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https://www.readbyqxmd.com/read/29790966/tcrmodel-high-resolution-modeling-of-t-cell-receptors-from-sequence
#1
Ragul Gowthaman, Brian G Pierce
T cell receptors (TCRs), along with antibodies, are responsible for specific antigen recognition in the adaptive immune response, and millions of unique TCRs are estimated to be present in each individual. Understanding the structural basis of TCR targeting has implications in vaccine design, autoimmunity, as well as T cell therapies for cancer. Given advances in deep sequencing leading to immune repertoire-level TCR sequence data, fast and accurate modeling methods are needed to elucidate shared and unique 3D structural features of these molecules which lead to their antigen targeting and cross-reactivity...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790960/complexcontact-a-web-server-for-inter-protein-contact-prediction-using-deep-learning
#2
Hong Zeng, Sheng Wang, Tianming Zhou, Feifeng Zhao, Xiufeng Li, Qing Wu, Jinbo Xu
ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29789087/individual-differences-in-adaptability-to-isolated-confined-and-extreme-environments
#3
Paul T Bartone, Gerald P Krueger, Jocelyn V Bartone
INTRODUCTION: Future deep space missions will expose astronauts to more intense stressors than previously encountered. Isolation will be greater and more prolonged, living and work areas more confined, and communications and resupply channels to Earth longer and less reliable. Astronauts will need to function more autonomously, with less guidance and support from Earth. Thus, it is important to select and train astronauts who can adapt and function effectively under extreme and variable conditions...
June 1, 2018: Aerospace Medicine and Human Performance
https://www.readbyqxmd.com/read/29776185/master-stability-functions-reveal-diffusion-driven-pattern-formation-in-networks
#4
Andreas Brechtel, Philipp Gramlich, Daniel Ritterskamp, Barbara Drossel, Thilo Gross
We study diffusion-driven pattern formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing random walks, while they can be created or destroyed by reactions between or within a layer. We show that the stability of homogeneous steady states can be analyzed with a master stability function approach that reveals a deep analogy between pattern formation in networks and pattern formation in continuous space...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29760112/macronutrient-and-carbon-supply-uptake-and-cycling-across-the-antarctic-peninsula-shelf-during-summer
#5
Sian F Henley, Elizabeth M Jones, Hugh J Venables, Michael P Meredith, Yvonne L Firing, Ribanna Dittrich, Sabrina Heiser, Jacqueline Stefels, Julie Dougans
The West Antarctic Peninsula shelf is a region of high seasonal primary production which supports a large and productive food web, where macronutrients and inorganic carbon are sourced primarily from intrusions of warm saline Circumpolar Deep Water. We examined the cross-shelf modification of this water mass during mid-summer 2015 to understand the supply of nutrients and carbon to the productive surface ocean, and their subsequent uptake and cycling. We show that nitrate, phosphate, silicic acid and inorganic carbon are progressively enriched in subsurface waters across the shelf, contrary to cross-shelf reductions in heat, salinity and density...
June 28, 2018: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29753964/a-web-based-system-for-neural-network-based-classification-in-temporomandibular-joint-osteoarthritis
#6
Priscille de Dumast, Clément Mirabel, Lucia Cevidanes, Antonio Ruellas, Marilia Yatabe, Marcos Ioshida, Nina Tubau Ribera, Loic Michoud, Liliane Gomes, Chao Huang, Hongtu Zhu, Luciana Muniz, Brandon Shoukri, Beatriz Paniagua, Martin Styner, Steve Pieper, Francois Budin, Jean-Baptiste Vimort, Laura Pascal, Juan Carlos Prieto
OBJECTIVE: The purpose of this study is to describe the methodological innovations of a web-based system for storage, integration and computation of biomedical data, using a training imaging dataset to remotely compute a deep neural network classifier of temporomandibular joint osteoarthritis (TMJOA). METHODS: This study imaging dataset consisted of three-dimensional (3D) surface meshes of mandibular condyles constructed from cone beam computed tomography (CBCT) scans...
