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https://www.readbyqxmd.com/read/29228186/aether-leveraging-linear-programming-for-optimal-cloud-computing-in-genomics
#1
Jacob M Luber, Braden T Tierney, Evan M Cofer, Chirag J Patel, Aleksandar D Kostic
Motivation: Across biology we are seeing rapid developments in scale of data production without a corresponding increase in data analysis capabilities. Results: Here, we present Aether (http://aether.kosticlab.org), an intuitive, easy-to-use, cost-effective, and scalable framework that uses linear programming (LP) to optimally bid on and deploy combinations of underutilized cloud computing resources. Our approach simultaneously minimizes the cost of data analysis and provides an easy transition from users' existing HPC pipelines...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29228172/spring-a-kinetic-interface-for-visualizing-high-dimensional-single-cell-expression-data
#2
Caleb Weinreb, Samuel Wolock, Allon Klein
Motivation: Single-cell gene expression profiling technologies can map the cell states in a tissue or organism. As these technologies become more common, there is a need for computational tools to explore the data they produce. In particular, visualizing continuous gene expression topologies can be improved, since current tools tend to fragment gene expression continua or capture only limited features of complex population topologies. Results: Force-directed layouts of k-nearest-neighbor graphs can visualize continuous gene expression topologies in a manner that preserves high-dimensional relationships and captures complex population topologies...
December 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29226795/treatment-of-sleep-disturbances-in-refugees-suffering-from-post-traumatic-stress-disorder
#3
Hinuga Sandahl, Erik Vindbjerg, Jessica Carlsson
Sleep disturbances are often referred to as the hallmark of Post-Traumatic Stress Disorder (PTSD). Although PTSD is prevalent in refugees, studies on sleep disturbances in trauma-affected refugees are scarce. This article presents the results of two studies: a systematic review of the literature on treatment of sleep disturbances in adult trauma-affected refugees and a study of the role of sleep disturbances in the PTSD symptom structure. Study 1, the literature review, identified five studies on treatment of sleep disturbances: four studies were on pharmacological treatment and one study on music therapy...
October 2017: Transcultural Psychiatry
https://www.readbyqxmd.com/read/29226792/posttraumatic-world-assumptions-among-treatment-seeking-refugees
#4
F Jackie June Ter Heide, Marieke Sleijpen, Niels van der Aa
The clinical relevance of negative changes in cognitions about oneself, others, and the world is reflected in the diagnostic criteria for posttraumatic stress disorder (PTSD) in the DSM-5 and complex posttraumatic stress disorder in the ICD-11. Although such changes in cognition have been posited to be especially relevant for traumatised refugees, few studies have examined this in refugee populations. The present study used a cross-sectional design to compare negative cognitions among 213 adult treatment-seeking refugees with those in previously published samples from the general population, veterans with combat-related PTSD, and whiplash victims...
October 2017: Transcultural Psychiatry
https://www.readbyqxmd.com/read/29226791/counting-the-cost-of-afrophobia-post-migration-adaptation-and-mental-health-challenges-of-african-refugees-in-south-africa
#5
Lindokuhle Thela, Andrew Tomita, Varsha Maharaj, Mpho Mhlongo, Jonathan K Burns
There are few studies on the role of migration within sub-Saharan Africa and its relation to the development of mental illness. We investigated post-resettlement adaptation and mental health challenges of African refugees/migrants in Durban, South Africa. We interviewed 335 African help-seeking refugees/migrants for anxiety, depression (25-item Hopkins Symptom Checklist) and post-traumatic stress symptoms (30-item Harvard Trauma Questionnaire). Socio-demographic and migration history, focusing on post-migration circumstances and experiences of discrimination in the host country, were obtained...
October 2017: Transcultural Psychiatry
https://www.readbyqxmd.com/read/29209996/understanding-ownership-of-patient-care-a%C3%A2-dual-site-qualitative-study-of-faculty-and-residents-from-medicine-and-psychiatry
#6
Deborah S Cowley, Jesse D Markman, Jennifer A Best, Erica L Greenberg, Michael J Grodesky, Suzanne B Murray, Kelli A Corning, Mitchell R Levy, William E Greenberg
INTRODUCTION: With changes in duty hours and supervision requirements, educators have raised concerns about erosion of patient care ownership by resident physicians. However, the definition of ownership is unclear. This qualitative study investigated definitions of ownership in medicine and psychiatry faculty and residents. METHODS: The authors distributed an anonymous online survey regarding definitions of ownership to faculty and residents at the psychiatry and internal medicine residency programs at the University of Washington and the Harvard Longwood psychiatry residency and conducted a qualitative analysis of free-text responses to identify emergent themes...
December 5, 2017: Perspectives on Medical Education
https://www.readbyqxmd.com/read/29196944/scientometric-evaluation-of-the-global-research-in-spine-an-update-on-the-pioneering-study-by-wei-et-al
#7
REVIEW
Ozcan Konur
PURPOSE: Wei et al. evaluated the global research in spine using scientometric methods based on a sample of 13,115 papers published in 5 spine journals from 2004 to 2013. This study builds on this pioneering study and provides up-to-date and thorough information on spine based on a sample of 166,962 papers for the stakeholders. METHOD: 'Articles' and 'reviews' published in 'English' in the journals indexed by the 'Web of Science' primary databases between 1980 and 2017 were retrieved through the use of an optimal keyword set for titles of both papers and ten spine journals...
