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https://www.readbyqxmd.com/read/28334409/siapopr-a-computational-method-to-simulate-evolutionary-branching-trees-for-analysis-of-tumor-clonal-evolution
#1
Thomas O McDonald, Franziska Michor
Summary: SIApopr (Simulating Infinite-Allele populations) is an R package to simulate homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334344/estimating-gene-regulatory-networks-with-pandar
#2
Daniel Schlauch, Joseph N Paulson, Albert Young, Kimberly Glass, John Quackenbush
PANDA (Passing Attributes betweenNetworks forData Assimilation) is a gene regulatory network inference method that begins with amodel of transcription factor-target gene interactions and usesmessage passing to update the network model given available transcriptomic and protein-protein interaction data. PANDA is used to estimate networks for each experimental group and the network models are then compared between groups to explore transcriptional processes that distinguish the groups. We present pandaR (bioconductor...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334167/identification-of-genetic-outliers-due-to-sub-structure-and-cryptic-relationships
#3
Daniel Schlauch, Heide Fier, Christoph Lange
Motivation: In order to minimize the effects of genetic confounding on the analysis of high-throughput genetic association studies, e.g. (whole-genome) sequencing (WGS) studies, genome-wide association studies (GWAS), etc., we propose a general framework to assess and to test formally for genetic heterogeneity among study subjects. As the approach fully utilizes the recent ancestor information captured by rare variants, it is especially powerful in WGS studies. Even for relatively moderate sample sizes, the proposed testing framework is able to identify study subjects that are genetically too similar, e...
February 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28328735/building-workforce-capacity-abroad-while-strengthening-global-health-programs-at-home-participation-of-seven-harvard-affiliated-institutions-in-a-health-professional-training-initiative-in-rwanda
#4
Corrado Cancedda, Robert Riviello, Kim Wilson, Kirstin W Scott, Meenu Tuteja, Jane R Barrow, Bethany Hedt-Gauthier, Gene Bukhman, Jennifer Scott, Danny Milner, Giuseppe Raviola, Barbara Weissman, Stacy Smith, Tej Nuthulaganti, Craig D McClain, Barbara E Bierer, Paul E Farmer, Anne E Becker, Agnes Binagwaho, Joseph Rhatigan, David E Golan
A consortium of 22 U.S. academic institutions is currently participating in the Rwanda Human Resources for Health Program (HRH Program). Led by the Rwandan Ministry of Health and funded by both the U.S. Government and the Global Fund to Fight AIDS, Tuberculosis and Malaria, the primary goal of this seven-year initiative is to help Rwanda train the number of health professionals necessary to reach the country's health workforce targets. Since 2012, the participating U.S. academic institutions have deployed faculty from a variety of health-related disciplines and clinical specialties to Rwanda...
March 21, 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/28328493/a-balancing-act-scientists-seek-to-reduce-the-risk-of-falls-in-the-elderly
#5
Jennifer Berglund
It was the inaugural day of the study in 2005 when Brad Manor went out into the hot Louisiana sun to meet his first patient, a gentleman we'll call James. Manor, now director of the Mobility and Brain Function Lab at the Harvard-affiliated Institute for Aging Research, was, at that time, a Ph.D. student at Louisiana State University (Figure 1). James, a man in his early 70s, suffered from peripheral neuropathy, a condition that caused significant nerve damage in his legs and feet. James got out of his car, carrying his cane in his hand, and walked with Manor to the lab...
March 2017: IEEE Pulse
https://www.readbyqxmd.com/read/28320355/severe-war-related-trauma-and-personality-pathology-a-case-control-study
#6
Jasna Munjiza, Dolores Britvic, Maja Radman, Mike J Crawford
BACKGROUND: Exposure to war-related trauma has long been recognised to have an adverse effect on mental health. We attempted to investigate whether people who have clinically significant personality-related problems 15 years after a war are more likely to have been exposed to severe war-related trauma than those who do not have significant personality difficulties. METHODS: A case -control study was conducted in southern Croatia, fifteen years after the 1991-1995 war...
