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https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#1
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637296/omixcore-a-web-server-for-prediction-of-protein-interactions-with-large-rna
#2
Alexandros Armaos, Davide Cirillo, Gian Gaetano Tartaglia
Summary: Here we introduce omiXcore, a server for calculations of protein binding to large RNAs (> 500 nucleotides). Our webserver allows (i) use of both protein and RNA sequences without size restriction; (ii) pre-compiled library for exploration of human long intergenic RNAs (lincRNAs) interactions; (iii) prediction of binding sites. Results: omiXcore was trained and tested on enhanced UV Cross-Linking and ImmunoPrecipitation (eCLIP) data. The method discriminates interacting and non-interacting protein-RNA pairs and identifies RNA binding sites with Areas under the ROC curve > 0...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637159/methane-production-and-fertilizing-value-of-organic-waste-organic-matter-characterization-for-a-better-prediction-of-valorization-pathways
#3
Julie Jimenez, Han Lei, Jean-Philippe Steyer, Sabine Houot, Dominique Patureau
Organic wastes are potential sources of both energy as well as crop production fertilizers. Correlations and models, involving organic matter characterization, have been previously described by several authors although there is still a lack in knowledge on the potential of simultaneous predictions of methane and organic fertilizer quality to optimize the wastes treatments. A methodology combining chemical accessibility and fluorescence spectroscopy was used to characterize 82 different organic wastes. Characterization data were compared with the biochemical methane potential (BMP), and with the biodegradable organic carbon obtained by soil incubation (C_bio)...
May 31, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28637130/community-integration-and-life-satisfaction-among-individuals-with-spinal-cord-injury-living-in-the-community-after-receiving-institutional-care-in-bangladesh
#4
Nayeema Ahmed, Mohammad Morshedul Quadir, Mohammad Akhlasur Rahman, Hasanat Alamgir
PURPOSE: This study reports level of community integration and life satisfaction among individuals who sustained traumatic spinal cord injuries, received institutional rehabilitation care services, and went back to live in the community in Bangladesh. It examines the impact of type of injury, demographic characteristics, socio-economic profile, and secondary health conditions on community integration and life satisfaction and explores the association between these two measures. METHOD: Individuals with spinal cord injury were telephone interviewed by the Centre for the Rehabilitation of the Paralysed, Bangladesh from February to June of 2014...
February 7, 2017: Disability and Rehabilitation
https://www.readbyqxmd.com/read/28637065/evaluation-of-an-e-learning-system-for-diagnosis-of-gastric-lesions-using-magnifying-narrow-band-imaging-a-multicenter-randomized-controlled-study
#5
Hiroyoshi Nakanishi, Hisashi Doyama, Hideki Ishikawa, Noriya Uedo, Takuji Gotoda, Mototsugu Kato, Shigeaki Nagao, Yasuaki Nagami, Hiroyuki Aoyagi, Atsushi Imagawa, Junichi Kodaira, Shinya Mitsui, Nozomu Kobayashi, Manabu Muto, Hajime Takatori, Takashi Abe, Masahiko Tsujii, Jiro Watari, Shuhei Ishiyama, Ichiro Oda, Hiroyuki Ono, Kazuhiro Kaneko, Chizu Yokoi, Tetsuya Ueo, Kunihisa Uchita, Kenshi Matsumoto, Takashi Kanesaka, Yoshinori Morita, Shinichi Katsuki, Jun Nishikawa, Katsuhisa Inamura, Tetsu Kinjo, Katsumi Yamamoto, Daisuke Yoshimura, Hiroshi Araki, Hiroshi Kashida, Ayumu Hosokawa, Hirohito Mori, Haruhiro Yamashita, Osamu Motohashi, Kazuhiko Kobayashi, Michiaki Hirayama, Hiroyuki Kobayashi, Masaki Endo, Hiroo Yamano, Kazunari Murakami, Tomoyuki Koike, Kingo Hirasawa, Youichi Miyaoka, Hidetaka Hamamoto, Takuto Hikichi, Norihiro Hanabata, Ryo Shimoda, Shinichiro Hori, Tadashi Sato, Shinya Kodashima, Hiroyuki Okada, Tomohiko Mannami, Shojiro Yamamoto, Yasumasa Niwa, Kazuo Yashima, Satoshi Tanabe, Hiro Satoh, Fumisato Sasaki, Tetsuro Yamazato, Yoshiou Ikeda, Hogara Nishisaki, Masahiro Nakagawa, Akio Matsuda, Fumio Tamura, Hitoshi Nishiyama, Keiko Arita, Keisuke Kawasaki, Kazushige Hoppo, Masashi Oka, Shinichi Ishihara, Michita Mukasa, Hiroaki Minamino, Kenshi Yao
Background and study aim Magnifying narrow-band imaging (M-NBI) is useful for the accurate diagnosis of early gastric cancer (EGC). However, acquiring skill at M-NBI diagnosis takes substantial effort. An Internet-based e-learning system to teach endoscopic diagnosis of EGC using M-NBI has been developed. This study evaluated its effectiveness. Participants and methods This study was designed as a multicenter randomized controlled trial. We recruited endoscopists as participants from all over Japan. After completing Test 1, which consisted of M-NBI images of 40 gastric lesions, participants were randomly assigned to the e-learning or non-e-learning groups...
