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https://www.readbyqxmd.com/read/28092692/smile-seq-identifies-binding-motifs-of-single-and-dimeric-transcription-factors
#1
Alina Isakova, Romain Groux, Michael Imbeault, Pernille Rainer, Daniel Alpern, Riccardo Dainese, Giovanna Ambrosini, Didier Trono, Philipp Bucher, Bart Deplancke
Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq). SMiLE-seq is neither limited by DNA bait length nor biased toward strong affinity binders; it probes the DNA-binding properties of TFs over a wide affinity range in a fast and cost-effective fashion. We validated SMiLE-seq by analyzing 58 full-length human, mouse, and Drosophila TFs from distinct structural classes...
January 16, 2017: Nature Methods
https://www.readbyqxmd.com/read/28092564/static-vs-dynamic-decoding-algorithms-in-a-non-invasive-body-machine-interface
#2
Ismael Seanez-Gonzalez, Camilla Pierella, Ali Farshchiansadegh, Elias Barry Thorp, Farnaz Abdollahi, Jessica P Pedersen, Ferdinando A Mussa-Ivaldi
In this study, we consider a non-invasive bodymachine interface that captures body motions still available to people with spinal cord injury (SCI) and maps them into a set of signals for controlling a computer user interface while engaging in a sustained level of mobility and exercise. We compare the effectiveness of two decoding algorithms that transform a highdimensional body-signal vector into a lower dimensional control vector on 6 subjects with high-level SCI and 8 controls. One algorithm is based on a static map from current body signals to the current value of the control vector set through principal component analysis (PCA), the other on dynamic mapping a segment of body signals to the value and the temporal derivatives of the control vector set through a Kalman filter...
December 15, 2016: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/28092562/line-graph-or-scatter-plot-automatic-selection-of-methods-for-visualizing-trends-in-time-series
#3
Yunhai Wang, Fubo Han, Lifeng Zhu, Oliver Deussen, Baoquan Chen
Line graphs are usually considered to be the best choice for visualizing time series data, whereas sometimes also scatter plots are used for showing main trends. So far there are no guidelines that indicate which of these visualization methods better display trends in time series for a given canvas. Assuming that the main information in a time series is its overall trend, we propose an algorithm that automatically picks the visualization method that reveals this trend best. This is achieved by measuring the visual consistency between the trend curve represented by a LOESS fit and the trend described by a scatter plot or a line graph...
January 16, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28092537/detail-enhanced-multi-scale-exposure-fusion
#4
Zhengguo Li, Zhe Wei, Changyun Wen, Jinghong Zheng
Multi-scale exposure fusion is an effective image enhancement technique for a high dynamic range (HDR) scene. In this paper, a new multi-scale exposure fusion algorithm is proposed to merge differently exposed low dynamic range (LDR) images by using the weighted guided image filter (WGIF) to smooth the Gaussian pyramids of weight maps for all the LDR images. Details in the brightest and darkest regions of the HDR scene are preserved better by the proposed algorithm without relative brightness change in the fused image...
January 16, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28092494/zebrafish-are-able-to-detect-ethanol-in-their-environment
#5
Steven Tran, Hayden Chow, Benjamin Tsang, Amanda Facciol, Prabhlene Gandhi, Priyanka Desai, Robert Gerlai
Zebrafish have become a popular animal model for studying the development of alcohol addiction. Several behavioral paradigms for studying alcohol addiction have been developed for zebrafish, including conditioned place preference, alcohol-induced tolerance, and withdrawal. However, alcohol choice preference tasks have not been established in zebrafish as of yet. The ability of zebrafish to detect alcohol in their environment is required in alcohol choice or preference tasks. To our knowledge, it is currently unknown whether zebrafish are able to detect alcohol in their environment immediately following bath immersion...