March 21, 2017: BMC Psychiatry
https://www.readbyqxmd.com/read/28315741/individual-classification-of-alzheimer-s-disease-with-diffusion-magnetic-resonance-imaging
#7
Tijn M Schouten, Marisa Koini, Frank de Vos, Stephan Seiler, Mark de Rooij, Anita Lechner, Reinhold Schmidt, Martijn van den Heuvel, Jeroen van der Grond, Serge A R B Rombouts
Diffusion magnetic resonance imaging (MRI) is a powerful non-invasive method to study white matter integrity, and is sensitive to detect differences in Alzheimer's disease (AD) patients. Diffusion MRI may be able to contribute towards reliable diagnosis of AD. We used diffusion MRI to classify AD patients (N=77), and controls (N=173). We use different methods to extract information from the diffusion MRI data. First, we use the voxel-wise diffusion tensor measures that have been skeletonised using tract based spatial statistics...
March 15, 2017: NeuroImage
https://www.readbyqxmd.com/read/28304396/associations-between-genetic-variants-in-mrna-splicing-related-genes-and-risk-of-lung-cancer-a-pathway-based-analysis-from-published-gwass
#8
Yongchu Pan, Hongliang Liu, Yanru Wang, Xiaozheng Kang, Zhensheng Liu, Kouros Owzar, Younghun Han, Li Su, Yongyue Wei, Rayjean J Hung, Yonathan Brhane, John McLaughlin, Paul Brennan, Heike Bickeböller, Albert Rosenberger, Richard S Houlston, Neil Caporaso, Maria Teresa Landi, Joachim Heinrich, Angela Risch, Xifeng Wu, Yuanqing Ye, David C Christiani, Christopher I Amos, Qingyi Wei
mRNA splicing is an important mechanism to regulate mRNA expression. Abnormal regulation of this process may lead to lung cancer. Here, we investigated the associations of 11,966 single-nucleotide polymorphisms (SNPs) in 206 mRNA splicing-related genes with lung cancer risk by using the summary data from six published genome-wide association studies (GWASs) of Transdisciplinary Research in Cancer of the Lung (TRICL) (12,160 cases and 16,838 controls) and another two lung cancer GWASs of Harvard University (984 cases and 970 controls) and deCODE (1,319 cases and 26,380 controls)...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28300521/volitional-and-nonvolitional-responses-to-hypnotic-suggestions-predictors-and-subjective-experience
#9
John C Mohl, Meriel J Schutkofsky
This investigation combined the data from two studies that used modified scoring of the Harvard Group Scale of Hypnotic Susceptibility (Shor & Orne, 1962) to evaluate deliberate, volitional responses to suggestions. One study also employed subjective ratings of each item of the Harvard Scale, with comparisons of nonvolitional, volitional, and non-responses. Based on the assumption that participants would have marked volitional responses as positive responses using the traditional scale, the traditional scoring method was found to inflate mean hypnotic responsiveness by nearly one point...
April 2017: American Journal of Clinical Hypnosis
https://www.readbyqxmd.com/read/28287025/assessing-interprofessional-education-in-a-student-faculty-collaborative-practice-network
#10
Grace J Young, Marya J Cohen, Bonnie B Blanchfield, Meissa M Jones, Patricia A Reidy, Amy R Weinstein
Although interprofessional relationships are ubiquitous in clinical practice, undergraduate medical students have limited opportunities to develop these relationships in the clinical setting. A few student-faculty collaborative practice networks (SFCPNs) have been working to address this issue, but limited data exist examining the nature and extent of these practices. A systematic survey at a Harvard-affiliated SFCPN is utilised to evaluate the quantity and quality of interprofessional interactions, isolate improvements, and identify challenges in undergraduate interprofessional education (IPE)...
March 12, 2017: Education for Primary Care
https://www.readbyqxmd.com/read/28285181/gender-differences-of-neuropsychological-profiles-in-cognitively-normal-older-people-without-amyloid-pathology
#11
Jie Zhang, Wenjun Zhou, Lijun Wang, Xiangyang Zhang
OBJECTIVE: To investigate the impact of sex on cognition among cognitively normal older people without amyloid pathology. METHODS: The study sample consisted of 83 males (mean age 74years, ranging from 65 to 88years) and 111 females (mean age 72years, ranging from 65 to 89years) who were cognitively normal without amyloid pathology confirmed by Pittsburgh compound B PET scan. We examined the sex discrepancies in cognition using a comprehensive neuropsychological battery...