May 1, 2018: Computerized Medical Imaging and Graphics: the Official Journal of the Computerized Medical Imaging Society
https://www.readbyqxmd.com/read/29741075/-selection-of-isotopic-baselines-in-marine-ecosystems
#7
Yi Gong, Ling Chen, Yun Kai Li
Stable isotope analysis has been widely used in marine food web studies. An appropriate isotopic baseline is essential for calculating diet or trophic position of marine organisms when using stable isotopic data. This paper provided an overview of the selection of isotopic baselines for four ty-pical marine ecosystems, i.e. estuary and bay, neritic zone, oceanic zone, and deep sea. The interferential factors of baseline selection and the significance of compound specific stable isotope in minimizing the effects of temporal-spatial variations of isotopic baseline were summarized, and the issues needed to be solved in this field and several directions for further research were presented...
July 18, 2017: Ying Yong Sheng Tai Xue Bao, the Journal of Applied Ecology
https://www.readbyqxmd.com/read/29727761/systematic-review-and-meta-analyses-of-tranexamic-acid-use-for-bleeding-reduction-in-prostate-surgery
#8
REVIEW
Marcelo A Longo, Bárbara T Cavalheiro, Getúlio R de Oliveira Filho
BACKGROUND: Prostate cancer and benign prostatic hyperplasia have an increased incidence with aging. The most effective treatments are radical prostatectomy and transurethral resection of the prostate. To reduce perioperative bleeding in these surgeries, an approach is the use of tranexamic acid (TXA). Studies show that TXA is effective in reducing the blood loss and the need for transfusion in cardiac, orthopedic, and gynecological surgeries. In prostate surgeries, its efficacy and safety have not been established yet...
May 1, 2018: Journal of Clinical Anesthesia
https://www.readbyqxmd.com/read/29690534/a-system-based-on-the-internet-of-things-for-real-time-particle-monitoring-in-buildings
#9
Gonçalo Marques, Cristina Roque Ferreira, Rui Pitarma
Occupational health can be strongly influenced by the indoor environment as people spend 90% of their time indoors. Although indoor air quality (IAQ) is not typically monitored, IAQ parameters could be in many instances very different from those defined as healthy values. Particulate matter (PM), a complex mixture of solid and liquid particles of organic and inorganic substances suspended in the air, is considered the pollutant that affects more people. The most health-damaging particles are the ≤PM10 (diameter of 10 microns or less), which can penetrate and lodge deep inside the lungs, contributing to the risk of developing cardiovascular and respiratory diseases, as well as of lung cancer...
April 21, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29651054/integrated-design-execution-and-analysis-of-arrayed-and-pooled-crispr-genome-editing-experiments
#10
Matthew C Canver, Maximilian Haeussler, Daniel E Bauer, Stuart H Orkin, Neville E Sanjana, Ophir Shalem, Guo-Cheng Yuan, Feng Zhang, Jean-Paul Concordet, Luca Pinello
CRISPR (clustered regularly interspaced short palindromic repeats) genome-editing experiments offer enormous potential for the evaluation of genomic loci using arrayed single guide RNAs (sgRNAs) or pooled sgRNA libraries. Numerous computational tools are available to help design sgRNAs with optimal on-target efficiency and minimal off-target potential. In addition, computational tools have been developed to analyze deep-sequencing data resulting from genome-editing experiments. However, these tools are typically developed in isolation and oftentimes are not readily translatable into laboratory-based experiments...
May 2018: Nature Protocols
https://www.readbyqxmd.com/read/29625252/the-deep-lymphatic-anatomy-of-the-hand
#11
Chuan-Xiang Ma, Wei-Ren Pan, Zhi-An Liu, Fan-Qiang Zeng, Zhi-Qiang Qiu
BACKGROUND: The deep lymphatic anatomy of the hand still remains the least described in medical literature. METHODS: Eight hands were harvested from four nonembalmed human cadavers amputated above the wrist. A small amount of 6% hydrogen peroxide was employed to detect the lymphatic vessels around the superficial and deep palmar vascular arches, in webs from the index to little fingers, the thenar and hypothenar areas. A 30-gauge needle was inserted into the vessels and injected with a barium sulphate compound...