January 16, 2017: Zebrafish
https://www.readbyqxmd.com/read/28092444/engineering-of-the-bacillus-circulans-%C3%AE-galactosidase-product-specificity
#6
Huifang Yin, Tjaard Pijning, Xiangfeng Meng, Lubbert Dijkhuizen, Sander Sebastiaan van Leeuwen
Microbial β-galactosidase enzymes are widely used as biocatalysts in industry to produce prebiotic galactooligosaccharides (GOS) from lactose. GOS mixtures are used as beneficial additives in infant formula to mimic the prebiotic effects of human milk oligosaccharides (hMOS). The structural variety in GOS mixtures is significantly lower than in hMOS. Since this structural complexity is considered as the basis for the multiple biological functions of hMOS, it is important to broaden the variety of GOS structures...
January 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28092439/molecular-details-of-the-ph-domain-of-acap1-bar-ph-protein-binding-to-pip-containing-membrane
#7
Chun Chan, Lanyuan Lu, Fei Sun, Jun Fan
ACAP1 proteins were previously reported to specifically bind PIP2-containing cell membranes and form well-structured protein lattices in order to conduct membrane tubulation. We carried out molecular dynamics simulations to characterize orientation of the PH domains with respect to the BAR domains inside the protein dimer. Followed by molecular dynamics simulations, we present a comprehensive orientation analysis of PH domain under different states including unbound and bound with lipids. We have examined two binding pockets on the PH domain and present PMF profiles of the two pockets to account for their preference to PIP2 lipids...
January 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28092429/residents-understanding-of-adult-congenital-heart-disease
#8
Paul Cooper, Morgan Hindes, Timothy M Maul, Stephen C Cook
OBJECTIVE: Medical residents are exposed to increasing numbers of adults with congenital heart disease (ACHD). While inadequate ACHD knowledge may lead to inappropriate practice, this educational deficit has not been investigated. Our aim was to analyze residents' attitudes, perceived ability, and knowledge of ACHD medicine. DESIGN, METHODS, OUTCOME MEASURES: A single center, multiprogram cross-sectional study was conducted in 2015 using an electronic survey to assess 472 medical residents' perceived knowledge and self-assessed skills related to ACHD medicine...
January 16, 2017: Congenital Heart Disease
https://www.readbyqxmd.com/read/28092272/material-dependent-implant-artifact-reduction-using-semac-vat-and-mavric-a-prospective-mri-phantom-study
#9
Lukas Filli, Lukas Jud, Roger Luechinger, Daniel Nanz, Gustav Andreisek, Val M Runge, Sebastian Kozerke, Nadja A Farshad-Amacker
OBJECTIVE: The aim of this study was to compare the degree of artifact reduction in magnetic resonance imaging achieved with slice encoding for metal artifact correction (SEMAC) in combination with view angle tilting (VAT) and multiacquisition variable resonance image combination (MAVRIC) for standard contrast weightings and different metallic materials. METHODS: Four identically shaped rods made of the most commonly used prosthetic materials (stainless steel, SS; titanium, Ti; cobalt-chromium-molybdenum, CoCr; and oxidized zirconium, oxZi) were scanned at 3 T...
January 13, 2017: Investigative Radiology
https://www.readbyqxmd.com/read/28092255/-the-importance-of-promoting-the-bioethical-seeds-in-the-university
#10
Paola Pérez-Polanco, Luis Manuel Montaño-Zetina
One of the main scopes for institutions dedicated to preparing professionals in health is to increase their bioethics profile. To achieve this scope, these institutions have included lessons in bioethics into their study plans. Another way to increase the profile of the students, as the authors of this article propose, is creating bioethics seeds through a bioethics interest diagnostic on the students' preferences in their first year of the Justo Sierra University using a particular clinical case. The results found indicated that students show more interest in learning the physiopathology, diagnostics, and therapy of the pathologies than bioethics...