December 1, 2017: European Spine Journal
https://www.readbyqxmd.com/read/29194469/biobakery-a-meta-omic-analysis-environment
#8
Lauren J McIver, Galeb Abu-Ali, Eric A Franzosa, Randall Schwager, Xochitl C Morgan, Levi Waldron, Nicola Segata, Curtis Huttenhower
Summary: bioBakery is a meta'omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured analysis modules also joined into workflows for reproducibility. Availability: bioBakery (http://huttenhower.sph.harvard.edu/biobakery) is publicly available for local installation as individual modules and as a virtual machine image...
November 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29194088/the-range-and-impact-of-postmigration-stressors-during-treatment-of-trauma-affected-refugees
#9
Maja Bruhn, Susan Rees, Mohammed Mohsin, Derrick Silove, Jessica Carlsson
Trauma-affected refugees commonly experience postmigration stressors, which can compound conflict-related emotional distress. Our study aimed to assess clinician-rated frequency and types of postmigration stressors deemed to be interfering with the treatment of refugees attending a service for trauma-related mental distress. A total of 116 patients completed 6 months of multidisciplinary treatment. Clinician-rated postmigration stressors were registered at each session. Outcome measures were Harvard Trauma Questionnaire and Global Assessment of Functioning, function (GAF-F) and symptom...
November 29, 2017: Journal of Nervous and Mental Disease
https://www.readbyqxmd.com/read/29186292/satori-a-system-for-ontology-guided-visual-exploration-of-biomedical-data-repositories
#10
Fritz Lekschas, Nils Gehlenborg
Motivation: The ever-increasing number of biomedical data sets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating data sets. Visualizing this rich network of relationships can improve the explorability of large data repositories and help researchers find data sets of interest. Results: We developed SATORI -an integrative search and visual exploration interface for the exploration of biomedical data repositories...
November 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29176305/correlations-between-fracture-load-of-zirconia-implant-supported-single-crowns-and-mechanical-properties-of-restorative-material-and-cement
#11
Nadja Rohr, Sabrina Märtin, Jens Fischer
Zirconia implants that were restored with veneered zirconia displayed severe chipping rates of the restorations in clinical studies. Purpose of this study was to evaluate the fracture load of different zirconia implant supported monolithic crown materials (zirconia, alumina, lithium disilicate, feldspar ceramic and polymer-infiltrated ceramic) cemented with various cements (Harvard LuteCem SE, Harvard Implant Semi-permanent, Multilink Automix, VITA Adiva F-Cem). Flexural strength and fracture toughness of crown materials and compressive strength of the cements were measured...
November 23, 2017: Dental Materials Journal
https://www.readbyqxmd.com/read/29176087/in-pursuit-of-educational-integrity-professional-identity-formation-in-the-harvard-medical-school-cambridge-integrated-clerkship
#12
Elizabeth Gaufberg, David Bor, Perry Dinardo, Edward Krupat, Elizabeth Pine, Barbara Ogur, David A Hirsh
Graduates of Harvard Medical School's Cambridge Integrated Clerkship (CIC) describe several core processes that may underlie professional identity formation (PIF): encouragement to integrate pre-professional and professional identities; support for learner autonomy in discovering meaningful roles and responsibilities; learning through caring relationships; and a curriculum and an institutional culture that make values explicit. The authors suggest that the benefits of educational integrity accrue when idealistic learners inhabit an educational model that aligns with their own core values, and when professional development occurs in the context of an institutional home that upholds these values...
2017: Perspectives in Biology and Medicine
https://www.readbyqxmd.com/read/29174008/-the-use-of-the-debriefing-assessment-for-simulation-in-healthcare-dash-in-a-simulation-based-team-learning-program-for-newborn-resuscitation-in-the-delivery-room
#13
C Durand, T Secheresse, M Leconte
OBJECTIVE: To evaluate the contribution of the Debriefing Assessment for Simulation in Healthcare (DASH, Centre for Medical Simulation, Harvard) in a high-fidelity simulation in situ program used for newborn resuscitation training. METHODS: The DASH was scored by trainees and instructors at the end of the session. The instructors' feedback and opinions were collected. RESULTS: The study included 16 training sessions (ten maternity units) with 156 trainees and ten instructors (45 DASH)...
November 21, 2017: Archives de Pédiatrie: Organe Officiel de la Sociéte Française de Pédiatrie
https://www.readbyqxmd.com/read/29171194/third-person-self-talk-reduces-ebola-worry-and-risk-perception-by-enhancing-rational-thinking
#14
Ethan Kross, Brian D Vickers, Ariana Orvell, Izzy Gainsburg, Tim P Moran, Margaret Boyer, John Jonides, Jason Moser, Ozlem Ayduk
BACKGROUND: During the fall of 2014, the threat of an Ebola outbreak gripped the United States (Poll, 8-12 October 2014; see Harvard School of Public Health & SSRS, 2014), creating a unique opportunity to advance basic knowledge concerning how emotion regulation works in consequential contexts and translate existing research in this area to inform public health and policy. METHOD: We addressed these issues by examining whether third-person self-talk, a simple technique that promotes emotion regulation, could nudge people into reasoning about Ebola more rationally...