March 1, 2017: Comprehensive Psychiatry
https://www.readbyqxmd.com/read/28280852/tantigen-a-comprehensive-database-of-tumor-t-cell-antigens
#12
Lars Rønn Olsen, Songsak Tongchusak, Honghuang Lin, Ellis L Reinherz, Vladimir Brusic, Guang Lan Zhang
Tumor T cell antigens are both diagnostically and therapeutically valuable molecules. A large number of new peptides are examined as potential tumor epitopes each year, yet there is no infrastructure for storing and accessing the results of these experiments. We have retroactively cataloged more than 1000 tumor peptides from 368 different proteins, and implemented a web-accessible infrastructure for storing and accessing these experimental results. All peptides in TANTIGEN are labeled as one of the four categories: (1) peptides measured in vitro to bind the HLA, but not reported to elicit either in vivo or in vitro T cell response, (2) peptides found to bind the HLA and to elicit an in vitro T cell response, (3) peptides shown to elicit in vivo tumor rejection, and (4) peptides processed and naturally presented as defined by physical detection...
March 9, 2017: Cancer Immunology, Immunotherapy: CII
https://www.readbyqxmd.com/read/28270892/molecular-analysis-of-factor-viii-and-factor-ix-genes-in-hemophilia-patients-identification-of-novel-mutations-and-molecular-dynamics-studies
#13
Faisal A Al-Allaf, Mohiuddin M Taher, Zainularifeen Abduljaleel, Abdellatif Bouazzaoui, Mohammed Athar, Neda M Bogari, Halah A Abalkhail, Tarek Ma Owaidah
BACKGROUND: Hemophilias A and B are X-linked bleeding disorders caused by mutations in the factor VIII and factor IX genes, respectively. Our objective was to identify the spectrum of mutations of the factor VIII and factor IX genes in Saudi Arabian population and determine the genotype and phenotype correlations by molecular dynamics (MD) simulation. METHODS: For genotyping, blood samples from Saudi Arabian patients were collected, and the genomic DNA was amplified, and then sequenced by Sanger method...
April 2017: Journal of Clinical Medicine Research
https://www.readbyqxmd.com/read/28265252/post-traumatic-stress-disorder-symptoms-resulting-from-torture-and-other-traumatic-events-among-syrian-kurdish-refugees-in-kurdistan-region-iraq
#14
Hawkar Ibrahim, Chiya Q Hassan
Political violence is known to cause psychological distress. There is a large body of empirical studies drawing correlations between war trauma, torture, and post-traumatic stress disorder (PTSD). However, there are few studies on the effects of war-related trauma among Syrian refugees after events following the 'Arab Spring' uprisings between 2010 and 2012. This study examines the association of PTSD symptoms with torture and other traumatic events among Syrian Kurdish refugees living in Kurdistan Region, Iraq...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28259520/derivation-and-external-validation-of-the-plasmic-score-for-rapid-assessment-of-adults-with-thrombotic-microangiopathies-a-cohort-study
#15
Pavan K Bendapudi, Shelley Hurwitz, Ashley Fry, Marisa B Marques, Stephen W Waldo, Ang Li, Lova Sun, Vivek Upadhyay, Ayad Hamdan, Andrew M Brunner, John M Gansner, Srinivas Viswanathan, Richard M Kaufman, Lynne Uhl, Christopher P Stowell, Walter H Dzik, Robert S Makar
BACKGROUND: Among the syndromes characterised by thrombotic microangiopathy, thrombotic thrombocytopenic purpura is distinguished by a severe deficiency in the ADAMTS13 enzyme. Patients with this disorder need urgent treatment with plasma exchange. Because ADAMTS13 activity testing typically requires prolonged turnaround times and might be unavailable in resource-poor settings, a method to rapidly assess the likelihood of severe ADAMTS13 deficiency is needed. METHODS: All consecutive adult patients presenting to three large academic medical centres in Boston, MA, USA, with thrombotic microangiopathy and a possible diagnosis of thrombotic thrombocytopenic purpura between Jan 8, 2004, and Dec 6, 2015, were included in an ongoing multi-institutional registry (the Harvard TMA Research Collaborative)...