January 2017: Revista Médica del Instituto Mexicano del Seguro Social
https://www.readbyqxmd.com/read/28092224/visual-map-and-instruction-based-bicycle-navigation-a-comparison-of-effects-on-behaviour
#11
Dick de Waard, Frank Westerhuis, Danielle Joling, Stella Weiland, Ronja Stadtbäumer, Leonie Kaltofen
Cycling with a classic paper map was compared with navigating with a moving map displayed on a smartphone, and with auditory, and visual turn-by-turn route guidance. Spatial skills were found to be related to navigation performance, however only when navigating from a paper or electronic map, not with turn-by-turn (instruction based) navigation. While navigating, 25% of the time cyclists fixated at the devices that present visual information. Navigating from a paper map required most mental effort and both young and older cyclists preferred electronic over paper map navigation...
January 16, 2017: Ergonomics
https://www.readbyqxmd.com/read/28092144/exergaming-boxing-versus-heavy-bag-boxing-are-these-equipotent-for-individuals-with-spinal-cord-injury
#12
Maziah Mat Rosly, Hadi Mat Rosly, Nazirah Hasnan, Glen M Davis, Ruby Husain
BACKGROUND: Current strategies for increased physical activity and exercise in individuals with spinal cord injury (SCI) face many challenges with regards to maintaining their continuity of participation. Barriers cited often include problems with accessing facilities, mundane, monotonous or boring exercises and expensive equipment that is often not adapted for wheelchair users. AIM: To compare the physiological responses and user preferences between conventional heavy bag boxing against a novel form of video game boxing, known as exergaming boxing...
January 13, 2017: European Journal of Physical and Rehabilitation Medicine
https://www.readbyqxmd.com/read/28092092/domains-of-daily-physical-activity-in-children-with-mitochondrial-disease-a-3d-accelerometry-approach
#13
Saskia Koene, Ilse Dirks, Esmee van Mierlo, Pascal R de Vries, Anjo J W M Janssen, Jan A M Smeitink, Arjen Bergsma, Hans Essers, Kenneth Meijer, Imelda J M de Groot
Feasible, sensitive and clinically relevant outcome measures are of extreme importance when designing clinical trials. For paediatric mitochondrial disease, no robust end point has been described to date. The aim of this study was to select the domains of daily physical activity, which can be measured by 3D accelerometry, that could serve as sensitive end points in future clinical trials in children with mitochondrial disorders.In this exploratory observational study, 17 patients with mitochondrial disease and 16 age- and sex-matched controls wore 3D accelerometers at the upper leg, upper arm, lower arm and chest during one weekend...
January 17, 2017: JIMD Reports
https://www.readbyqxmd.com/read/28092086/anxiety-related-behaviours-associated-with-microrna-206-3p-and-bdnf-expression-in-pregnant-female-mice-following-psychological-social-stress
#14
Zhuang Miao, Fengbiao Mao, Jialong Liang, Moshe Szyf, Yan Wang, Zhong Sheng Sun
Stress during pregnancy can induce various psychological disorders in women. However, the association linking psychological stress during pregnancy with abnormal behaviours in females remains largely unknown. We employed a novel psychological stress model by introducing pregnant mice to witness the defeat process of their mated partner (WDPMP) and examined the effects of WDPMP on depression-/anxiety-like behaviours and on the expression of brain-derived neurotrophic factor (BDNF) and miR-206-3p in the hippocampus, medial prefrontal cortex (mPFC) and amygdala...
January 14, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28092044/high-throughput-quantification-of-sh2-domain-phosphopeptide-interactions-with-cellulose-peptide-conjugate-microarrays
#15
Brett W Engelmann
The Src Homology 2 (SH2) domain family primarily recognizes phosphorylated tyrosine (pY) containing peptide motifs. The relative affinity preferences among competing SH2 domains for phosphopeptide ligands define "specificity space," and underpins many functional pY mediated interactions within signaling networks. The degree of promiscuity exhibited and the dynamic range of affinities supported by individual domains or phosphopeptides is best resolved by a carefully executed and controlled quantitative high-throughput experiment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092020/early-life-social-isolation-induced-depressive-like-behavior-in-rats-results-in-microglial-activation-and-neuronal-histone-methylation-that-are-mitigated-by-minocycline
#16
Hong-Tao Wang, Fu-Lian Huang, Zhao-Lan Hu, Wen-Juan Zhang, Xiao-Qing Qiao, Yan-Qing Huang, Ru-Ping Dai, Fang Li, Chang-Qi Li
Early-life stress is a potent risk factor for development of psychiatric conditions such as depression. The underlying mechanisms remain poorly understood. Here, we used the early-life social isolation (ESI) model of early-life stress in rats to characterize development of depressive-like behavior, the role of microglia, levels of histone methylation, as well as expression of glutamate receptor subunits in the hippocampus. We found that depressive-like behavior was induced after ESI as determined by sucrose preference and forced swimming tests...