November 2017: Applied Psychology. Health and Well-being
https://www.readbyqxmd.com/read/29162139/effect-of-aging-and-curing-mode-on-the-compressive-and-indirect-tensile-strength-of-resin-composite-cements
#15
Nadja Rohr, Jens Fischer
BACKGROUND: Resin composite cements are used in dentistry to bond ceramic restorations to the tooth structure. In the oral cavity these cements are subjected to aging induced by masticatory and thermal stresses. Thermal cycling between 5 and 55 °C simulates the effect of varying temperatures in vitro. Purpose of this study was to compare indirect tensile to compressive strength of different cements before and after thermal cycling. The effect of the curing mode was additionally assessed...
November 21, 2017: Head & Face Medicine
https://www.readbyqxmd.com/read/29155944/molecular-interaction-search-tool-mist-an-integrated-resource-for-mining-gene-and-protein-interaction-data
#16
Yanhui Hu, Arunachalam Vinayagam, Ankita Nand, Aram Comjean, Verena Chung, Tong Hao, Stephanie E Mohr, Norbert Perrimon
Model organism and human databases are rich with information about genetic and physical interactions. These data can be used to interpret and guide the analysis of results from new studies and develop new hypotheses. Here, we report the development of the Molecular Interaction Search Tool (MIST; http://fgrtools.hms.harvard.edu/MIST/). The MIST database integrates biological interaction data from yeast, nematode, fly, zebrafish, frog, rat and mouse model systems, as well as human. For individual or short gene lists, the MIST user interface can be used to identify interacting partners based on protein-protein and genetic interaction (GI) data from the species of interest as well as inferred interactions, known as interologs, and to view a corresponding network...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29150135/effect-of-different-resin-luting-cements-on-the-marginal-fit-of-lithium-disilicate-pressed-crowns
#17
Radek Mounajjed, Thomas J Salinas, Tomas Ingr, Basel Azar
STATEMENT OF PROBLEM: The vertical marginal discrepancy of restorations can increase upon cementation, and poor marginal fit can lead to cement dissolution, marginal discoloration, microleakage, and secondary caries. The amount of increase is related to the type of luting cement used, but how lithium disilicate pressed crowns are affected by different resin cements is unclear. PURPOSE: The purpose of this in vitro study was to compare the effect of using different resin luting cements on the vertical marginal discrepancy of lithium disilicate pressed crowns...
November 15, 2017: Journal of Prosthetic Dentistry
https://www.readbyqxmd.com/read/29130373/book-review-youval-rotman-insanity-and-sanctity-in-byzantium-the-ambiguity-of-religious-experience-rotman-youval-insanity-and-sanctity-in-byzantium-the-ambiguity-of-religious-experience-harvard-university-press-cambridge-ma-2016-256-pp-9780674057616-29-95-hbk
#18
https://www.readbyqxmd.com/read/29124043/activities-of-daily-living-measured-by-the-harvard-automated-phone-task-track-with-cognitive-decline-over-time-in-non-demented-elderly
#19
Gad A Marshall, Sarah L Aghjayan, Maria Dekhtyar, Joseph J Locascio, Kamal Jethwani, Rebecca E Amariglio, Keith A Johnson, Reisa A Sperling, Dorene M Rentz
Background: Impairment in activities of daily living is a major burden to both patients and caregivers. Mild impairment in instrumental activities of daily living is often seen at the stage of mild cognitive impairment. The field of Alzheimer's disease is moving toward earlier diagnosis and intervention and more sensitive and ecologically valid assessments of instrumental or complex activities of daily living are needed. The Harvard Automated Phone Task, a novel performance-based activities of daily living instrument, has the potential to fill this gap...
2017: Journal of Prevention of Alzheimer's Disease
https://www.readbyqxmd.com/read/29118161/dietary-nutrient-intake-ethnicity-and-epigenetic-silencing-of-lung-cancer-genes-detected-in-sputum-in-new-mexican-smokers
#20
Shuguang Leng, Maria A Picchi, Huining Kang, Guodong Wu, Piotr T Filipczak, Daniel E Juri, Xiequn Zhang, W James Gauderman, Frank D Gilliland, Steven A Belinsky
Lung cancer (LC) gene methylation detected in sputum assesses field cancerization and predicts LC incidence. Hispanic smokers have higher LC susceptibility compared to non-Hispanic Whites (NHW). We aimed to identify novel dietary nutrients affecting LC gene methylation and determine the degree of ethnic disparity in methylation explained by diet. Dietary intakes of 139 nutrients were assessed using a validated Harvard food frequency questionnaire in 327 Hispanics and 1502 NHWs from the Lovelace Smokers cohort (LSC)...
November 8, 2017: Cancer Prevention Research
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