains a serious problem. Without early detection and preventative care, melanoma can quickly spread to become fatal (Stage IV 5-year survival rate is 20-10%) from a once localized skin lesion (Stage IA 5- year survival rate is 97%). There is no biomarker for melanoma in clinical use, and the current diagnostic criteria for skin lesions remains subjective and imprecise. Accurate diagnosis of melanoma relies on a histopathologic gold standard; thus, aggressive excision of melanocytic skin lesions has been the mainstay of treatment...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28811326/-10m-gift-supports-data-recycling-at-ucsf
#14
(no author information available yet)
The University of California, San Francisco's Institute for Computational Health Sciences has received a $10 million gift to support "data recycling" investigations. The approach to medical research involves mining existing data to potentially uncover new uses for existing drugs and help improve clinical care.
August 15, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28736970/report-from-the-2016-university-of-california-san-francisco-center-for-reproductive-sciences-retreat
#15
Paolo F Rinaudo, Marco Conti
No abstract text is available yet for this article.
October 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/28732459/crispulator-a-discrete-simulation-tool-for-pooled-genetic-screens
#16
Tamas Nagy, Martin Kampmann
BACKGROUND: The rapid adoption of CRISPR technology has enabled biomedical researchers to conduct CRISPR-based genetic screens in a pooled format. The quality of results from such screens is heavily dependent on the selection of optimal screen design parameters, which also affects cost and scalability. However, the cost and effort of implementing pooled screens prohibits experimental testing of a large number of parameters. RESULTS: We present CRISPulator, a Monte Carlo method-based computational tool that simulates the impact of screen parameters on the robustness of screen results, thereby enabling users to build intuition and insights that will inform their experimental strategy...
July 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28724802/partially-exhausted-tumor-infiltrating-lymphocytes-predict-response-to-combination-immunotherapy
#17
Kimberly Loo, Katy K Tsai, Kelly Mahuron, Jacqueline Liu, Mariela L Pauli, Priscila M Sandoval, Adi Nosrati, James Lee, Lawrence Chen, Jimmy Hwang, Lauren S Levine, Matthew F Krummel, Alain P Algazi, Michael D Alvarado, Michael D Rosenblum, Adil I Daud
BACKGROUND: Programmed death 1 (PD-1) inhibition activates partially exhausted cytotoxic T lymphocytes (peCTLs) and induces tumor regression. We previously showed that the peCTL fraction predicts response to anti-PD-1 monotherapy. Here, we sought to correlate peCTL and regulatory T lymphocyte (Treg) levels with response to combination immunotherapy, and with demographic/disease characteristics, in metastatic melanoma patients. METHODS: Pretreatment melanoma samples underwent multiparameter flow cytometric analysis...
July 20, 2017: JCI Insight
https://www.readbyqxmd.com/read/28713803/the-institute-for-global-orthopedics-and-traumatology-a-model-for-academic-collaboration-in-orthopedic-surgery
#18
Devin James Conway, Richard Coughlin, Amber Caldwell, David Shearer
In 2006, surgeons at the University of California, San Francisco (UCSF) established the Institute for Global Orthopedics and Traumatology (IGOT), an initiative within the department of orthopedic surgery. The principal aim of IGOT is to create long-term, sustainable solutions to the growing burden of musculoskeletal injury in low- and middle-income countries (LMICs) through academic partnership. IGOT currently has relationships with teaching hospitals in Ghana, Malawi, Tanzania, Nicaragua, and Nepal. The organizational structure of IGOT is built on four pillars: Global Surgical Education (GSE), Global Knowledge Exchange (GKE), Global Research Initiative (GRI), and Global Leadership and Advocacy...
2017: Frontiers in Public Health
https://www.readbyqxmd.com/read/28710774/ucsf-chimerax-meeting-modern-challenges-in-visualization-and-analysis
#19
Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin
UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This paper highlights some specific advances in the areas of visualization and usability, performance, and extensibility...
July 14, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28654694/ethnic-differences-in-lens-parameters-measured-by-ocular-biometry-in-a-cataract-surgery-population
#20
Dajiang Wang, Behzad Amoozgar, Travis Porco, Zhen Wang, Shan C Lin
PURPOSE: To investigate whether differences exist in lens position and other lens parameters among major ethnic groups with cataractous eyes, which may help explain racial differences in angle closure risk. METHODS: This retrospective, cross-sectional study included 807 adult patients who had cataract surgery between years 2014 and 2016 at the University of California, San Francisco (UCSF). Adult patients of white, Asian, Hispanic and African-American ethnicity were included...
2017: PloS One
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