June 21, 2017: Endoscopy
https://www.readbyqxmd.com/read/28637051/teaching-transnasal-endoscopy-to-graduate-students-without-a-hospital-or-simulation-laboratory-pool-noodles-and-cadavers
#6
Shari Salzhauer Berkowitz
Purpose: This study reports on a training opportunity in endoscopy in which speech-language pathology graduate students use inanimate objects and cadavers. Best practices for transnasal endoscopy in vivo require a physician to be nearby, but many graduate programs do not have this access. Method: Endoscopy was offered as a graduate elective. Students (13 women) initially learned to manipulate the endoscope through the lumen of a swimming pool noodle that was embedded with trinkets...
June 20, 2017: American Journal of Speech-language Pathology
https://www.readbyqxmd.com/read/28636978/psychiatric-comorbidity-with-hypothalamic-hamartoma-systematic-review-for-predictive-clinical-features
#7
REVIEW
Zachary Killeen, Raymond Bunch, John F Kerrigan
OBJECTIVE: We conducted a systematic review of the English-language literature to identify clinical features associated with a higher risk of psychiatric symptoms (aggression and rage behaviors) in patients with hypothalamic hamartoma (HH) and epilepsy. METHODS: Two publicly-accessible databases (PubMed and Cochrane Library) were searched for Hypothalamic Hamartoma AND Epilepsy. We identified peer-reviewed original research publications (case reports or clinical series; N=19) in which clinical data was provided on an individual basis...
June 18, 2017: Epilepsy & Behavior: E&B
https://www.readbyqxmd.com/read/28636905/a-kepler-workflow-tool-for-reproducible-amber-gpu-molecular-dynamics
#8
Shweta Purawat, Pek U Ieong, Robert D Malmstrom, Garrett J Chan, Alan K Yeung, Ross C Walker, Ilkay Altintas, Rommie E Amaro
With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636834/implementation-of-medical-homes-in-federally-qualified-health-centers
#9
Justin W Timbie, Claude M Setodji, Amii Kress, Tara A Lavelle, Mark W Friedberg, Peter J Mendel, Emily K Chen, Beverly A Weidmer, Christine Buttorff, Rosalie Malsberger, Mallika Kommareddi, Afshin Rastegar, Aaron Kofner, Lisa Hiatt, Ammarah Mahmud, Katherine Giuriceo, Katherine L Kahn
Background From 2011 through 2014, the Federally Qualified Health Center Advanced Primary Care Practice Demonstration provided care management fees and technical assistance to a nationwide sample of 503 federally qualified health centers to help them achieve the highest (level 3) medical-home recognition by the National Committee for Quality Assurance, a designation that requires the implementation of processes to improve access, continuity, and coordination. Methods We examined the achievement of medical-home recognition and used Medicare claims and beneficiary surveys to measure utilization of services, quality of care, patients' experiences, and Medicare expenditures in demonstration sites versus comparison sites...
June 21, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28636815/accurate-characterization-of-the-pore-volume-in-microporous-crystalline-materials
#10
Daniele Ongari, Peter G Boyd, Senja Barthel, Matthew Witman, Maciej Haranczyk, Berend Smit
Pore volume is one of the main properties for the characterization of microporous crystals. It is experimentally measurable and it can also be obtained from the refined unit cell by a number of computational techniques. In this work we assess the accuracy and the discrepancies between the different computational methods which are commonly used for this purpose, i.e, geometric, helium and probe center pore volume, by studying a database of more than 5000 frameworks. We developed a new technique to fully characterize the internal void of a microporous material and to compute the probe accessible and occupiable pore volume...
