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https://www.readbyqxmd.com/read/28651329/high-speed-and-high-ratio-referential-genome-compression
#1
Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li
Motivation: The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28651111/the-rise-of-zika-infection-and-microcephaly-what-can-we-learn-from-a-public-health-emergency
#2
REVIEW
B McCloskey, T Endericks
OBJECTIVES: To consider why Zika was declared a Public Health Emergency of International Concern (PHEIC), why it stopped being one and what we can learn from this for the future. STUDY DESIGN: This paper reviews the sequence of events and evidence base for the decision to declare Zika a PHEIC, the global response to this, the challenges in maintaining an evidence-based approach to outbreak response and identifies learning outcomes. METHODS: Evidence review, all published articles in reputable UK and international journals were identified...
June 23, 2017: Public Health
https://www.readbyqxmd.com/read/28651045/photoinduced-charge-transfer-versus-fragmentation-pathways-in-lanthanum-cyclopentadienyl-complexes
#3
Yulun Han, Qingguo Meng, Bakhtiyor Rasulev, P Stanley May, Mary T Berry, Dmitri S Kilin
This study compares two competing pathways of photoexcitations in gas-phase metal-organic complexes: first, a sequence of phonon-assisted electronic transitions leading to dissipation of the energy of photoexcitations and second, a sequence of light-driven electronic transitions leading to photolysis. Phonon-assisted charge carrier dynamics is investigated by combination of the density matrix formalism and on-the-fly nonadiabatic couplings. Light-driven fragmentation is modeled by a time-dependent excited-state molecular dynamics (TDESMD) algorithm based on Rabi theory and principles similar to the trajectory surface hopping approximation...
June 26, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28650843/can-canmeds-competencies-be-developed-in-medical-school-anatomy-laboratories-a-literature-review
#4
REVIEW
Joshua Hefler, Christopher J Ramnanan
Objectives: The purpose of this literature review was to identify potential ways in which undergraduate medical anatomy education may be relevant to the CanMEDS Roles, a competency-based framework used throughout Canadian medical training. Methods: A scoping review of medical education literature was conducted in March 2017 for English language publications that included key words related to anatomy education and to key competencies formally described for each of the Roles in the CanMEDS 2015 framework...
June 16, 2017: International Journal of Medical Education
https://www.readbyqxmd.com/read/28650355/axillary-dissection-and-nodal-irradiation-can-be-avoided-for-most-node-positive-z0011-eligible-breast-cancers-a-prospective-validation-study-of-793-patients
#5
Monica Morrow, Kimberly J Van Zee, Sujata Patil, Oriana Petruolo, Anita Mamtani, Andrea V Barrio, Deborah Capko, Mahmoud El-Tamer, Mary L Gemignani, Alexandra S Heerdt, Laurie Kirstein, Melissa Pilewskie, George Plitas, Virgilio S Sacchini, Lisa M Sclafani, Alice Ho, Hiram S Cody
OBJECTIVE: To determine rates of axillary dissection (ALND) and nodal recurrence in patients eligible for ACOSOG Z0011. BACKGROUND: Z0011 demonstrated that patients with cT1-2N0 breast cancers and 1 to 2 involved sentinel lymph nodes (SLNs) having breast-conserving therapy had no difference in locoregional recurrence or survival after SLN biopsy alone or ALND. The generalizability of the results and importance of nodal radiotherapy (RT) is unclear. METHODS: Patients eligible for Z0011 had SLN biopsy alone...
July 22, 2017: Annals of Surgery
https://www.readbyqxmd.com/read/28649921/leader-trust-competence-lmx-and-member-performance
#6
Gukdo Byun, Ye Dai, Soojin Lee, Seungwan Kang
Based on social exchange theory, this study examines the influence of leaders' trusting behavior and competence in in-role activities on members' perceived leader-member exchange (LMX) relationships. Our study proposes that a leader's trust in a member contributes to the member's perceived LMX, and that the leader's competence in in-role activities moderates this relationship. Furthermore, our study suggests that perceived LMX mediates the relationship between the leader's trust and members' task performance...
January 1, 2017: Psychological Reports
https://www.readbyqxmd.com/read/28649626/investigation-of-simulated-microgravity-effects-on-streptococcus-mutans-physiology-and-global-gene-expression
#7
Silvia S Orsini, April M Lewis, Kelly C Rice
Astronauts have been previously shown to exhibit decreased salivary lysozyme and increased dental calculus and gingival inflammation in response to space flight, host factors that could contribute to oral diseases such as caries and periodontitis. However, the specific physiological response of caries-causing bacteria such as Streptococcus mutans to space flight and/or ground-based simulated microgravity has not been extensively investigated. In this study, high aspect ratio vessel S. mutans simulated microgravity and normal gravity cultures were assessed for changes in metabolite and transcriptome profiles, H2O2 resistance, and competence in sucrose-containing biofilm media...
