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https://www.readbyqxmd.com/read/28343097/strait-razor-v2s-advancing-sequence-based-str-allele-reporting-and-beyond-to-other-marker-systems
#1
Jonathan L King, Frank R Wendt, Jie Sun, Bruce Budowle
STRait Razor has provided the forensic community a free-to-use, open-source tool for short tandem repeat (STR) analysis of massively parallel sequencing (MPS) data. STRait Razor v2s (SRv2s) allows users to capture physically phased haplotypes within the full amplicon of both commercial (ForenSeq) and "early access" panels (PowerSeq, Mixture ID). STRait Razor v2s may be run in batch mode to facilitate population-level analysis and is supported by all Unix distributions (including MAC OS). Data are reported in tables in string (haplotype), length-based (e...
March 12, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28342523/early-experience-with-a-modified-preloaded-system-for-fenestrated-endovascular-aortic-repair
#2
Blandine Maurel, Tim Resch, Rafaelle Spear, Blayne Roeder, Umberto M Bracale, Stephan Haulon, Tara M Mastracci
OBJECTIVE: Preloaded endovascular delivery systems expand the anatomic eligibility for complex aortic repair by requiring only one iliac access vessel and providing a stable platform for guiding sheaths into challenging target vessels. This article reports the lessons learned and early clinical outcomes using a modified preloaded delivery system for fenestrated endovascular aneurysm repair (FEVAR) in three aortic centers in Europe. METHODS: From October 2015 to March 2016, consecutive patients presenting with extensive aortic aneurysm treated with a modified preloaded FEVAR were prospectively enrolled from three high volume European aortic centers...
April 2017: Journal of Vascular Surgery
https://www.readbyqxmd.com/read/28340354/mechanism-of-substrate-translocation-in-an-alternating-access-transporter
#3
Naomi R Latorraca, Nathan M Fastman, A J Venkatakrishnan, Wolf B Frommer, Ron O Dror, Liang Feng
Transporters shuttle molecules across cell membranes by alternating among distinct conformational states. Fundamental questions remain about how transporters transition between states and how such structural rearrangements regulate substrate translocation. Here, we capture the translocation process by crystallography and unguided molecular dynamics simulations, providing an atomic-level description of alternating access transport. Simulations of a SWEET-family transporter initiated from an outward-open, glucose-bound structure reported here spontaneously adopt occluded and inward-open conformations...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28339669/in-their-own-words-young-adults-menthol-cigarette-initiation-perceptions-experiences-and-regulation-perspectives
#4
Olivia A Wackowski, Kiameesha R Evans, Melissa B Harrell, Alexandra Loukas, M Jane Lewis, Cristine D Delnevo, Cheryl L Perry
Background: Menthol cigarettes are disproportionately used by young people and have been called smoking starter products. However, limited qualitative research exists on young adults' perceptions of and experiences with these products, with much of it based on document reviews of the tobacco industry's research. Methods: We conducted six focus groups with young adult (ages 18-24) menthol smokers in New Jersey (half with black smokers) between December 2014 and March 2015...
February 17, 2017: Nicotine & Tobacco Research: Official Journal of the Society for Research on Nicotine and Tobacco
https://www.readbyqxmd.com/read/28339355/psychometric-properties-of-sleep-and-coping-numeric-rating-scales-in-rheumatoid-arthritis-a-subanalysis-of-an-etanercept-trial
#5
Pedro Avila-Ribeiro, Yves Brault, Maxime Dougados, Laure Gossec
OBJECTIVES: In rheumatoid arthritis, quality of sleep and ability to cope are important for patients; however their usefulness as outcome measures is not well established. METHODS: Post-hoc analysis of an open-label 12-week trial of etanercept in biologic-naïve rheumatoid arthritis patients with visits at screening, baseline and over 12 weeks. Outcomes measured included Disease Activity Score 28 erythrocyte sedimentation rate (DAS28), numeric rating scales for sleep, coping, patient and physician-global assessment, pain and fatigue, and modified-HAQ...
