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https://www.readbyqxmd.com/read/28073746/mirdis-a-web-tool-for-endogenous-and-exogenous-microrna-discovery-based-on-deep-sequencing-data-analysis
#1
Hanyuan Zhang, Bruno Vieira Resende E Silva, Juan Cui
Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28067221/quantum-chemical-insights-from-deep-tensor-neural-networks
#2
Kristof T Schütt, Farhad Arbabzadah, Stefan Chmiela, Klaus R Müller, Alexandre Tkatchenko
Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol(-1)) predictions in compositional and configurational chemical space for molecules of intermediate size...
January 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28060704/segnet-a-deep-convolutional-encoder-decoder-architecture-for-scene-segmentation
#3
Vijay Badrinarayanan, Alex Kendall, Roberto Cipolla
We present a novel and practical deep fully convolutional neural network architecture for semantic pixel-wise segmentation termed SegNet. This core trainable segmentation engine consists of an encoder network, a corresponding decoder network followed by a pixel-wise classification layer. The architecture of the encoder network is topologically identical to the 13 convolutional layers in the VGG16 network [1]. The role of the decoder network is to map the low resolution encoder feature maps to full input resolution feature maps for pixel-wise classification...
January 2, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28056627/needle-like-instruments-for-steering-through-solid-organs-a-review-of-the-scientific-and-patent-literature
#4
Marta Scali, Tim P Pusch, Paul Breedveld, Dimitra Dodou
High accuracy and precision in reaching target locations inside the human body is necessary for the success of percutaneous procedures, such as tissue sample removal (biopsy), brachytherapy, and localized drug delivery. Flexible steerable needles may allow the surgeon to reach targets deep inside solid organs while avoiding sensitive structures (e.g. blood vessels). This article provides a systematic classification of possible mechanical solutions for three-dimensional steering through solid organs. A scientific and patent literature search of steerable instrument designs was conducted using Scopus and Web of Science Derwent Innovations Index patent database, respectively...
December 1, 2016: Proceedings of the Institution of Mechanical Engineers. Part H, Journal of Engineering in Medicine
https://www.readbyqxmd.com/read/28056090/accurate-de-novo-prediction-of-protein-contact-map-by-ultra-deep-learning-model
#5
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu
MOTIVATION: Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. METHOD: This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks...
January 5, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28049134/mirandb-a-resource-of-online-services-for-mirna-research
#6
Seyed Hamid Aghaee-Bakhtiari, Ehsan Arefian, Pierre Lau
Recent discovery of thousands of small and large noncoding RNAs, in parallel to technical improvements enabling scientists to study the transcriptome in much higher depth, has resulted in massive data generation. This burst of information prompts the development of easily accessible resources for storage, retrieval and analysis of raw and processed data, and hundreds of Web-based tools dedicated to these tasks have been made available. However, the increasing number and diversity of bioinformatics tools, each covering a specific and specialized area, as well as their redundancies, represent potential sources of complication for end users...
January 3, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28046049/health-care-needs-and-support-for-patients-undergoing-treatment-for-prosthetic-joint-infection-following-hip-or-knee-arthroplasty-a-systematic-review
#7
Setor K Kunutsor, Andrew D Beswick, Tim J Peters, Rachael Gooberman-Hill, Michael R Whitehouse, Ashley W Blom, Andrew J Moore
BACKGROUND: Hip and knee arthroplasty are common interventions for the treatment of joint conditions, most notably osteoarthritis. Although many patients benefit from surgery, approximately 1% of patients develop infection afterwards known as deep prosthetic joint infection (PJI), which often requires further major surgery. OBJECTIVE: To assess support needs of patients undergoing treatment for PJI following hip or knee arthroplasty and to identify and evaluate what interventions are routinely offered to support such patients...
2017: PloS One
https://www.readbyqxmd.com/read/28030740/repetitive-transcranial-magnetic-stimulation-for-the-acute-treatment-of-major-depressive-episodes-a-systematic-review-with-network-meta-analysis
#8
Andre R Brunoni, Anna Chaimani, Adriano H Moffa, Lais B Razza, Wagner F Gattaz, Zafiris J Daskalakis, Andre F Carvalho
Importance: Although several strategies of repetitive transcranial magnetic stimulation (rTMS) have been investigated as treatment of major depressive disorder (MDD), their comparative efficacy and acceptability is unknown. Objective: To establish the relative efficacy and acceptability of the different modalities of rTMS used for MDD by performing a network meta-analysis, obtaining a clinically meaningful treatment hierarchy. Data Sources: PubMed/MEDLINE, EMBASE, PsycInfo, and Web of Science were searched up until October 1, 2016...