April 3, 2018: Annals of Anatomy, Anatomischer Anzeiger: Official Organ of the Anatomische Gesellschaft
https://www.readbyqxmd.com/read/29590297/deep-learning-improves-antimicrobial-peptide-recognition
#12
Daniel Veltri, Uday Kamath, Amarda Shehu
Motivation: Bacterial resistance to antibiotics is a growing concern. Antimicrobial peptides (AMPs), natural components of innate immunity, are popular targets for developing new drugs. Machine learning methods are now commonly adopted by wet-laboratory researchers to screen for promising candidates. Results: In this work we utilize deep learning to recognize antimicrobial activity. We propose a neural network model with convolutional and recurrent layers that leverage primary sequence composition...
March 24, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29579268/an-overview-of-the-use-of-bromelain-based-enzymatic-debridement-nexobrid%C3%A2-in-deep-partial-full-thickness-burns-appraising-the-evidence
#13
Yew L Loo, Benjamin K L Goh, S Jeffery
Aim: Recent introduction of rapid bromelain-based enzymatic debridement has been increasingly popular in its use in non-surgical debridement in deep partial and full thickness burns. We designed this study to evaluate the evidence suggested by current studies on the perceived benefits of using Nexobrid® as compared to traditional surgical standard of care (SOC) in burns wound debridement. Method: A comprehensive search on electronic databases Pubmed, Embase and Web of Science was done to identify studies published between 1986 to 2017 involving the use of Nexobrid in deep partial and full thickness burns...
March 22, 2018: Journal of Burn Care & Research: Official Publication of the American Burn Association
https://www.readbyqxmd.com/read/29570741/time-and-depth-wise-trophic-niche-shifts-in-antarctic-benthos
#14
Edoardo Calizza, Giulio Careddu, Simona Sporta Caputi, Loreto Rossi, Maria Letizia Costantini
Climate change is expected to affect resource-consumer interactions underlying stability in polar food webs. Polar benthic organisms have adapted to the marked seasonality characterising their habitats by concentrating foraging and reproductive activity in summer months, when inputs from sympagic and pelagic producers increase. While this enables the persistence of biodiverse food webs, the mechanisms underlying changes in resource use and nutrient transfer are poorly understood. Thus, our understanding of how temporal and spatial variations in the supply of resources may affect food web structure and functioning is limited...
2018: PloS One
https://www.readbyqxmd.com/read/29564707/zinc-in-an-ultraoligotrophic-lake-food-web
#15
Juan Cruz Montañez, María A Arribére, Andrea Rizzo, Marina Arcagni, Linda Campbell, Sergio Ribeiro Guevara
Zinc (Zn) bioaccumulation and trophic transfer were analyzed in the food web of Lake Nahuel Huapi, a deep, unpolluted ultraoligotrophic system in North Patagonia. Benthic macroinvertebrates, plankton, and native and introduced fish were collected at three sites. The effect of pyroclastic inputs on Zn levels in lacustrine food webs was assessed by studying the impact of the eruption of Puyehue-Cordón Caulle volcanic complex (PCCVC) in 2011, by performing three sampling campaigns immediately before and after the PCCVC eruption, and after 2 years of recovery of the ecosystem...
March 21, 2018: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29558847/variations-in-the-origins-and-absence-of-the-common-digital-arteries-of-the-hand-a-cadaveric-study
#16
Ahmed M Hashem, Rebecca W Knackstedt, Steven Bernard, Mark Hendrickson, Jennifer M McBride, Risal Djohan
We studied anomalies of the common digital arteries by dissecting 33 fresh cadaver hands under magnification. In the majority of the dissected hands (25 hands), common digital arteries took off from the superficial palmar arch and ran superficial and parallel to the flexor tendons. Variations were found in eight out of 33 hands. In four hands the common digital artery to the second web space was replaced by an atypical vessel, originating from the deep palmar arch, that crossed posterior to the index flexor tendons proximal to the A1 pulley...