2017: NPJ Microgravity
https://www.readbyqxmd.com/read/28649352/tracking-a-single-pigeon-using-a-shadowing-filter-algorithm
#8
Ayham Zaitouny, Thomas Stemler, Michael Small
Miniature GPS devices now allow for measurement of the movement of animals in real time and provide high- quality and high-resolution data. While these new data sets are a great improvement, one still encounters some measurement errors as well as device failures. Moreover, these devices only measure position and require further reconstruction techniques to extract the full dynamical state space with the velocity and acceleration. Direct differentiation of position is generally not adequate. We report on the successful implementation of a shadowing filter algorithm that (1) minimizes measurement errors and (2) reconstructs at the same time the full phase-space from a position recording of a flying pigeon...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28648761/improved-jpeg-anti-forensics-with-better-image-visual-quality-and-forensic-undetectability
#9
Gurinder Singh, Kulbir Singh
There is an immediate need to validate the authenticity of digital images due to the availability of powerful image processing tools that can easily manipulate the digital image information without leaving any traces. The digital image forensics most often employs the tampering detectors based on JPEG compression. Therefore, to evaluate the competency of the JPEG forensic detectors, an anti-forensic technique is required. In this paper, two improved JPEG anti-forensic techniques are proposed to remove the blocking artifacts left by the JPEG compression in both spatial and DCT domain...
June 10, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28647895/systematic-design-for-trait-introgression-projects
#10
John N Cameron, Ye Han, Lizhi Wang, William D Beavis
Using an Operations Research approach, we demonstrate design of optimal trait introgression projects with respect to competing objectives. We demonstrate an innovative approach for designing Trait Introgression (TI) projects based on optimization principles from Operations Research. If the designs of TI projects are based on clear and measurable objectives, they can be translated into mathematical models with decision variables and constraints that can be translated into Pareto optimality plots associated with any arbitrary selection strategy...
June 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28647393/the-effect-and-use-of-milestones-in-the-assessment-of-neurological-surgery-residents-and-residency-programs
#11
Lisa N Conforti, Nicholas A Yaghmour, Stanley J Hamstra, Eric S Holmboe, Benjamin Kennedy, Jesse J Liu, Heidi Waldo, Nathan R Selden
OBJECTIVES: The purpose of this study was to determine the effect of the Accreditation Council for Graduate Medical Education Milestones on the assessment of neurological surgery residents. The authors sought to determine the feasibility, acceptability, and utility of this new framework in making judgments of progressive competence, its implementation within programs, and the influence on curricula. Residents were also surveyed to elicit the effect of Milestones on their educational experience and professional development...
June 21, 2017: Journal of Surgical Education
https://www.readbyqxmd.com/read/28647303/the-predictors-of-metabolic-syndrome-based-on-walker-health-promoting-lifestyle-in-iran-2016
#12
REVIEW
Maryam Mohammadi, Ali Ramezankhani, Shabnam Mohammadi, Shakiba Zahed, Farahnaz Khabiri, Soheila Khodakarim, Mohsen Roshani, Majid Ghayur
BACKGROUND: Understanding the metabolic syndrome has been the center of attention in recent years as a major risk factor of many diseases. Given the rising incidence of this disease and as the patient can compete against this disease with choosing healthy lifestyle, in the present study, we investigated the predictors of metabolic syndrome, based on Walker's health-promoting lifestyle in two large cities in Iran, in 2016. METHODS: This cross-sectional study used two-stage cluster sampling to select 1128 patients, among patients who referred to health centers in Isfahan and Yazd...
May 17, 2017: Diabetes & Metabolic Syndrome
https://www.readbyqxmd.com/read/28647064/efficacy-of-the-doktormitsdm-training-module-in-supporting-shared-decision-making-results-from-a-multicenter-double-blind-randomized-controlled-trial
#13
Friedemann Geiger, Katrin Liethmann, Daniela Reitz, Razvan Galalae, Jürgen Kasper
OBJECTIVE: Training to improve physicians' shared decision making (SDM) competencies with proven effectiveness and efficiency is rare. This study evaluated the brief in situ training module 'doktormitSDM'. METHODS: In a multicenter RCT, each physician recorded four consultations, each of which included a diagnostic or treatment decision (N=152 consultations from seven medical specialties). The doktormitSDM training module included two video-based individual coaching sessions (15min) at the physicians' workplaces, supplemented by a manual and a video tutorial...
June 19, 2017: Patient Education and Counseling
https://www.readbyqxmd.com/read/28646877/sbmlmod-a-python-based-web-application-and-web-service-for-efficient-data-integration-and-model-simulation
#14
Sascha Schäuble, Anne-Kristin Stavrum, Mathias Bockwoldt, Pål Puntervoll, Ines Heiland
BACKGROUND: Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. RESULTS: We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models...
