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https://www.readbyqxmd.com/read/28339468/pbmda-a-novel-and-effective-path-based-computational-model-for-mirna-disease-association-prediction
#1
Zhu-Hong You, Zhi-An Huang, Zexuan Zhu, Gui-Ying Yan, Zheng-Wei Li, Zhenkun Wen, Xing Chen
In the recent few years, an increasing number of studies have shown that microRNAs (miRNAs) play critical roles in many fundamental and important biological processes. As one of pathogenetic factors, the molecular mechanisms underlying human complex diseases still have not been completely understood from the perspective of miRNA. Predicting potential miRNA-disease associations makes important contributions to understanding the pathogenesis of diseases, developing new drugs, and formulating individualized diagnosis and treatment for diverse human complex diseases...
March 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28335897/mitral-loop-cerclage-annuloplasty-for-secondary-mitral-regurgitation-first-human-results
#2
Yong-Hyun Park, Min-Ku Chon, Robert J Lederman, Si-Chan Sung, Hyung-Gon Je, Ki-Seok Choo, Sang-Hyun Lee, Eun-Seok Shin, Jeong-Su Kim, Ki-Won Hwang, Soo-Yong Lee, Kook-Jin Chun, Cheol-Min Kim, June-Hong Kim
OBJECTIVES: This is an early feasibility clinical test of mitral loop cerclage annuloplasty to treat secondary mitral valve regurgitation. BACKGROUND: Secondary mitral regurgitation is characterized by cardiomyopathy, mitral annular enlargement, and leaflet traction contributing to malcoaptation. Transcatheter mitral loop cerclage applies circumferential compression to the mitral annulus by creating a loop through the coronary sinus across the interventricular septum, protecting entrapped coronary arteries from compression, and interactive annular reduction under echocardiographic guidance...
March 27, 2017: JACC. Cardiovascular Interventions
https://www.readbyqxmd.com/read/28335409/the-formyl-peptide-receptors-diversity-of-ligands-and-mechanism-for-recognition
#3
REVIEW
Hui-Qiong He, Richard D Ye
The formyl peptide receptors (FPRs) are G protein-coupled receptors that transduce chemotactic signals in phagocytes and mediate host-defense as well as inflammatory responses including cell adhesion, directed migration, granule release and superoxide production. In recent years, the cellular distribution and biological functions of FPRs have expanded to include additional roles in homeostasis of organ functions and modulation of inflammation. In a prototype, FPRs recognize peptides containing N-formylated methionine such as those produced in bacteria and mitochondria, thereby serving as pattern recognition receptors...
March 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28334697/constraint-based-stoichiometric-modelling-from-single-organisms-to-microbial-communities
#4
REVIEW
Willi Gottstein, Brett G Olivier, Frank J Bruggeman, Bas Teusink
Microbial communities are ubiquitously found in Nature and have direct implications for the environment, human health and biotechnology. The species composition and overall function of microbial communities are largely shaped by metabolic interactions such as competition for resources and cross-feeding. Although considerable scientific progress has been made towards mapping and modelling species-level metabolism, elucidating the metabolic exchanges between microorganisms and steering the community dynamics remain an enormous scientific challenge...
November 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28331548/discovering-feature-relevancy-and-dependency-by-kernel-guided-probabilistic-model-building-evolution
#5
Nestor Rodriguez, Sergio Rojas-Galeano
BACKGROUND: Discovering relevant features (biomarkers) that discriminate etiologies of a disease is useful to provide biomedical researchers with candidate targets for further laboratory experimentation while saving costs; dependencies among biomarkers may suggest additional valuable information, for example, to characterize complex epistatic relationships from genetic data. The use of classifiers to guide the search for biomarkers (the so-called wrapper approach) has been widely studied...
2017: BioData Mining
https://www.readbyqxmd.com/read/28327660/quantitative-volumetric-raman-imaging-of-three-dimensional-cell-cultures
#6
Charalambos Kallepitis, Mads S Bergholt, Manuel M Mazo, Vincent Leonardo, Stacey C Skaalure, Stephanie A Maynard, Molly M Stevens
The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment...
March 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28323040/-machine-learning-based-identification-of-endogenous-cellular-microrna-sponges-against-viral-micrornas
#7
Soowon Kang, Seunghyun Park, Sungroh Yoon, Hyeyoung Min
A "miRNA sponge" is an artificial oligonucleotide-based miRNA inhibitor containing multiple binding sites for a specific miRNA. Each miRNA sponge can bind and sequester several miRNA copies, thereby decreasing the cellular levels of the target miRNA. In addition to developing artificial miRNA sponges, scientists have sought endogenous RNA transcripts and found that long non-coding RNAs, competing endogenous RNAs, pseudogenes, circular RNAs, and coding RNAs could act as miRNA sponges under precise conditions...