December 28, 2016: JAMA Psychiatry
https://www.readbyqxmd.com/read/28011771/improving-protein-disorder-prediction-by-deep-bidirectional-long-short-term-memory-recurrent-neural-networks
#9
Jack Hanson, Yuedong Yang, Kuldip Paliwal, Yaoqi Zhou
MOTIVATION: Capturing long-range interactions between structural but not sequence neighbors of proteins is a long-standing challenging problem in bioinformatics. Recently, long short-term memory (LSTM) networks have significantly improved the accuracy of speech and image classification problems by remembering useful past information in long sequential events. Here, we have implemented deep bidirectional LSTM recurrent neural networks in the problem of protein intrinsic disorder prediction...
December 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28007690/deep-brain-stimulation-for-tremor-tractographic-versus-traditional-distinct-study-protocol-of-a-randomized-controlled-feasibility-trial
#10
Bastian Elmar Alexander Sajonz, Florian Amtage, Peter Christoph Reinacher, Carolin Jenkner, Tobias Piroth, Jürgen Kätzler, Horst Urbach, Volker Arnd Coenen
BACKGROUND: Essential tremor is a movement disorder that can result in profound disability affecting the quality of life. Medically refractory essential tremor can be successfully reduced by deep brain stimulation (DBS) traditionally targeting the thalamic ventral intermediate nucleus (Vim). Although this structure can be identified with magnetic resonance (MR) imaging nowadays, Vim-DBS electrodes are still implanted in the awake patient with intraoperative tremor testing to achieve satisfactory tremor control...
December 22, 2016: JMIR Research Protocols
https://www.readbyqxmd.com/read/28002321/is-combined-topical-with-intravenous-tranexamic-acid-superior-than-topical-intravenous-tranexamic-acid-alone-and-control-groups-for-blood-loss-controlling-after-total-knee-arthroplasty-a-meta-analysis
#11
Chunmei Lin, Yingmei Qi, Li Jie, Hong-Biao Li, Xi-Cheng Zhao, Lei Qin, Xin-Qiang Jiang, Zhen-Hua Zhang, Liping Ma
BACKGROUND: The purpose of this systematic review and meta-analysis of randomized controlled trials (RCTs) was to evaluate the efficacy and safety of combined topical with intravenous tranexamic acid (TXA) versus topical, intravenous TXA alone or control for reducing blood loss after a total knee arthroplasty (TKA). METHODS: In May 2016, a systematic computer-based search was conducted in the PubMed, Embase, Cochrane Library, Web of Science, and Chinese Wanfang database...
December 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27995611/disruptive-potential-of-the-internet-to-transform-illicit-drug-markets-and-impact-on-future-patterns-of-drug-consumption
#12
P Griffiths, J Mounteney
The internet facilitates rapid and covert communication, knowledge transfer, and has the potential to disrupt and transform drug market models and associated consumption patterns. Innovation and new trends diffuse rapidly through this medium and new operational models are emerging. Although the online drug markets currently only account for a small share of all drug transactions, the potential of the surface and deep web to provide a new platform for drug sale and exchanges is considerable.
November 7, 2016: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/27992409/in-vivo-high-throughput-profiling-of-crispr-cpf1-activity
#13
Hui K Kim, Myungjae Song, Jinu Lee, A Vipin Menon, Soobin Jung, Young-Mook Kang, Jae W Choi, Euijeon Woo, Hyun C Koh, Jin-Wu Nam, Hyongbum Kim
CRISPR from Prevotella and Francisella 1 (Cpf1) is an effector endonuclease of the class 2 CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) gene editing system. We developed a method for evaluating Cpf1 activity, based on target sequence composition in mammalian cells, in a high-throughput manner. A library of >11,000 target sequence and guide RNA pairs was delivered into human cells using lentiviral vectors. Subsequent delivery of Cpf1 into this cell library induced insertions and deletions (indels) at the integrated synthetic target sequences, which allowed en masse evaluation of Cpf1 activity by using deep sequencing...
December 19, 2016: Nature Methods
https://www.readbyqxmd.com/read/27986266/general-dentists-pediatric-dentists-and-endodontists-diagnostic-assessment-and-treatment-strategies-for-deep-carious-lesions-a-comparative-analysis
#14
Mahshid Majlessi Koopaeei, Marita R Inglehart, Neville McDonald, Margherita Fontana
BACKGROUND: There is a large variation among clinicians when managing deep carious lesions (DCLs). The purpose of this study was to assess general dentists' (GDs), pediatric dentists' (PDs), and endodontists' (EDs) diagnostic methods, clinical decision-making considerations, treatment strategies, and knowledge, behavior, and attitudes related to the diagnosis and treatment of DCLs. METHODS: A total of 175 GDs, 511 PDs, and 377 EDs responded to a nationwide Web-based survey...