June 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28646413/integrated-in-silico-in-vitro-identification-and-characterization-of-the-sh3-mediated-interaction-between-human-pttg-and-its-cognate-partners-in-medulloblastoma
#15
Jiangang Liu, Dapeng Wang, Yanyan Li, Hui Yao, Nan Zhang, Xuewen Zhang, Fangping Zhong, Yulun Huang
The human pituitary tumor-transforming gene is an oncogenic protein which serves as a central hub in the cellular signaling network of medulloblastoma. The protein contains two vicinal PxxP motifs at its C terminus that are potential binding sites of peptide-recognition SH3 domains. Here, a synthetic protocol that integrated in silico analysis and in vitro assay was described to identify the SH3-binding partners of pituitary tumor-transforming gene in the gene expression profile of medulloblastoma. In the procedure, a variety of structurally diverse, non-redundant SH3 domains with high gene expression in medulloblastoma were compiled, and their three-dimensional structures were either manually retrieved from the protein data bank database or computationally modeled through bioinformatics technique...
June 24, 2017: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28646094/immune-mediated-effects-targeting-hepatitis-c-virus-in-a-syngeneic-replicon-cell-transplantation-mouse-model
#16
Sepideh Levander, Fredrik Holmström, Lars Frelin, Gustaf Ahlén, Daniel Rupp, Gang Long, Ralf Bartenschlager, Matti Sällberg
OBJECTIVE: HCV is characterised by its ability to establish chronic infection in hepatocytes and to replicate in the presence of an inflammation. We mimicked this situation in vivo in immune-competent mice by syngeneic transplantation of HCV replicon-containing mouse hepatoma cells. DESIGN: A total of 5 million H-2(b) positive Hep56.1D cells, carrying a subgenomic genotype (gt) 2a replicon (HCV replicon cells) or stably expressing comparable levels of the HCV NS3/4A protease/helicase complex (NS3/4A hepatoma cells), were injected subcutaneously into syngeneic H-2(b)-restricted mice...
June 23, 2017: Gut
https://www.readbyqxmd.com/read/28645619/supporting-and-caring-for-transgender-and-gender-nonconforming-youth-in-the-urology-practice
#17
REVIEW
L E Conard
INTRODUCTION: Gender identity is a person's internal sense of gender, which may be different than the sex they were assigned at birth. Pediatric urologists are starting to see more transgender and gender non-conforming (TGN) youth and need to be able to provide culturally competent and appropriate care for these patients and their caregivers. This review will discuss common transgender terminology, specific health concerns and treatment options. METHODS AND MATERIALS: A systematic literature review was performed on Medline(®), PubMed(®), and Google Scholar™ for key words transgender, gender dysphoria and gender identity disorder...
June 2017: Journal of Pediatric Urology
https://www.readbyqxmd.com/read/28645250/labour-market-marginalisation-after-mental-disorders-among-young-natives-and-immigrants-living-in-sweden
#18
Magnus Helgesson, Petter Tinghög, Thomas Niederkrotenthaler, Fredrik Saboonchi, Ellenor Mittendorfer-Rutz
BACKGROUND: The aim was to investigate the associations between mental disorders and three different measures of labour-market marginalisation, and differences between native Swedes and immigrants. METHODS: The study comprised 1,753,544 individuals, aged 20-35 years, and resident in Sweden 2004. They were followed 2005-2011 with regard to disability pension, sickness absence (≥90 days) and unemployment (≥180 days). Immigrants were born in Western countries (Nordic countries, EU, Europe outside EU or North-America/Oceania), or in non-Western countries (Africa, Asia or South-America)...
June 23, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28644873/circular-rna-expression-profiling-of-human-granulosa-cells-during-maternal-aging-reveals-novel-transcripts-associated-with-assisted-reproductive-technology-outcomes
#19
Jing Cheng, Jia Huang, Suzhen Yuan, Su Zhou, Wei Yan, Wei Shen, Yun Chen, Xi Xia, Aiyue Luo, Da Zhu, Shixuan Wang
Circular RNAs (circRNAs) are a unique class of endogenous RNAs which could be used as potential diagnostic and prognostic biomarkers of many diseases. Our study aimed to investigate circRNA profiles in human granulosa cells (GCs) during maternal aging and to uncover age-related circRNA variations that potentially reflect decreased oocyte competence. CircRNAs in GCs from in vitro fertilization (IVF) patients with young age (YA, ≤ 30 years) and advanced age (AA, ≥ 38 years) were profiled by microarray, and validated in 20 paired samples...
2017: PloS One
https://www.readbyqxmd.com/read/28644772/risk-stratification-for-second-primary-lung-cancer
#20
Summer S Han, Gabriel A Rivera, Martin C Tammemägi, Sylvia K Plevritis, Scarlett L Gomez, Iona Cheng, Heather A Wakelee
Purpose This study estimated the 10-year risk of developing second primary lung cancer (SPLC) among survivors of initial primary lung cancer (IPLC) and evaluated the clinical utility of the risk prediction model for selecting eligibility criteria for screening. Methods SEER data were used to identify a population-based cohort of 20,032 participants diagnosed with IPLC between 1988 and 2003 and who survived ≥ 5 years after the initial diagnosis. We used a proportional subdistribution hazards model to estimate the 10-year risk of developing SPLC among survivors of lung cancer LC in the presence of competing risks...
June 23, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
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