March 23, 2017: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/28338480/the-challenges-in-predicting-ecmo-survival-and-a-path-forward
#6
Marco Huesch, Christopher Brehm
Extracorporeal membrane oxygenation (ECMO) support is a life-saving but complex technique for patients suffering from severe cardiac and/or pulmonary dysfunction. Increasingly greater utilization in the last 15 years means that a suite of mortality risk analytics is both feasible for researchers and required by clinicians, patients, administrators and insurers. We argue that to date, research into such risk analytics has been insufficient and does not adequately reflect the various indications and configurations of ECLS...
March 22, 2017: ASAIO Journal: a Peer-reviewed Journal of the American Society for Artificial Internal Organs
https://www.readbyqxmd.com/read/28337576/robotic-video-assisted-thoracoscopy-minimally-invasive-approach-for-management-of-mediastinal-tumors
#7
Pejman Radkani, Devendra Joshi, Tushar Barot, Roy Williams
In spite of difficult anatomic access for tumors of mediastinum, surgical resection remains the best diagnostic and therapeutic approach. Widespread acceptance of video-assisted thoracoscopy (VATS) is restricted by the limiting nature of instruments and suboptimal visualization. Robotic assisted minimally invasive surgery seems to hold most promise in remote, narrow anatomical regions. After obtaining approval from Institutional Review Board (IRB), a retrospective review of prospectively collected database on patients that underwent Robotic VATS between 2009 and 2013 was conducted...
March 23, 2017: Journal of Robotic Surgery
https://www.readbyqxmd.com/read/28337092/patronage-and-cost-of-malaria-treatment-in-private-hospitals-in-ibadan-north-l-g-a-south-western-nigeria
#8
A T Salawu, O I Fawole, M D Dairo
BACKGROUND: Malaria accounts for about 60% of all clinic attendance in Nigeria. About 300,000 children die of malaria annually while an estimated 4,500 pregnant women are lost annually on account of malaria in Nigeria alone. High cost of treatment is a barrier to the uptake of health services in low resource settings, therefore an exploration of the cost of malaria management will reveal possible components that may benefit from intervention and thus reveal important clues for improving access to malaria treatment...
December 2016: Annals of Ibadan Postgraduate Medicine
https://www.readbyqxmd.com/read/28336202/medical-surgical-activity-and-the-current-state-of-training-of-urology-residents-in-spain-results-of-a-national-survey
#9
M E Rodríguez-Socarrás, J Gómez Rivas, M García-Sanz, L Pesquera, L Tortolero-Blanco, M Ciappara, A Melnick, J Colombo, G Patruno, Á Serrano-Pascual, J Bachiller-Burgos, J M Cozar-Olmo
OBJECTIVES: To determine the actual state of medical-surgical activity and training for urology residents in Spain. MATERIAL AND METHOD: We designed 2 anonymous surveys, which were uploaded with the Google Docs(©) tool so that the respondents could answer the surveys online. The online collection period was September 2015 to January 2016. The collected data were processing using the statistical programme IBM SPSS for Windows, Version 21.0 and the programme R version 3...
March 20, 2017: Actas Urologicas Españolas
https://www.readbyqxmd.com/read/28336200/systematic-review-of-transgastric-ercp-in-roux-en-y-gastric-bypass-patients
#10
Nikhil Banerjee, Mayur Parepally, T Karl Byrne, Rana C Pullatt, Gregory A Coté, B Joseph Elmunzer
Balloon-assisted endoscopic retrograde cholangiopancreatoscopy (ERCP) in Roux-en-Y gastric bypass (RYGB) patients is technically challenging due to anatomic and accessory constraints, thus success rates are modest. Transgastric ERCP (TG-ERCP) offers a viable alternative. We aimed to systematically review the literature on TG-ERCP in RYGB patients to better define the technical approaches, success rates, and adverse events of this procedure. A computer-assisted search of the Embase and PubMed databases was performed to identify studies that focused on the techniques and clinical outcomes of TG-ERCP...