June 21, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28636809/visible-light-driven-aza-ortho-quinone-methide-generation-enables-a-multicomponent-reaction
#11
Wen-Jing Xiao, Yi-Ying Liu, Xiao-Ye Yu, Miao-Maio Qiao, Xiaotian Qi, Jia-Rong Chen, De-Qing Shi
A visible light photoredox-catalyzed and radical-mediated strategy for the in situ generation of aza-ortho-quinone methides from readily accessible alkenylanilines and alkyl radical precursors has been accomplished for the first time. This protocol enables an efficient multicomponent cascade reaction of alkenylanilines, halides and sulfur ylides, and shows wide substrate scope and high functional group tolerance with respect to each component. Treatment of the initially formed cycloaddition products with a base leads to a convergent and streamlined synthesis of densely functionalized indoles in a single flask operation...
June 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28636751/using-experimentation-to-understand-the-10-year-snowshoe-hare-cycle-in-the-boreal-forest-of-north-america
#12
C J Krebs, R Boonstra, S Boutin
Population cycles have long fascinated ecologists from the time of Charles Elton in the 1920s. The discovery of large population fluctuations in undisturbed ecosystems challenged the idea that pristine nature was in a state of balance. The 10-year cycle of snowshoe hares (Lepus americanus Erxleben) across the boreal forests of Canada and Alaska is a classic cycle, recognized by fur traders for more than 300 years. Since the 1930s ecologists have investigated the mechanisms that might cause these cycles. Proposed causal mechanisms have varied from sunspots to food supplies, parasites, diseases, predation, and social behaviour...
June 21, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28636680/unifying-the-microscopic-picture-of-his-containing-turns-from-gas-phase-model-peptides-to-crystallized-proteins
#13
Woon Yong Sohn, Sana Habka, Eric Gloaguen, Michel Mons
The presence in crystallized proteins of a local anchoring between the side chain of a His residue, located in the central position of a γ- or β-turn, and its local main chain environment, was assessed by the comparison of protein structures with relevant isolated model peptides. Gas phase laser spectroscopy, combined with relevant quantum chemistry methods, was used to characterize the γ- and β-turn structures in these model peptides. A conformer-selective NH stretch infrared study provided evidence for the formation in vacuo of two types of short-range H-bonded motifs, labelled ε-6(δ) and δ-(δ)7/π(H), bridging the His side chain (in its gauche+ rotamer) to the neighbouring NH(i) and CO(i) sites of the backbone; each side chain-backbone motif was found to be specific of the tautomer (ε or δ) adopted by the His side chain in its neutral form...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28636676/mitochondrion-to-endoplasmic-reticulum-apposition-length-in-zebrafish-embryo-spinal-progenitors-is-unchanged-in-response-to-perturbations-associated-with-alzheimer-s-disease
#14
Morgan Newman, Lena Halter, Anne Lim, Michael Lardelli
Mutations in the human genes PRESENILIN1 (PSEN1), PRESENILIN2 (PSEN2) and AMYLOID BETA A4 PRECURSOR PROTEIN (APP) have been identified in familial Alzheimer's disease (AD). The length of mitochondrion-endoplasmic reticulum (M-ER) appositions is increased in Psen1-/-/Psen2-/- double knockout murine embryonic fibroblasts and in fibroblasts from AD-affected individuals. Development of an easily accessible, genetically manipulable, in vivo system for studying M-ER appositions would be valuable so we attempted to manipulate M-ER apposition length in zebrafish (Danio rerio) embryos...
2017: PloS One
https://www.readbyqxmd.com/read/28636669/exploring-factors-associated-with-art-adherence-and-retention-in-care-under-option-b-strategy-in-malawi-a-qualitative-study
#15
Salem Gugsa, Katy Potter, Hannock Tweya, Sam Phiri, Odala Sande, Pascal Sikwese, Janet Chikonda, Gabrielle O'Malley
Although several studies have documented challenges related to inadequate adherence to antiretroviral therapy (ART) and high loss to follow-up (LTFU) among Option B+ women, there is limited understanding of why these challenges occur and how to address them. This qualitative study examines women's experiences with ART adherence and retention in care. Between July and October 2015, in-depth interviews were conducted with 39 pregnant and lactating women who initiated ART at Bwaila Hospital in Lilongwe, Malawi...