December 13, 2016: Journal of the American Dental Association
https://www.readbyqxmd.com/read/27977593/comparing-efficacy-and-safety-of-2-methods-of-tranexamic-acid-administration-in-reducing-blood-loss-following-total-knee-arthroplasty-a-meta-analysis
#15
Yu Fu, Zhigang Shi, Bing Han, Yong Ye, Tao You, Juehua Jing, Jun Li
BACKGROUND: The purpose of this systematic review and meta-analysis of randomized controlled trials (RCTs) were to gather data to evaluate the efficacy and safety of topical tranexamic acid (TXA) versus intravenous (IV) TXA for blood loss after a total knee arthroplasty (TKA). METHODS: Electronic databases: Pubmed, Web of Science, Cochrane library, and Embase from inception to June 2016 were searched. RCTs that comparing topical with IV TXA for blood loss control in patients prepared for TKA were included in this meta-analysis...
December 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27959801/webly-supervised-fine-grained-visual-categorization-via-deep-domain-adaptation
#16
Zhe Xu, Shaoli Huang, Ya Zhang, Dacheng Tao
Learning visual representations from web data has recently attracted attention for object recognition. Previous studies have mainly focused on overcoming label noise and data bias and have shown promising results by learning directly from web data. However, we argue that it might be better to transfer knowledge from existing human labeling resources to improve performance at nearly no additional cost. In this paper, we propose a new semi-supervised method for learning via web data. Our method has the unique design of exploiting strong supervision, i...
December 8, 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/27939268/the-efficiency-and-safety-of-fibrin-sealant-for-reducing-blood-loss-in-primary-total-hip-arthroplasty-a-systematic-review-and-meta-analysis
#17
REVIEW
Zhiyuan Wang, Lin Xiao, Hao Guo, Guanghui Zhao, Jianbing Ma
OBJECTIVE: Total hip arthroplasty (THA) is associated with substantial blood loss. The objective of present systematic review and meta-analysis is to provide evidence from randomized controlled trials (RCTs) on the efficiency and safety of administration of fibrin sealant (FS) for reducing blood loss in patients undergoing primary THA. METHODS: Potential relevant studies were identified from electronic databases including Medline, PubMed, Embase, ScienceDirect, web of science and Cochrane Library...
December 8, 2016: International Journal of Surgery
https://www.readbyqxmd.com/read/27930683/deep-insight-into-the-phosphatomes-of-parasitic-protozoa-and-a-web-resource-protozphosdb
#18
Tamanna Anwar, Samudrala Gourinath
Phosphorylation dynamically regulates the function of proteins by maintaining a balance between protein kinase and phosphatase activity. A comprehensive understanding of the role phosphatases in cellular signaling is lacking in case of protozoans of medical and veterinary importance worldwide. The drugs used to treat protozoal diseases have many undesired effects and the development of resistance, highlights the need for new effective and safer antiprotozoal agents. In the present study we have analyzed phosphatomes of 15 protozoans of medical significance...
2016: PloS One
https://www.readbyqxmd.com/read/27913236/effect-of-different-postoperative-limb-positions-on-blood-loss-and-range-of-motion-in-total-knee-arthroplasty-an-updated-meta-analysis-of-randomized-controlled-trials
#19
REVIEW
Yuangang Wu, Timin Yang, Yi Zeng, Haibo Si, Canfeng Li, Bin Shen
BACKGROUND: Postoperative limb positioning has been reported to be an efficient and simple way to reduce blood loss and improve range of motion following total knee arthroplasty (TKA). This meta-analysis was designed to compare the effectiveness of two different limb positions in primary TKA. MATERIALS AND METHODS: A meta-analysis of the PubMed, CENTRAL, Web of Science, EMBASE and Google Search Engine electronic databases was performed. In this meta-analysis, two postoperative limb positions were considered: mild-flexion (flexion less than 60°) and high-flexion (flexion at 60° or more)...
November 30, 2016: International Journal of Surgery
https://www.readbyqxmd.com/read/27900461/microbial-food-web-drivers-in-tropical-reservoirs
#20
Carolina Davila Domingues, Lucia Helena Sampaio da Silva, Luciana Machado Rangel, Leonardo de Magalhães, Adriana de Melo Rocha, Lúcia Meirelles Lobão, Rafael Paiva, Fábio Roland, Hugo Sarmento
Element cycling in aquatic systems is driven chiefly by planktonic processes, and the structure of the planktonic food web determines the efficiency of carbon transfer through trophic levels. However, few studies have comprehensively evaluated all planktonic food-web components in tropical regions. The aim of this study was to unravel the top-down controls (metazooplankton community structure), bottom-up controls (resource availability), and hydrologic (water residence time) and physical (temperature) variables that affect different components of the microbial food web (MFW) carbon stock in tropical reservoirs, through structural equation models (SEM)...
November 29, 2016: Microbial Ecology
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