January 16, 2017: Neurotoxicity Research
https://www.readbyqxmd.com/read/28092000/direct-and-indirect-effects-of-wastewater-use-and-herd-environment-on-the-occurrence-of-animal-diseases-and-animal-health-in-pakistan
#17
Ehsan Elahi, Liqin Zhang, Muhammad Abid, Muhammad Tariq Javed, Han Xinru
The use of wastewater for rearing domestic animals is a common phenomenon in most of the developing countries like Pakistan that face a serious shortage of freshwater resources. However, most of the literature has only focused on the indirect effects of wastewater use on animal health or productivity, and literature on the direct effects of wastewater use is rare. Therefore, this study aims to investigate the direct and indirect effects of wastewater usage on the prevalence of animal diseases and animal health in Pakistan...
January 14, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28091847/using-the-newly-developed-floor-sitting-movement-analysis-proforma-to-study-the-effect-of-age-and-activity-on-floor-sitting-in-indian-adults
#18
Anjana Nagrajan, Sebestina A D'Souza
Floor-sitting is culturally relevant to the Indian context. The present study aimed to examine the effect of age and activity on the movement patterns used and time taken to perform floor-sitting in Indian adults. Video-recordings of 30 young (23.30 ± 2.53 years) and 30 older (69.67 ± 6.45 years) adults performing floor-sitting without and with an activity (simulated feeding) were analyzed using the Floor-sitting Movement Analysis Proforma (FMAP) developed for the study. For inter-rater reliability of the FMAP, two raters analyzed the performance of a random sample of 20 participants...
January 16, 2017: Journal of Cross-cultural Gerontology
https://www.readbyqxmd.com/read/28091840/test-of-gross-motor-development-3-tgmd-3-with-the-use-of-visual-supports-for-children-with-autism-spectrum-disorder-validity-and-reliability
#19
K A Allen, B Bredero, T Van Damme, D A Ulrich, J Simons
The validity and reliability of the Test of Gross Motor Development-3 (TGMD-3) were measured, taking into consideration the preference for visual learning of children with autism spectrum disorder (ASD). The TGMD-3 was administered to 14 children with ASD (4-10 years) and 21 age-matched typically developing children under two conditions: TGMD-3 traditional protocol, and TGMD-3 visual support protocol. Excellent levels of internal consistency, test-retest, interrater and intrarater reliability were achieved for the TGMD-3 visual support protocol...
January 13, 2017: Journal of Autism and Developmental Disorders
https://www.readbyqxmd.com/read/28091796/preferences-for-smoking-cessation-support-from-family-and-friends-among-adults-with-serious-mental-illness
#20
Kelly A Aschbrenner, John A Naslund, Lydia Gill, Stephen J Bartels, A James O'Malley, Mary F Brunette
Engaging natural supports may be a promising strategy to promote the use of evidence-based smoking cessation treatment for individuals with serious mental illness (SMI) who smoke. This qualitative study explored preferences for support for quitting from family and friends among individuals with SMI who participated in cessation treatment. Participants were 41 individuals with SMI enrolled in a Medicaid Demonstration Project of smoking cessation at community mental health centers. Open-ended questions asked during a social network interview explored participants' preferences for more support for quitting smoking from family and friends...
January 16, 2017: Psychiatric Quarterly
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