March 17, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28322827/structural-divergence-of-essential-triad-ribbon-synapse-proteins-among-placental-mammals-implications-for-preclinical-trials-in-photoreceptor-transplantation-therapy
#8
Christopher R J Laver, Joanne A Matsubara
As photoreceptor transplantation rapidly moves closer to the clinic, verifying graft efficacy in animal models may have unforeseen xenogeneic barriers. Although photoreceptor transplants have most convincingly exhibited functional synaptogenesis in conspecific studies, such evidence (while ruling out false-positives due to: viral graft labeling, fusion/cytosolic transfer, or neuroprotection) has not yet been shown for discordant xenografts. From this, a fundamental question should be raised: is useful xenosynaptogenesis likely between human photoreceptors and mouse retina? The triad ribbon synapse (TRS) that would normally form is unique and contains trans-synaptic proteins essential to its formation and function...
March 18, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/28322159/towards-predicting-the-cytochrome-p450-modulation-from-qsar-to-proteochemometric-modeling
#9
Watshara Shoombuatong, Philip Prathipati, Veda Prachayasittikul, Nalini Schaduangrat, Aijaz Ahmad Malik, Reny Pratiwi, Sompon Wanwimolruk, Jarl E S Wikberg, Matthew Paul Gleeson, Ola Spjuth, Chanin Nantasenamat
Drug metabolism determines the fate of a drug when it enters the human body and is a critical factor in defining their absorption, distribution, metabolism, excretion and toxicity (ADMET) characteristics. Among the various drug metabolizing enzymes, cytochrome P450s (CYP450) constitute an important protein family that aside from functioning in xenobiotic metabolism is also responsible for a diverse array of other roles encompassing steroid and cholesterol biosynthesis, fatty acid metabolism, calcium homeostasis, neuroendocrine functions and growth regulation...
March 20, 2017: Current Drug Metabolism
https://www.readbyqxmd.com/read/28321413/fluid-structure-interaction-in-abdominal-aortic-aneurysm-effect-of-modeling-techniques
#10
Shengmao Lin, Xinwei Han, Yonghua Bi, Siyeong Ju, Linxia Gu
In this work, the impact of modeling techniques on predicting the mechanical behaviors of abdominal aortic aneurysm (AAA) is systematically investigated. The fluid-structure interaction (FSI) model for simultaneously capturing the transient interaction between blood flow dynamics and wall mechanics was compared with its simplified techniques, that is, computational fluid dynamics (CFD) or computational solid stress (CSS) model. Results demonstrated that CFD exhibited relatively smaller vortexes and tends to overestimate the fluid wall shear stress, compared to FSI...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28320846/working-memory-load-strengthens-reward-prediction-errors
#11
Anne G E Collins, Brittany Ciullo, Michael J Frank, David Badre
Reinforcement learning in simple instrumental tasks is usually modeled as a monolithic process in which reward prediction errors are used to update expected values of choice options. This modeling ignores the different contributions of different memory and decision-making systems thought to contribute even to simple learning. In an fMRI experiment, we asked how working memory and incremental reinforcement learning processes interact to guide human learning. Working memory load was manipulated by varying the number of stimuli to be learned across blocks...
March 20, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28320670/bci-use-and-its-relation-to-adaptation-in-cortical-networks
#12
Kaitlyn Casimo, Kurt E Weaver, Jeremiah Wander, Jeffrey G Ojemann
Brain-computer interfaces (BCIs) carry great potential in the treatment of motor impairments. As a new motor output, BCIs interface with the native motor system, but acquisition of BCI proficiency requires a degree of learning to integrate this new function. In this review, we discuss how BCI designs often take advantage of the brain's motor system infrastructure as sources of command signals. We highlight a growing body of literature examining how this approach leads to changes in activity across cortex, including beyond motor regions, as a result of learning the new skill of BCI control...
March 13, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/28320651/collaborative-active-visual-recognition-from-crowds-a-distributed-ensemble-approach
#13
Gang Hua, Chengjiang Long, Ming Yang, Yan Gao
Active learning is an effective way of engaging users to interactively train models for visual recognition more efficiently. The vast majority of previous works focused on active learning with a single human oracle. The problem of active learning with multiple oracles in a collaborative setting has not been well explored. We present a collaborative computational model for active learning with multiple human oracles, the input from whom may be subject to different levels of noise. It leads to not only an ensemble kernel machine that is robust to label noise, but also a principled label quality measure to online detect irresponsible labelers...