January 1, 2018: Journal of Hand Surgery, European Volume
https://www.readbyqxmd.com/read/29548962/the-50-most-cited-articles-in-invasive-neuromodulation
#17
Max Ward, Joseph Doran, Boris Paskhover, Antonios Mammis
OBJECTIVE: Bibliometric analysis is a commonly used analytic tool for objective determination of the most influential and peer-recognized articles within a given field. This study is the first bibliometric analysis of the literature in the field of invasive neuromodulation, excluding deep brain stimulation. The objectives of this study are to identify the 50 most cited articles in invasive neuromodulation, provide an overview of the literature to assist in clinical education, and evaluate the effect of impact factor on manuscript recognition...
March 14, 2018: World Neurosurgery
https://www.readbyqxmd.com/read/29538399/generalising-better-applying-deep-learning-to-integrate-deleteriousness-prediction-scores-for-whole-exome-snv-studies
#18
Ilia Korvigo, Andrey Afanasyev, Nikolay Romashchenko, Mikhail Skoblov
Many automatic classifiers were introduced to aid inference of phenotypical effects of uncategorised nsSNVs (nonsynonymous Single Nucleotide Variations) in theoretical and medical applications. Lately, several meta-estimators have been proposed that combine different predictors, such as PolyPhen and SIFT, to integrate more information in a single score. Although many advances have been made in feature design and machine learning algorithms used, the shortage of high-quality reference data along with the bias towards intensively studied in vitro models call for improved generalisation ability in order to further increase classification accuracy and handle records with insufficient data...
2018: PloS One
https://www.readbyqxmd.com/read/29531367/coccolithovirus-facilitation-of-carbon-export-in-the-north-atlantic
#19
Christien P Laber, Jonathan E Hunter, Filipa Carvalho, James R Collins, Elias J Hunter, Brittany M Schieler, Emmanuel Boss, Kuldeep More, Miguel Frada, Kimberlee Thamatrakoln, Christopher M Brown, Liti Haramaty, Justin Ossolinski, Helen Fredricks, Jozef I Nissimov, Rebecca Vandzura, Uri Sheyn, Yoav Lehahn, Robert J Chant, Ana M Martins, Marco J L Coolen, Assaf Vardi, Giacomo R DiTullio, Benjamin A S Van Mooy, Kay D Bidle
Marine phytoplankton account for approximately half of global primary productivity 1 , making their fate an important driver of the marine carbon cycle. Viruses are thought to recycle more than one-quarter of oceanic photosynthetically fixed organic carbon 2 , which can stimulate nutrient regeneration, primary production and upper ocean respiration 2 via lytic infection and the 'virus shunt'. Ultimately, this limits the trophic transfer of carbon and energy to both higher food webs and the deep ocean 2 . Using imagery taken by the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard the Aqua satellite, along with a suite of diagnostic lipid- and gene-based molecular biomarkers, in situ optical sensors and sediment traps, we show that Coccolithovirus infections of mesoscale (~100 km) Emiliania huxleyi blooms in the North Atlantic are coupled with particle aggregation, high zooplankton grazing and greater downward vertical fluxes of both particulate organic and particulate inorganic carbon from the upper mixed layer...
May 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29530780/ajo-centennial-ajo-contributions-to-ophthalmic-genetics
#20
Ian M MacDonald, Pamela C Sieving
PURPOSE: To review the contributions to ophthalmic genetics through the American Journal of Ophthalmology (AJO). DESIGN: Perspective. METHODS: A literature search to retrieve original articles, letters, editorials, and published lectures from 1966 to 2017, providing a 50-year review. Titles were excluded that gave no reference to genetics or that presented findings related to a nongenetic ocular condition. RESULTS: From a search of the Scopus database, 719 articles were ascertained...
March 9, 2018: American Journal of Ophthalmology
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