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https://www.readbyqxmd.com/read/29151135/classification-of-g-protein-coupled-receptors-based-on-a-rich-generation-of-convolutional-neural-network-n-gram-transformation-and-multiple-sequence-alignments
#1
Man Li, Cheng Ling, Qi Xu, Jingyang Gao
Sequence classification is crucial in predicting the function of newly discovered sequences. In recent years, the prediction of the incremental large-scale and diversity of sequences has heavily relied on the involvement of machine-learning algorithms. To improve prediction accuracy, these algorithms must confront the key challenge of extracting valuable features. In this work, we propose a feature-enhanced protein classification approach, considering the rich generation of multiple sequence alignment algorithms, N-gram probabilistic language model and the deep learning technique...
November 18, 2017: Amino Acids
https://www.readbyqxmd.com/read/29150140/visual-pathways-from-the-perspective-of-cost-functions-and-multi-task-deep-neural-networks
#2
REVIEW
H Steven Scholte, Max M Losch, Kandan Ramakrishnan, Edward H F de Haan, Sander M Bohte
Vision research has been shaped by the seminal insight that we can understand the higher-tier visual cortex from the perspective of multiple functional pathways with different goals. In this paper, we try to give a computational account of the functional organization of this system by reasoning from the perspective of multi-task deep neural networks. Machine learning has shown that tasks become easier to solve when they are decomposed into subtasks with their own cost function. We hypothesize that the visual system optimizes multiple cost functions of unrelated tasks and this causes the emergence of a ventral pathway dedicated to vision for perception, and a dorsal pathway dedicated to vision for action...
October 7, 2017: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/29149772/natural-history-of-infantile-onset-spinal-muscular-atrophy
#3
Stephen J Kolb, Christopher S Coffey, Jon W Yankey, Kristin Krosschell, W David Arnold, Seward B Rutkove, Kathryn J Swoboda, Sandra P Reyna, Ai Sakonju, Basil T Darras, Richard Shell, Nancy Kuntz, Diana Castro, Julie Parsons, Anne M Connolly, Claudia A Chiriboga, Craig McDonald, W Bryan Burnette, Klaus Werner, Mathula Thangarajh, Perry B Shieh, Erika Finanger, Merit E Cudkowicz, Michelle M McGovern, D Elizabeth McNeil, Richard Finkel, Susan T Iannaccone, Edward Kaye, Allison Kingsley, Samantha R Renusch, Vicki L McGovern, Xueqian Wang, Phillip G Zaworski, Thomas W Prior, Arthur H M Burghes, Amy Bartlett, John T Kissel
OBJECTIVE: Infantile-onset spinal muscular atrophy (SMA) is the most common genetic cause of infant mortality, typically resulting in death prior to age 2. Clinical trials in this population require an understanding of disease progression and identification of meaningful biomarkers to hasten therapeutic development and predict outcomes. METHODS: A longitudinal, multi-center, prospective natural history study enrolled 26 SMA infants, and 27 control infants less than six months of age...
November 17, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/29149660/a-systems-level-approach-for-investigating-organophosphorus-pesticide-toxicity
#4
Jingbo Zhu, Jing Wang, Yan Ding, Baoyue Liu, Wei Xiao
The full understanding of the single and joint toxicity of a variety of organophosphorus (OP) pesticides is still unavailable, because of the extreme complex mechanism of action. This study established a systems-level approach based on systems toxicology to investigate OP pesticide toxicity by incorporating ADME/T properties, protein prediction, and network and pathway analysis. The results showed that most OP pesticides are highly toxic according to the ADME/T parameters, and can interact with significant receptor proteins to cooperatively lead to various diseases by the established OP pesticide -protein and protein-disease networks...
November 14, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29146995/gaba-concentrations-in-the-anterior-temporal-lobe-predict-human-semantic-processing
#5
JeYoung Jung, Stephen R Williams, Faezeh Sanaei Nezhad, Matthew A Lambon Ralph
There is now considerable convergent evidence from multiple methodologies and clinical studies that the human anterior temporal lobe (ATL) is a semantic representational hub. However, the neurochemical nature of the ATL in the semantic processing remains unclear. The current study investigated the neurochemical mechanism underlying semantic processing in the ATL. We combined functional magnetic resonance imaging (fMRI) with resting-state magnetic resonance spectroscopy (MRS) to measure task-related blood-oxygen level-dependent (BOLD) signal changes during sematic processing and resting-state GABA concentrations in the ATL...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29145121/role-of-acid-alkali-treatment-in-primary-sludge-anaerobic-fermentation-insights-into-microbial-community-structure-functional-shifts-and-metabolic-output-by-high-throughput-sequencing
#6
Xiao Huang, Wenyi Dong, Hongjie Wang, Yangyang Feng
This study aimed to investigate the effect of acid- or alkali-treatment on volatile fatty acids (VFAs) production and microbiological mechanism during primary sludge anaerobic fermentation. Seven fermentation experiments were conducted at different pH (3-12). Results showed that the optimal pH was 10 for accumulation of VFAs. High-throughput sequencing results indicated that acid and alkali treatment could inhibit Erysipelotrichaceae_UCG-004 and norank_p_Aminicenantes, instead of promoting Pseudomonas and Tissierella at acidic and alkaline condition, respectively...
