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https://www.readbyqxmd.com/read/28092029/an-efficient-semi-supervised-learning-approach-to-predict-sh2-domain-mediated-interactions
#1
Kousik Kundu, Rolf Backofen
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to facilitate various molecular functions. For determining the subtle binding specificities of SH2 domains, it is very important to understand the intriguing mechanisms by which these domains recognize their target peptides in a complex cellular environment. There are several attempts have been made to predict SH2-peptide interactions using high-throughput data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28087697/development-of-high-affinity-and-high-specificity-inhibitors-of-metalloproteinase-14-through-computational-design-and-directed-evolution
#2
Valeria Arkadash, Gal Yosef, Jason Shirian, Itay Cohen, Yuval Horev, Moran Grossman, Irit Sagi, Evette S Radisky, Julia M Shifman, Niv Papo
Degradation of the extracellular matrices in the human body is controlled by matrix metalloproteinases (MMPs), a family of more than 20 homologous enzymes. Imbalance in MMP activity can result in many diseases, such as arthritis, cardiovascular diseases, neurological disorders, fibrosis, and cancers. Thus, MMPs present attractive targets for drug design and have been a focus for inhibitor design for as long as three decades. Yet, to date, all MMP inhibitors have failed in clinical trials because of their broad activity against numerous MMP family members and the serious side effects of the proposed treatment...
January 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28087242/brains-for-birds-and-babies-neural-parallels-between-birdsong-and-speech-acquisition
#3
REVIEW
Jonathan Prather, Kazuo Okanoya, Johan J Bolhuis
Language as a computational cognitive mechanism appears to be unique to the human species. However, there are remarkable behavioral similarities between song learning in songbirds and speech acquisition in human infants that are absent in non-human primates. Here we review important neural parallels between birdsong and speech. In both cases there are separate but continually interacting neural networks that underlie vocal production, sensorimotor learning, and auditory perception and memory. As in the case of human speech, neural activity related to birdsong learning is lateralized, and mirror neurons linking perception and performance may contribute to sensorimotor learning...
January 10, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28081260/comparative-genome-sequencing-reveals-within-host-genetic-changes-in-neisseria-meningitidis-during-invasive-disease
#4
Johanna Klughammer, Marcus Dittrich, Jochen Blom, Vera Mitesser, Ulrich Vogel, Matthias Frosch, Alexander Goesmann, Tobias Müller, Christoph Schoen
Some members of the physiological human microbiome occasionally cause life-threatening disease even in immunocompetent individuals. A prime example of such a commensal pathogen is Neisseria meningitidis, which normally resides in the human nasopharynx but is also a leading cause of sepsis and epidemic meningitis. Using N. meningitidis as model organism, we tested the hypothesis that virulence of commensal pathogens is a consequence of within host evolution and selection of invasive variants due to mutations at contingency genes, a mechanism called phase variation...
2017: PloS One
https://www.readbyqxmd.com/read/28079528/assessing-the-evolution-of-redundancy-synergy-of-spontaneous-variability-regulation-with-age
#5
Alberto Porta, Vlasta Bari, Beatrice De Maria, Natália Maria Perseguini, Juliana Milan, Patricia Rehder-Santos, Vinícius Minatel, Anielle Takahashi, Aparecida Catai
We exploited a model-based Wiener-Granger causality method in the information domain for the evaluation of the transfer entropy (TE) and interaction TE (ITE), the latter taken as a measure of the net balance between redundancy and synergy, to describe the interactions between the spontaneous variability of heart period (HP) and systolic arterial pressure (SAP) and the effect of respiration (R) on both variables. Cardiac control was typified via the genuine TE from SAP to HP, that from R to HP, and the ITE from SAP and R to HP, while vascular control was characterized via the genuine TE from HP to SAP, that from R to SAP, and the ITE from HP and R to SAP...
January 12, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28079249/fractal-analysis-of-visual-search-activity-for-mass-detection-during-mammographic-screening
#6
Folami Alamudun, Hong-Jun Yoon, Kathleen B Hudson, Garnetta Morin-Ducote, Tracy Hammond, Georgia D Tourassi
PURPOSE: The objective of this study is to assess the complexity of human visual search activity during mammographic screening using fractal analysis and to investigate its relationship with case and reader characteristics. METHODS: The study was performed for the task of mammographic screening with simultaneous viewing of four coordinated breast views as typically done in clinical practice. Eye-tracking data and diagnostic decisions collected for 100 mammographic cases (25 normal, 25 benign, 50 malignant) and 10 readers (three board certified radiologists and seven radiology residents), formed the corpus data for this study...