February 10, 2017: Surgery for Obesity and related Diseases: Official Journal of the American Society for Bariatric Surgery
https://www.readbyqxmd.com/read/28336138/preparation-of-an-epitope-imprinted-polymer-with-antibody-like-selectivity-for-beta2-microglobulin-and-application-in-serum-sample-analysis-with-a-facile-method-of-on-line-solid-phase-extraction-coupling-with-high-performance-liquid-chromatography
#11
Fangfang Yang, Dandan Deng, Xiangchao Dong, Shen Lin
Molecularly imprinted polymers (MIPs) for protein recognition have great application potential in the biological analysis. However, preparation of protein imprinted polymer is still facing challenge. Beta2-microglobulin (β2m) is a protein biomarker that can be used in diagnosis of different diseases. In this research, a novel MIP with ability of β2m recognition has been developed by epitope and surface-confined imprinting approaches. A peptide with sequence of MIQRTPKIQ was selected as template. A strategy of combination of hierarchical imprinting and template immobilization was employed in the β2m-MIP synthesis...
March 9, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28335700/cochlear-implants-in-the-management-of-hearing-loss-in-neurofibromatosis-type-2
#12
Frances Harris, James R Tysome, Neil Donnelly, Juliette Durie-Gair, Gemma Crundwell, Yu Chuen Tam, Richard D Knight, Zebunnisa H Vanat, Nicola Folland, Patrick Axon
OBJECTIVE: Review of cochlear implant (CI) outcomes in patients with Neurofibromatosis Type 2 (NF2), implanted in the presence of an ipsilateral vestibular schwannoma (VS). Hearing restoration was combined in some cases with a Bevacizumab regime. METHOD: Retrospective review of 12 patients, managed over the period 2009-2016, at a tertiary referral multidisciplinary NF2 clinic. The patients are grouped by hearing outcomes to explore likely protective factors, and to generate a proposed decision-making tool for the selection of either CI or Auditory Brainstem Implant (ABI)...
March 24, 2017: Cochlear Implants International
https://www.readbyqxmd.com/read/28335009/open-chromatin-profiling-of-human-postmortem-brain-infers-functional-roles-for-non-coding-schizophrenia-loci
#13
John F Fullard, Claudia Giambartolomei, Mads E Hauberg, Ke Xu, Georgios Voloudakis, Zhiping Shao, Christopher Bare, Joel T Dudley, Manuel Mattheisen, Nikolaos K Robakis, Vahram Haroutunian, Panos Roussos
Open chromatin provides access to DNA binding proteins for the correct spatiotemporal regulation of gene expression. Mapping chromatin accessibility has been widely used to identify the location of cis regulatory elements (CREs) including promoters and enhancers. CREs show tissue- and cell-type specificity and disease-associated variants are often enriched for CREs in the tissues and cells that pertain to a given disease. To better understand the role of CREs in neuropsychiatric disorders we applied the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) to neuronal and non-neuronal nuclei isolated from frozen postmortem human brain by fluorescence-activated nuclear sorting (FANS)...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334978/therapeutic-window-of-dopamine-d2-3-receptor-occupancy-to-treat-psychosis-in-alzheimer-s-disease
#14
Suzanne Reeves, Emma McLachlan, Julie Bertrand, Fabrizia D Antonio, Stuart Brownings, Akshay Nair, Suki Greaves, Alan Smith, David Taylor, Joel Dunn, Paul Marsden, Robert Kessler, Robert Howard
Antipsychotic drugs, originally developed to treat schizophrenia, are used to treat psychosis, agitation and aggression in Alzheimer's disease. In the absence of dopamine D2/3 receptor occupancy data to inform antipsychotic prescribing for psychosis in Alzheimer's disease, the mechanisms underpinning antipsychotic efficacy and side effects are poorly understood. This study used a population approach to investigate the relationship between amisulpride blood concentration and central D2/3 occupancy in older people with Alzheimer's disease by combining: (i) pharmacokinetic data (280 venous samples) from a phase I single (50 mg) dose study in healthy older people (n = 20, 65-79 years); (ii) pharmacokinetic, 18F-fallypride D2/3 receptor imaging and clinical outcome data on patients with Alzheimer's disease who were prescribed amisulpride (25-75 mg daily) to treat psychosis as part of an open study (n = 28; 69-92 years; 41 blood samples, five pretreatment scans, 19 post-treatment scans); and (iii) 18F-fallypride imaging of an antipsychotic free Alzheimer's disease control group (n = 10, 78-92 years), to provide additional pretreatment data...
