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https://www.readbyqxmd.com/read/28642848/mycobacterium-tuberculosis-glyceraldehyde-3-phosphate-dehydrogenase-gapdh-functions-as-a-receptor-for-human-lactoferrin
#1
Himanshu Malhotra, Anil Patidar, Vishant M Boradia, Rajender Kumar, Rakesh D Nimbalkar, Ajay Kumar, Zahid Gani, Rajbeer Kaur, Prabha Garg, Manoj Raje, Chaaya I Raje
Iron is crucial for the survival of living cells, particularly the human pathogen Mycobacterium tuberculosis (M.tb) which uses multiple strategies to acquire and store iron. M.tb synthesizes high affinity iron chelators (siderophores), these extract iron from host iron carrier proteins such as transferrin (Tf) and lactoferrin (Lf). Recent studies have revealed that M.tb may also relocate several housekeeping proteins to the cell surface for capture and internalization of host iron carrier protein transferrin...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28641235/computer-aided-training-sensorimotor-cortex-functions-in-humans-before-the-upper-limb-transplantation-using-virtual-reality-and-sensory-feedback
#2
Marek Kurzynski, Anna Jaskolska, Jaroslaw Marusiak, Andrzej Wolczowski, Przemyslaw Bierut, Lukasz Szumowski, Jerzy Witkowski, Katarzyna Kisiel-Sajewicz
One of the biggest problems of upper limb transplantation is lack of certainty as to whether a patient will be able to control voluntary movements of transplanted hands. Based on findings of the recent research on brain cortex plasticity, a premise can be drawn that mental training supported with visual and sensory feedback can cause structural and functional reorganization of the sensorimotor cortex, which leads to recovery of function associated with the control of movements performed by the upper limbs. In this study, authors - based on the above observations - propose the computer-aided training (CAT) system, which generating visual and sensory stimuli, should enhance the effectiveness of mental training applied to humans before upper limb transplantation...
June 15, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28638896/a-scalable-cyberinfrastructure-for-interactive-visualization-of-terascale-microscopy-data
#3
A Venkat, C Christensen, A Gyulassy, B Summa, F Federer, A Angelucci, V Pascucci
The goal of the recently emerged field of connectomics is to generate a wiring diagram of the brain at different scales. To identify brain circuitry, neuroscientists use specialized microscopes to perform multichannel imaging of labeled neurons at a very high resolution. CLARITY tissue clearing allows imaging labeled circuits through entire tissue blocks, without the need for tissue sectioning and section-to-section alignment. Imaging the large and complex non-human primate brain with sufficient resolution to identify and disambiguate between axons, in particular, produces massive data, creating great computational challenges to the study of neural circuits...
August 2016: N Y Sci Data Summit NYSDS
https://www.readbyqxmd.com/read/28638442/computational-dynamic-approaches-for-temporal-omics-data-with-applications-to-systems-medicine
#4
REVIEW
Yulan Liang, Arpad Kelemen
Modeling and predicting biological dynamic systems and simultaneously estimating the kinetic structural and functional parameters are extremely important in systems and computational biology. This is key for understanding the complexity of the human health, drug response, disease susceptibility and pathogenesis for systems medicine. Temporal omics data used to measure the dynamic biological systems are essentials to discover complex biological interactions and clinical mechanism and causations. However, the delineation of the possible associations and causalities of genes, proteins, metabolites, cells and other biological entities from high throughput time course omics data is challenging for which conventional experimental techniques are not suited in the big omics era...