January 12, 2017: Medical Physics
https://www.readbyqxmd.com/read/28077563/the-bioc-biogrid-corpus-full-text-articles-annotated-for-curation-of-protein-protein-and-genetic-interactions
#7
Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-Aryamontri, Christie S Chang, Rose Oughtred, Jennifer Rust, W John Wilbur, Donald C Comeau, Kara Dolinski, Mike Tyers
A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data. This data is provided in a standardized computationally tractable format and includes structured annotation of experimental evidence. BioGRID curation necessarily involves substantial human effort by expert curators who must read each publication to extract the relevant information...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28076954/identification-of-genes-associated-with-breast-cancer-metastasis-to-bone-on-a-protein-protein-interaction-network-with-a-shortest-path-algorithm
#8
Yu-Dong Cai, Qing Zhang, Yu-Hang Zhang, Lei Chen, Tao Huang
Tumor metastasis is defined as the spread of tumor cells from one organ or part to another that is not directly connected to it, which significantly contributes to the progression and aggravation of tumorigenesis. Because it always involves multiple organs, the metastatic process is difficult to study in its entirety. Complete identification of the genes related to this process is an alternative way to study metastasis. In this study, we developed a computational method to identify such genes. To test our method, we selected breast cancer bone metastasis...
January 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28076446/downscaling-global-emissions-and-its-implications-derived-from-climate-model-experiments
#9
Shinichiro Fujimori, Manabu Abe, Tsuguki Kinoshita, Tomoko Hasegawa, Hiroaki Kawase, Kazuhide Kushida, Toshihiko Masui, Kazutaka Oka, Hideo Shiogama, Kiyoshi Takahashi, Hiroaki Tatebe, Minoru Yoshikawa
In climate change research, future scenarios of greenhouse gas and air pollutant emissions generated by integrated assessment models (IAMs) are used in climate models (CMs) and earth system models to analyze future interactions and feedback between human activities and climate. However, the spatial resolutions of IAMs and CMs differ. IAMs usually disaggregate the world into 10-30 aggregated regions, whereas CMs require a grid-based spatial resolution. Therefore, downscaling emissions data from IAMs into a finer scale is necessary to input the emissions into CMs...
2017: PloS One
https://www.readbyqxmd.com/read/28068295/support-vector-machines-to-detect-physiological-patterns-for-eeg-and-emg-based-human-computer-interaction-a-review
#10
L R Quitadamo, F Cavrini, L Sbernini, F Riillo, L Bianchi, S Seri, G Saggio
Support vector machines (SVMs) are widely used classifiers for detecting physiological patterns in human-computer interaction (HCI). Their success is due to their versatility, robustness and large availability of free dedicated toolboxes. Frequently in the literature, insufficient details about the SVM implementation and/or parameters selection are reported, making it impossible to reproduce study analysis and results. In order to perform an optimized classification and report a proper description of the results, it is necessary to have a comprehensive critical overview of the applications of SVM...
January 9, 2017: Journal of Neural Engineering
https://www.readbyqxmd.com/read/28068146/a-natural-language-based-presentation-of-cognitive-stimulation-to-people-with-dementia-in-assistive-technology-a-pilot-study
#11
Nina Dethlefs, Maarten Milders, Heriberto Cuayáhuitl, Turkey Al-Salkini, Lorraine Douglas
Currently, an estimated 36 million people worldwide are affected by Alzheimer's disease or related dementias. In the absence of a cure, non-pharmacological interventions, such as cognitive stimulation, which slow down the rate of deterioration can benefit people with dementia and their caregivers. Such interventions have shown to improve well-being and slow down the rate of cognitive decline. It has further been shown that cognitive stimulation in interaction with a computer is as effective as with a human...
January 9, 2017: Informatics for Health & Social Care
https://www.readbyqxmd.com/read/28067801/easy-handling-of-sensors-and-actuators-over-tcp-ip-networks-by-open-source-hardware-software
#12
Andrés Mejías, Reyes S Herrera, Marco A Márquez, Antonio José Calderón, Isaías González, José Manuel Andújar
There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented...
January 5, 2017: Sensors
https://www.readbyqxmd.com/read/28065846/the-association-of-heart-failure-related-micrornas-with-neurohormonal-signaling
#13
Yei-Tsung Chen, Juan Wang, Kai Sing Tong, Lee Lee Wong, Oi Wah Liew, Arthur Mark Richards
Heart failure (HF) is a widely prevalent syndrome imposing a significant burden of morbidity and mortality world-wide. Differential circulating microRNA profiles observed in HF cohorts suggest the diagnostic utility of microRNAs as biomarkers. Given their function in fine tuning gene expression, alternations in microRNA landscape could reflecting the underlying mechanisms of disease and present potential therapeutic targets. Using multiple computational target predicting algorithms together with the luciferase-based reporting platform, the interactions between HF-related microRNAs and the 3' untranslated regions (3'UTRs) of neurohormone associated genes were examined and compared...
January 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28062203/semi-mechanistic-computer-simulation-of-psychotic-symptoms-in-schizophrenia-with-a-model-of-a-humanized-cortico-striatal-thalamocortical-loop
#14
Athan Spiros, Patrick Roberts, Hugo Geerts
Despite new insights into the pathophysiology of schizophrenia and clinical trials with highly selective drugs, no new therapeutic breakthroughs have been identified. We present a semi-mechanistic Quantitative Systems Pharmacology (QSP) computer model of a biophysically realistic cortical-striatal-thalamo-cortical loop. The model incorporates the direct, indirect and hyperdirect pathway of the basal ganglia and CNS drug targets that modulate neuronal firing, based on preclinical data about their localization and coupling to voltage-gated ion channels...