February 4, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334478/different-structural-origins-of-the-enantioselectivity-of-haloalkane-dehalogenases-toward-linear-%C3%AE-haloalkanes-open-solvated-versus-occluded-desolvated-active-sites
#15
Veronika Liskova, Veronika Stepankova, David Bednar, Jan Brezovsky, Zbynek Prokop, Radka Chaloupkova, Jiri Damborsky
The enzymatic enantiodiscrimination of linear β-haloalkanes is difficult because the simple structures of the substrates prevent directional interactions. Herein we describe two distinct molecular mechanisms for the enantiodiscrimination of the β-haloalkane 2-bromopentane by haloalkane dehalogenases. Highly enantioselective DbjA has an open, solvent-accessible active site, whereas the engineered enzyme DhaA31 has an occluded and less solvated cavity but shows similar enantioselectivity. The enantioselectivity of DhaA31 arises from steric hindrance imposed by two specific substitutions rather than hydration as in DbjA...
March 23, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28334338/synmap2-synmap3d-web-based-whole-genome-synteny-browsers
#16
Asher Haug-Baltzell, Sean Stephens, Sean Davey, Carlos Scheidegger, Eric Lyons
Summary: Current synteny visualization tools either focus on small regions of sequence and do not illustrate genome-wide trends, or are complicated to use and create visualizations that are difficult to interpret. To address this challenge, The Comparative Genomics Platform (CoGe) has developed two web-based tools to visualize synteny across whole genomes. SynMap2 and SynMap3D allow researchers to explore whole genome synteny patterns (across two or three genomes, respectively) in responsive, web-based visualization and virtual reality environments...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334291/smartr-an-open-source-platform-for-interactive-visual-analytics-for-translational-research-data
#17
Sascha Herzinger, Wei Gu, Venkata Satagopam, Serge Eifes, Kavita Rege, Adriano Barbosa Da Silva, Reinhard Schneider
In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical, or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies...
March 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334127/managed-bumble-bees-bombus-impatiens-hymenoptera-apidae-caged-with-blueberry-bushes-at-high-density-did-not-increase-fruit-set-or-fruit-weight-compared-to-open-pollination
#18
J W Campbell, J O'Brien, J H Irvin, C B Kimmel, J C Daniels, J D Ellis
Highbush blueberry (Vaccinium corymbosum L.) is an important crop grown throughout Florida. Currently, most blueberry growers use honey bees (Apis mellifera L.) to provide pollination services for highbush blueberries even though bumble bees (Bombus spp.) have been shown to be more efficient at pollinating blueberries on a per bee basis. In general, contribution of bumble bees to the pollination of commercial highbush blueberries in Florida is unknown. Herein, we determined if managed bumble bees could contribute to highbush blueberry pollination...
February 17, 2017: Environmental Entomology
https://www.readbyqxmd.com/read/28334105/biojava-modfinder-identification-of-protein-modifications-in-3d-structures-from-the-protein-data-bank
#19
Jianjiong Gao, Andreas Prlic, Chunxiao Bi, Wolfgang F Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E Bourne, Peter W Rose
Summary: We developed a new software tool, BioJava-ModFinder, for identifying protein modifications observed in 3D structures archived in the Protein Data Bank (PDB). Information on more than 400 types of protein modifications were collected and curated from annotations in PDB, RESID, and PSI-MOD. We divided these modifications into three categories: modified residues, attachment modifications, and cross-links. We have developed a systematic method to identify these modifications in 3D protein structures...
February 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333841/audit-of-ca125-follow-up-after-first-line-therapy-for-ovarian-cancer
#20
Daniel Krell, Fran Said Battistino, Sarah Benafif, Lochani Ganegoda, Marcia Hall, Gordon J S Rustin
AIMS: The Medical Research Council OVO5/EORTC 55955 trial showed that patients in remission after first-line therapy for ovarian cancer did not benefit from routine measurement of CA125 during follow-up. Since the presentation of these results, we have counseled patients about the options for follow-up and provided them with an information leaflet about the trial results and the symptoms that should prompt an early appointment and CA125 measurement. We present an audit of practice after the presentation of those results...
March 23, 2017: International Journal of Gynecological Cancer
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