2017: BioData Mining
https://www.readbyqxmd.com/read/28638333/switching-adaptability-in-human-inspired-sidesteps-a-minimal-model
#5
Keisuke Fujii, Yuki Yoshihara, Hiroko Tanabe, Yuji Yamamoto
Humans can adapt to abruptly changing situations by coordinating redundant components, even in bipedality. Conventional adaptability has been reproduced by various computational approaches, such as optimal control, neural oscillator, and reinforcement learning; however, the adaptability in bipedal locomotion necessary for biological and social activities, such as unpredicted direction change in chase-and-escape, is unknown due to the dynamically unstable multi-link closed-loop system. Here we propose a switching adaptation model for performing bipedal locomotion by improving autonomous distributed control, where autonomous actuators interact without central control and switch the roles for propulsion, balancing, and leg swing...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28633385/timiner-ngs-data-mining-pipeline-for-cancer-immunology-and-immunotherapy
#6
Elias Tappeiner, Francesca Finotello, Pornpimol Charoentong, Clemens Mayer, Dietmar Rieder, Zlatko Trajanoski
Summary: Recently, a number of powerful computational tools for dissecting tumor-immune cell interactions from next-generation sequencing (NGS) data have been developed. However, the assembly of analytical pipelines and execution of multi-step workflows are laborious and involve a large number of intermediate steps with many dependencies and parameter settings. Here we present TIminer, an easy-to-use computational pipeline for mining tumor-immune cell interactions from NGS data. TIminer enables integrative immunogenomic analyses, including: human leukocyte antigens typing, neoantigen prediction, characterization of immune infiltrates, and quantification of tumor immunogenicity...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633280/motifhyades-expectation-maximization-for-de-novo-dna-motif-pair-discovery-on-paired-sequences
#7
Ka-Chun Wong
Motivation: In higher eukaryotes, protein-DNA binding interactions are the central activities in gene regulation. In particular, DNA motifs such as transcription factor binding sites are the key components in gene transcription. Harnessing the recently available chromatin interaction data, computational methods are desired for identifying the coupling DNA motif pairs enriched on long-range chromatin-interacting sequence pairs (e.g. promoter-enhancer pairs) systematically. Results: To fill the void, a novel probabilistic model (namely, MotifHyades) is proposed and developed for de novo DNA motif pair discovery on paired sequences...
June 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28632937/synthesis-biological-evaluation-and-docking-studies-of-trans-stilbene-methylthio-derivatives-as-cytochromes-p450-family-1-inhibitors
#8
Marcin Wierzchowski, Zbigniew Dutkiewicz, Agnieszka Gielara-Korzańska, Artur Korzański, Anna Teubert, Artur Teżyk, Tomasz Stefański, Wanda Baer-Dubowska, Renata Mikstacka
Cytochromes P450 family 1 (CYP1) are responsible for the metabolism of procarcinogens, e.g. polycyclic aromatic hydrocarbons and aromatic and heterocyclic amines. The inhibition of CYP1 activity is examined in terms of chemoprevention and cancer chemotherapy. We designed and synthesized a series of trans-stilbene derivatives possessing a combination of methoxy and methylthio functional groups attached in different positions to the trans-stilbene skeleton. We determined the effects of synthesized compounds on the activities of human recombinant CYP1A1, CYP1A2 and CYP1B1 and, to explain the variation of inhibitory potency of methoxystilbene derivatives and their methylthio analogs, we employed computational analysis...
June 20, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28631297/an-augmented-reality-tool-for-learning-spatial-anatomy-on-mobile-devices
#9
Nishant Jain, Patricia Youngblood, Matthew Hasel, Sakti Srivastava
INTRODUCTION: Augmented Realty (AR) offers a novel method of blending virtual and real anatomy for intuitive spatial learning. Our first aim in the study was to create a prototype AR tool for mobile devices. Our second aim was to complete a technical evaluation of our prototype AR tool focused on measuring the system's ability to accurately render digital content in the real world. MATERIALS AND METHODS: We imported Computed Tomography (CT) data derived virtual surface models into a 3D Unity engine environment and implemented an AR algorithm to display these on mobile devices...
June 20, 2017: Clinical Anatomy
https://www.readbyqxmd.com/read/28629518/analysis-of-the-asymmetry-of-activated-epo-receptor-enables-designing-small-molecule-agonists
#10
Frank Guarnieri
Amgen solved the high-resolution cocrystal structure of erythropoietin (EPO) bound to the extracellular part of the receptor (EPOR) in 1998, which reveals that the EPO-EPOR interaction surface is formed by 11 salt bridges, 17 H-bonds, and 2 hydrophobic clusters centered at a pair of crucial phenylalanines (F93). The EPOR has two domains, one that penetrates the membrane and a second extracellular domain that forms one arm of the binding site for the EPO ligand. The complete competent receptor-binding site is a homodimer of EPOR with the two arms forming a funnel-shaped cup where EPO binds...