March 1, 2017: Lancet Haematology
https://www.readbyqxmd.com/read/28259408/variants-of-%C3%AE-casofensin-a-bioactive-milk-peptide-differently-modulate-the-intestinal-barrier-in-vivo-and-ex-vivo-studies-in-rats
#16
Jérémie Bruno, Aurélie Nicolas, Sandra Pesenti, Jessica Schwarz, Jean-Luc Simon, Joëlle Léonil, Pascale Plaisancié
β-Casofensin is a bioactive milk peptide that modulates the intestinal barrier, particularly through its action on goblet cells. β-Casofensin corresponds to fragment (f) 94-123 of the bovine β-casein (β-CN) A2 variant. Fifteen genetic variants of bovine β-CN (A1-3, B-G, H1-2, I-L) are known, of which the A2, A1, and B forms are the most common. These variants differ from each other by the substitution of one or more AA, some of which are localized in f94 to 123. The aim of our study was to compare the intestinal effects of β-casofensin A2 and its 3 main variants: A1, A3, and B...
March 2, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28254549/assessing-the-factorial-structure-and-measurement-invariance-of-ptsd-by-gender-and-ethnic-groups-in-sri-lanka-an-analysis-of-the-modified-harvard-trauma-questionnaire-htq
#17
Alvin Kuowei Tay, Rohan Jayasuriya, Dinuk Jayasuriya, Derrick Silove
The Harvard Trauma Questionnaire (HTQ) remains the most widely used screening measure for post-traumatic stress disorder (PTSD) in the refugee and post-conflict field. The present study is the first to test the factorial structure and measurement invariance of the HTQ according to DSM-5 criteria across gender and ethnic groups in the ethnically diverse society of post-conflict Sri Lanka. The survey sample included 5136 participants (86% response rate) followed up 12 months after a baseline nationally representative survey undertaken in Sri Lanka in 2014...
February 3, 2017: Journal of Anxiety Disorders
https://www.readbyqxmd.com/read/28253546/fdg-metabolism-associated-with-tau-amyloid-interaction-predicts-memory-decline
#18
Bernard J Hanseeuw, Rebecca A Betensky, Aaron P Schultz, Kate V Papp, Elizabeth C Mormino, Jorge Sepulcre, John S Bark, Danielle M Cosio, Molly LaPoint, Jasmeer P Chhatwal, Dorene M Rentz, Reisa A Sperling, Keith Johnson
OBJECTIVE: To evaluate in normal older adults and preclinical Alzheimer's disease (AD) the impact of amyloid and regional tauopathy on cerebral glucose metabolism and subsequent memory decline. METHODS: We acquired positron emission tomography using F18 Flortaucipir (tau), C11 Pittsburgh Compound B (amyloid) and F18 Fluorodeoxyglucose in 90 clinically normal elderly of the Harvard Aging Brain Study. RESULTS: Posterior cingulate metabolism decreased when both amyloid and neocortical tau were high and predicted subsequent memory decline in a larger sample of normal elderly...
March 2, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/28253478/early-and-late-change-on-the-preclinical-alzheimer-s-cognitive-composite-in-clinically-normal-older-individuals-with-elevated-%C3%AE-amyloid
#19
Elizabeth C Mormino, Kathryn V Papp, Dorene M Rentz, Michael C Donohue, Rebecca Amariglio, Yakeel T Quiroz, Jasmeer Chhatwal, Gad A Marshall, Nancy Donovan, Jonathan Jackson, Jennifer R Gatchel, Bernard J Hanseeuw, Aaron P Schultz, Paul S Aisen, Keith A Johnson, Reisa A Sperling
INTRODUCTION: Sensitive detection of cognitive decline over the course of preclinical Alzheimer's disease is critical as the field moves toward secondary prevention trials. METHODS: We examined Aβ-related change in several variations of the preclinical Alzheimer cognitive composite (PACC) and each individual PACC component in clinically normal (CN) older participants in the Harvard Aging Brain Study. We then examined the PACC variations in the Alzheimer's Disease Cooperative Study Prevention Instrument Study as a replication cohort...
February 27, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28250037/the-relationship-between-dental-students-assessment-ability-and-preclinical-and-academic-performance-in-operative-dentistry
#20
Cliff Lee, Sheetal R Asher, Supattriya Chutinan, German O Gallucci, Hiroe Ohyama
Self-assessment is a critical skill for health care professionals. Because these professionals must be lifelong, self-directed learners and self-regulating practitioners, the ability to self-assess is essential for them. The aims of this study were to measure how dental students self-assessed and peer-assessed their performance in preclinical operative procedures and to evaluate any relationship between their assessment ability and preclinical skills or academic performance. The study was conducted from 2015 to 2016...
March 2017: Journal of Dental Education
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