2017: PloS One
https://www.readbyqxmd.com/read/28636654/characterization-of-human-fcrl4-positive-b-cells
#16
Michel Jourdan, Nicolas Robert, Maïlys Cren, Coraline Thibaut, Christophe Duperray, Alboukadel Kassambara, Michel Cogné, Karin Tarte, Bernard Klein, Jérôme Moreaux
FCRL4 is an immunoregulatory receptor that belongs to the Fc receptor-like (FCRL) family. In healthy individuals, FCRL4 is specifically expressed by memory B cells (MBCs) localized in sub-epithelial regions of lymphoid tissues. Expansion of FCRL4+ B cells has been observed in blood and other tissues in various infectious and autoimmune disorders. Currently, the mechanisms involved in pathological FCRL4+ B cell generation are actively studied, but they remain elusive. As in vivo FCRL4+ cells are difficult to access and to isolate, here we developed a culture system to generate in vitro FCRL4+ B cells from purified MBCs upon stimulation with soluble CD40 ligand and/or CpG DNA to mimic T-cell dependent and/or T-cell independent activation, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28636631/incidence-and-mortality-due-to-snakebite-in-the-americas
#17
Jean-Philippe Chippaux
BACKGROUND: Better knowledge of the epidemiological characteristics of snakebites could help to take measures to improve their management. The incidence and mortality of snakebites in the Americas are most often estimated from medical and scientific literature, which generally lack precision and representativeness. METHODOLOGY/PRINCIPAL FINDINGS: Authors used the notifications of snakebites treated in health centers collected by the Ministries of Health of the American countries to estimate their incidence and mortality...
June 21, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28636630/accessibility-and-socio-economic-development-of-human-settlements
#18
Samiul Hasan, Xiaoming Wang, Yong Bing Khoo, Greg Foliente
Access to facilities, services and socio-economic opportunities plays a critical role in the growth and decline of cities and human settlements. Previous attempts to explain changes in socio-economic indicators by differences in accessibility have not been convincing as countries with highly developed transport infrastructure have only seen marginal benefits of infrastructure improvements. Australia offers an ideal case for investigating the effects of accessibility on development since it is seen as home to some of the most liveable cities in the world while, at the same time, it also has some of the most isolated settlements...
2017: PloS One
https://www.readbyqxmd.com/read/28636623/the-basolateral-vesicle-sorting-machinery-and-basolateral-proteins-are-recruited-to-the-site-of-enteropathogenic-e-coli-microcolony-growth-at-the-apical-membrane
#19
Gitte A Pedersen, Helene H Jensen, Anne-Sofie B Schelde, Charlotte Toft, Hans N Pedersen, Maj Ulrichsen, Frédéric H Login, Manuel R Amieva, Lene N Nejsum
Foodborne Enteropathogenic Escherichia coli (EPEC) infections of the small intestine cause diarrhea especially in children and are a major cause of childhood death in developing countries. EPEC infects the apical membrane of the epithelium of the small intestine by attaching, effacing the microvilli under the bacteria and then forming microcolonies on the cell surface. We first asked the question where on epithelial cells EPEC attaches and grows. Using models of polarized epithelial monolayers, we evaluated the sites of initial EPEC attachment to the apical membrane and found that EPEC preferentially attached over the cell-cell junctions and formed microcolonies preferentially where three cells come together at tricellular tight junctions...
2017: PloS One
https://www.readbyqxmd.com/read/28636617/backup-development-and-evaluation-of-a-smart-phone-application-for-coping-with-suicidal-crises
#20
Kirsten Pauwels, Saskia Aerts, Ekke Muijzers, Eva De Jaegere, Kees van Heeringen, Gwendolyn Portzky
BACKGROUND: Suicide is a major public health issue and has large impact on the lives of many people. Innovative technologies such as smartphones could create new possibilities for suicide prevention, such as helping to overcome the barriers and stigma on help seeking in case of suicidal ideation. Due to their omnipresence, smartphone apps can offer suicide prevention tools very fast, they are easily-accessible, low-threshold and can help overcome some of the help-seeking barriers suicidal people experience...
2017: PloS One
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