March 15, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28303164/adverse-drug-reactions-triggered-by-the-common-hla-b-57-01-variant-a-molecular-docking-study
#14
George Van Den Driessche, Denis Fourches
BACKGROUND: Human leukocyte antigen (HLA) surface proteins are directly involved in idiosyncratic adverse drug reactions. Herein, we present a structure-based analysis of the common HLA-B*57:01 variant known to be responsible for several HLA-linked adverse effects such as the abacavir hypersensitivity syndrome. METHODS: First, we analyzed three X-ray crystal structures involving the HLA-B*57:01 protein variant, the anti-HIV drug abacavir, and different co-binding peptides present in the antigen-binding cleft...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28302551/role-of-structural-bioinformatics-in-drug-discovery-by-computational-snp-analysis-a-proposed-protocol-for-analyzing-variation-at-the-protein-level
#15
REVIEW
David K Brown, Özlem Tastan Bishop
With the completion of the human genome project at the beginning of the 21st century, the biological sciences entered an unprecedented age of data generation, and made its first steps toward an era of personalized medicine. This abundance of sequence data has led to the proliferation of numerous sequence-based techniques for associating variation with disease, such as genome-wide association studies and candidate gene association studies. However, these statistical methods do not provide an understanding of the functional effects of variation...
March 13, 2017: Global Heart
https://www.readbyqxmd.com/read/28300955/prototype-app-for-voice-therapy-a-peer-review
#16
Paula Lavaissiéri, Paulo Eduardo Damasceno Melo
Purpose: Voice speech therapy promotes changes in patients' voice-related habits and rehabilitation. Speech-language therapists use a host of materials ranging from pictures to electronic resources and computer tools as aids in this process. Mobile technology is attractive, interactive and a nearly constant feature in the daily routine of a large part of the population and has a growing application in healthcare. To develop a prototype application for voice therapy, submit it to peer assessment, and to improve the initial prototype based on these assessments...
March 9, 2017: CoDAS
https://www.readbyqxmd.com/read/28298218/systematic-identification-of-an-integrative-network-module-during-senescence-from-time-series-gene-expression
#17
Chihyun Park, So Jeong Yun, Sung Jin Ryu, Soyoung Lee, Young-Sam Lee, Youngmi Yoon, Sang Chul Park
BACKGROUND: Cellular senescence irreversibly arrests growth of human diploid cells. In addition, recent studies have indicated that senescence is a multi-step evolving process related to important complex biological processes. Most studies analyzed only the genes and their functions representing each senescence phase without considering gene-level interactions and continuously perturbed genes. It is necessary to reveal the genotypic mechanism inferred by affected genes and their interaction underlying the senescence process...
March 15, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28297277/application-programming-in-c-environment-with-recorded-user-software-interactions-and-its-application-in-autopilot-of-vmat-imrt-treatment-planning
#18
Henry Wang, Lei Xing
An autopilot scheme of volumetric-modulated arc therapy (VMAT)/intensity-modulated radiation therapy (IMRT) planning with the guidance of prior knowledge is established with recorded interactions between a planner and a commercial treatment planning system (TPS). Microsoft (MS) Visual Studio Coded UI is applied to record some common planner-TPS interactions as subroutines. The TPS used in this study is a Windows-based Eclipse system. The interactions of our application program with Eclipse TPS are realized through a series of subroutines obtained by prerecording the mouse clicks or keyboard strokes of a planner in operating the TPS...
November 2016: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28292943/molecular-details-underlying-dynamic-structures-and-regulation-of-the-human-26s-proteasome
#19
Xiaorong Wang, Peter Cimermancic, Clinton Yu, Andreas Schweitzer, Nikita Chopra, James L Engel, Charles H Greenberg, Alexander S Huszagh, Florian Beck, Eri Sakata, Yingying Yang, Eric J Novitsky, Alexander Leitner, Paolo Nanni, Abdullah Kahraman, Xing Guo, Jack E Dixon, Scott D Rychnovsky, Ruedi Aebersold, Wolfgang Baumeister, Andrej Sali, Lan Huang
The 26S proteasome is the macromolecular machine responsible for ATP/ubiquitin dependent degradation. As aberration in proteasomal degradation has been implicated in many human diseases, structural analysis of the human 26S proteasome complex is essential to advance our understanding of its action and regulation mechanisms. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for elucidating structural topologies of large protein assemblies, with its unique capability of studying protein complexes in cells...
March 14, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28291699/in-silico-investigation-of-cornea-deformation-during-irrigation-aspiration-in-phacoemulsification-in-cataract-surgery
#20
Dariush Bayatpour, Omid Abouali, Alireza Ghaffarieh, Goodarz Ahmadi
To analyze the stress, strain and displacement of the human cornea under the action of negative intraocular pressure, which occurs during phacoemulsification in cataract surgery, a multidisciplinary approach including biomedical engineering, solid mechanics, numerical analysis, and fluid dynamics was used. Fluid-structure interaction method was implemented using 3-dimensional nonlinear finite element analysis of cornea tissue in conjunction with CFD analysis of anterior chamber fluid flow to study the deformation of the cornea under negative gage pressure during irrigation and aspiration (I/A)...
March 10, 2017: Medical Engineering & Physics
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