January 3, 2017: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28061806/modular-combinatorial-binding-among-human-trans-acting-factors-reveals-direct-and-indirect-factor-binding
#15
Yuchun Guo, David K Gifford
BACKGROUND: The combinatorial binding of trans-acting factors (TFs) to the DNA is critical to the spatial and temporal specificity of gene regulation. For certain regulatory regions, more than one regulatory module (set of TFs that bind together) are combined to achieve context-specific gene regulation. However, previous approaches are limited to either pairwise TF co-association analysis or assuming that only one module is used in each regulatory region. RESULTS: We present a new computational approach that models the modular organization of TF combinatorial binding...
January 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28060906/steady-state-motion-visual-evoked-potential-ssmvep-based-on-equal-luminance-colored-enhancement
#16
Wenqiang Yan, Guanghua Xu, Min Li, Jun Xie, Chengcheng Han, Sicong Zhang, Ailing Luo, Chaoyang Chen
Steady-state visual evoked potential (SSVEP) is one of the typical stimulation paradigms of brain-computer interface (BCI). It has become a research approach to improve the performance of human-computer interaction, because of its advantages including multiple objectives, less recording electrodes for electroencephalogram (EEG) signals, and strong anti-interference capacity. Traditional SSVEP using light flicker stimulation may cause visual fatigue with a consequent reduction of recognition accuracy. To avoid the negative impacts on the brain response caused by prolonged strong visual stimulation for SSVEP, steady-state motion visual evoked potential (SSMVEP) stimulation method was used in this study by an equal-luminance colored ring-shaped checkerboard paradigm...
2017: PloS One
https://www.readbyqxmd.com/read/28059145/a-markov-state-based-quantitative-kinetic-model-of-sodium-release-from-the-dopamine-transporter
#17
Asghar M Razavi, George Khelashvili, Harel Weinstein
The dopamine transporter (DAT) belongs to the neurotransmitter:sodium symporter (NSS) family of membrane proteins that are responsible for reuptake of neurotransmitters from the synaptic cleft to terminate a neuronal signal and enable subsequent neurotransmitter release from the presynaptic neuron. The release of one sodium ion from the crystallographically determined sodium binding site Na2 had been identified as an initial step in the transport cycle which prepares the transporter for substrate translocation by stabilizing an inward-open conformation...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28059045/computational-screening-of-ccr5-inhibitors-as-potential-entry-inhibitor-microbicides-using-3d-qsar-studies-docking-and-molecular-dynamics-simulation
#18
Radhika Ramachandran, Muthusankar Aathi, D Durairaj Ruban, Shanmughavel Piramanyagam
BACKGROUND: The chemokine receptor CCR5 acts as a co-receptor for HIV binding and it is considered as an important target by CCR5 antagonists. Entry inhibitor based microbicides gain much importance nowadays as these drugs act at an early stage of HIV lifecycle and thus hinder the viral replication process in humans. The present study intends to identify a CCR5 antagonist which could be developed as a microbicide using computational approaches. METHOD: The pharmacophore modeling and 3D QSAR studies was used to identify CCR5 antagonists with enhanced antagonist activity...
January 6, 2017: Current HIV Research
https://www.readbyqxmd.com/read/28057571/acyl-chain-preference-and-inhibitor-identification-of-moraxella-catarrhalis-lpxa-insight-through-crystal-structure-and-computational-studies
#19
Shivendra Pratap, Pooja Kesari, Ravi Yadav, Aditya Dev, Manju Narwal, Pravindra Kumar
Lipopolysaccharide (LPS) is an important surface component and a potential virulence factor in the pathogenesis of Gram-negative bacteria. UDP-N-acetylglucosamine acyltransferase (LpxA) enzyme catalyzes the first reaction of LPS biosynthesis, reversible transfer of R-3-hydroxy-acyl moiety from donor R-3-hydroxy-acyl-acyl carrier protein to the 3' hydroxyl position of UDP-N-acetyl-glucosamine. LpxA enzyme's essentiality in bacterial survival and absence of any homologous protein in humans makes it a promising target for anti-bacterial drug development...
January 3, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28046412/we-ab-209-12-quasi-constrained-multi-criteria-optimization-for-automated-radiation-therapy-treatment-planning
#20
W T Watkins, J V Siebers
PURPOSE: To introduce quasi-constrained Multi-Criteria Optimization (qcMCO) for unsupervised radiation therapy optimization which generates alternative patient-specific plans emphasizing dosimetric tradeoffs and conformance to clinical constraints for multiple delivery techniques. METHODS: For N Organs At Risk (OARs) and M delivery techniques, qcMCO generates M(N+1) alternative treatment plans per patient. Objective weight variations for OARs and targets are used to generate alternative qcMCO plans...
June 2016: Medical Physics
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