2017: Vitamins and Hormones
https://www.readbyqxmd.com/read/28626431/artificial-intelligence-assisted-online-social-therapy-for-youth-mental-health
#11
Simon D'Alfonso, Olga Santesteban-Echarri, Simon Rice, Greg Wadley, Reeva Lederman, Christopher Miles, John Gleeson, Mario Alvarez-Jimenez
Introduction: Benefits from mental health early interventions may not be sustained over time, and longer-term intervention programs may be required to maintain early clinical gains. However, due to the high intensity of face-to-face early intervention treatments, this may not be feasible. Adjunctive internet-based interventions specifically designed for youth may provide a cost-effective and engaging alternative to prevent loss of intervention benefits. However, until now online interventions have relied on human moderators to deliver therapeutic content...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28625475/prediction-of-protein-protein-interactions-by-label-propagation-with-protein-evolutionary-and-chemical-information-derived-from-heterogeneous-network
#12
Yu-Ting Wen, Hai-Jun Lei, Zhu-Hong You, Bai-Ying Lei, Xing Chen, Li-Ping Li
Prediction of protein-protein interactions (PPIs) is of great significance. To achieve this, we propose a novel computational method for PPIs prediction based on a similarity network fusion (SNF) model for integrating the physical and chemical properties of proteins. Specifically, the physical and chemical properties of protein are the protein amino acid mutation rate and its hydrophobicity, respectively. The amino acid mutation rate is extracted using a BLOSUM62 matrix, which puts the protein sequence into block substitution matrix...
June 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28621357/computational-investigation-of-the-human-sod1-mutant-cys146arg-that-directs-familial-amyotrophic-lateral-sclerosis
#13
E Srinivasan, R Rajasekaran
The genetic substitution mutation of Cys146Arg in the SOD1 protein is predominantly found in the Japanese population suffering from familial amyotrophic lateral sclerosis (FALS). A complete study of the biophysical aspects of this particular missense mutation through conformational analysis and producing free energy landscapes could provide an insight into the pathogenic mechanism of ALS disease. In this study, we utilized general molecular dynamics simulations along with computational predictions to assess the structural characterization of the protein as well as the conformational preferences of monomeric wild type and mutant SOD1...
June 16, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28617227/in-silico-re-identification-of-properties-of-drug-target-proteins
#14
Baeksoo Kim, Jihoon Jo, Jonghyun Han, Chungoo Park, Hyunju Lee
BACKGROUND: Computational approaches in the identification of drug targets are expected to reduce time and effort in drug development. Advances in genomics and proteomics provide the opportunity to uncover properties of druggable genomes. Although several studies have been conducted for distinguishing drug targets from non-drug targets, they mainly focus on the sequences and functional roles of proteins. Many other properties of proteins have not been fully investigated. METHODS: Using the DrugBank (version 3...
May 31, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28616862/loops-d-e-and-g-in-the-drosophila-d%C3%AE-1-subunit-contribute-to-high-neonicotinoid-sensitivity-of-d%C3%AE-1-chicken-%C3%AE-2-nicotinic-acetylcholine-receptor
#15
Makoto Ihara, Mai Hikida, Hiroyuki Matsushita, Kyosuke Yamanaka, Yuya Kishimoto, Kazuki Kubo, Shun Watanabe, Mifumi Sakamoto, Koutaro Matsui, Akihiro Yamaguchi, Daiki Okuhara, Shogo Furutani, David B Sattelle, Kazuhiko Matsuda
BACKGROUND AND PURPOSE: Neonicotinoid insecticides interact with the orthosteric site formed at subunit interfaces of insect nicotinic acetylcholine receptors (insect nACh receptors). However, their interactions with the orthosteric sites at α-non α and α-α subunit interfaces remain poorly understood. The aim of this study was to elucidate the mechanism of neonicotinoid actions using the Drosophila Dα1-chicken β2 hybrid nACh receptor. EXPERIMENTAL APPROACH: Computer models of the (Dα1)3 (β2)2 nACh receptor in complex with imidacloprid and thiacloprid were generated...
June 14, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28615927/p-tsa-promoted-syntheses-of-5h-benzo-h-thiazolo-2-3-b-quinazoline-and-indeno-1-2-d-thiazolo-3-2-a-pyrimidine-analogs-molecular-modeling-and-in-vitro-antitumor-activity-against-hepatocellular-carcinoma
#16
Amit K Keshari, Ashok K Singh, Vinit Raj, Amit Rai, Prakruti Trivedi, Balaram Ghosh, Umesh Kumar, Atul Rawat, Dinesh Kumar, Sudipta Saha
In our efforts to address the rising incidence of hepatocellular carcinoma (HCC), we have made a commitment to the synthesis of novel molecules to combat Hep-G2 cells. A facile and highly efficient one-pot, multicomponent reaction has been successfully devised utilizing a p-toluenesulfonic acid (p-TSA)-catalyzed domino Knoevenagel/Michael/intramolecular cyclization approach for the synthesis of novel 5H-benzo[h]thiazolo[2,3-b]quinazoline and indeno[1,2-d] thiazolo[3,2-a]pyrimidine analogs bearing a bridgehead nitrogen atom...
2017: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/28615157/designing-prototyping-and-evaluating-digital-mindfulness-applications-a-case-study-of-mindful-breathing-for-stress-reduction
#17
Bin Zhu, Anders Hedman, Shuo Feng, Haibo Li, Walter Osika
BACKGROUND: During the past decade, there has been a rapid increase of interactive apps designed for health and well-being. Yet, little research has been published on developing frameworks for design and evaluation of digital mindfulness facilitating technologies. Moreover, many existing digital mindfulness applications are purely software based. There is room for further exploration and assessment of designs that make more use of physical qualities of artifacts. OBJECTIVE: The study aimed to develop and test a new physical digital mindfulness prototype designed for stress reduction...
June 14, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28610816/egocentric-distance-perception-and-performance-of-direct-pointing-in-stereoscopic-displays
#18
Chiuhsiang J Lin, Bereket H Woldegiorgis
In this study, the interaction performances and spatial perceptions in stereoscopic environments were investigated. The experiment compared direct user interactions during pointing at a target, which was continuously visible or presented briefly and disappeared, in both stereoscopic and real environments, at three parallax/depth levels. The position data, collected by a motion system, were used to compute accuracy, signed error, movement time, and throughput. The results showed inaccurate egocentric distance judgment in stereoscopic displays and accurate perceptions in the real world...
October 2017: Applied Ergonomics
https://www.readbyqxmd.com/read/28609757/a-molecular-docking-study-of-the-interactions-between-human-transferrin-and-seven-metallocene-dichlorides
#19
Jorge R Güette-Fernández, Enrique Meléndez, Wilson Maldonado-Rojas, Carlos Ortega-Zúñiga, Jesus Olivero-Verbel, Elsie I Parés-Matos
Human Transferrin (hTf) is a metal-binding protein found in blood plasma and is well known for its role in iron delivery. With only a 30% of its capacity for Fe(+3) binding, this protein has the potential ability to transport other metal ions or organometallic compounds from the blood stream to all cell tissues. In this perspective, recent studies have described seven metallocene dichlorides (Cp2M(IV)Cl2, M(IV)=V, Mo, W, Nb, Ti, Zr, Hf) suitable as anticancer drugs and less secondary effects than cisplatin...
May 30, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28608588/experimental-and-computational-characterization-on-the-binding-of-two-fluoroquinolones-to-bovine-hemoglobin
#20
Pengfei Qin, Xingren Pan, Rutao Liu, Jicai Qiu, Xiaoyan Fang
Ciprofloxacin (CPFX) and enrofloxacin (ENFX) are 2 representatives of widely used fluoroquinolones (FQs) with many human and veterinary applications. The residues of FQs in the environment are potentially harmful. Recently, great concern has been paid to their persistence and fate in the environment because of the potential adverse effects on humans and ecosystem functions. In the present study, we examined the interactions of bovine hemoglobin (BHb) with these 2 FQs by means of multiple spectroscopic and molecular docking methods under physiological conditions...
June 13, 2017: Journal of Molecular Recognition: JMR
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