November 4, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29145093/proteomic-profile-and-toxicity-pathway-analysis-in-zebrafish-embryos-exposed-to-bisphenol-a-and-di-n-butyl-phthalate-at-environmentally-relevant-levels
#7
Xing Dong, Xuchun Qiu, Shunlong Meng, Hai Xu, Xiangyang Wu, Ming Yang
Bisphenol A (BPA) and di-n-butyl phthalate (DBP) are well-known endocrine-disrupting chemicals (EDCs) that have human health risks. Chronic exposure to BPA and DBP increases the occurrence of human disease. Despite the potential for exposure in embryonic development, the mechanism of action of BPA and DBP on vertebrate development and disease still remains unclear. In the present study, we identified proteins and protein networks that are perturbed by BPA and DBP during zebrafish (Danio rerio) development. Zebrafish embryos were exposed to environmentally relevant levels of BPA (10 μg/L) and DBP (50 μg/L) for 96 h...
November 10, 2017: Chemosphere
https://www.readbyqxmd.com/read/29144390/rna-sequencing-and-coexpression-analysis-reveal-key-genes-involved-in-%C3%AE-linolenic-acid-biosynthesis-in-perilla-frutescens-seed
#8
Tianyuan Zhang, Chi Song, Li Song, Zhiwei Shang, Sen Yang, Dong Zhang, Wei Sun, Qi Shen, Degang Zhao
Perillafrutescen is used as traditional food and medicine in East Asia. Its seeds contain high levels of α-linolenic acid (ALA), which is important for health, but is scarce in our daily meals. Previous reports on RNA-seq of perilla seed had identified fatty acid (FA) and triacylglycerol (TAG) synthesis genes, but the underlying mechanism of ALA biosynthesis and its regulation still need to be further explored. So we conducted Illumina RNA-sequencing in seven temporal developmental stages of perilla seeds...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29144299/the-modelling-of-lead-removal-from-water-by-deep-eutectic-solvents-functionalized-cnts-artificial-neural-network-ann-approach
#9
Seef Saadi Fiyadh, Mohammed Abdulhakim AlSaadi, Mohamed Khalid AlOmar, Sabah Saadi Fayaed, Ako R Hama, Sharifah Bee, Ahmed El-Shafie
The main challenge in the lead removal simulation is the behaviour of non-linearity relationships between the process parameters. The conventional modelling technique usually deals with this problem by a linear method. The substitute modelling technique is an artificial neural network (ANN) system, and it is selected to reflect the non-linearity in the interaction among the variables in the function. Herein, synthesized deep eutectic solvents were used as a functionalized agent with carbon nanotubes as adsorbents of Pb(2+)...
November 2017: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/29143946/multi-scale-account-of-the-network-structure-of-macaque-visual-cortex
#10
Maximilian Schmidt, Rembrandt Bakker, Claus C Hilgetag, Markus Diesmann, Sacha J van Albada
Cortical network structure has been extensively characterized at the level of local circuits and in terms of long-range connectivity, but seldom in a manner that integrates both of these scales. Furthermore, while the connectivity of cortex is known to be related to its architecture, this knowledge has not been used to derive a comprehensive cortical connectivity map. In this study, we integrate data on cortical architecture and axonal tracing data into a consistent multi-scale framework of the structure of one hemisphere of macaque vision-related cortex...
November 16, 2017: Brain Structure & Function
https://www.readbyqxmd.com/read/29143409/chronnectome-fingerprinting-identifying-individuals-and-predicting-higher-cognitive-functions-using-dynamic-brain-connectivity-patterns
#11
Jin Liu, Xuhong Liao, Mingrui Xia, Yong He
The human brain is a large, interacting dynamic network, and its architecture of coupling among brain regions varies across time (termed the "chronnectome"). However, very little is known about whether and how the dynamic properties of the chronnectome can characterize individual uniqueness, such as identifying individuals as a "fingerprint" of the brain. Here, we employed multiband resting-state functional magnetic resonance imaging data from the Human Connectome Project (N = 105) and a sliding time-window dynamic network analysis approach to systematically examine individual time-varying properties of the chronnectome...
November 15, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/29143332/accurate-prediction-and-elucidation-of-drug-resistance-based-on-the-robust-and-reproducible-chemoresponse-communities
#12
Enyu Dai, Jing Wang, Feng Yang, Xu Zhou, Qian Song, Shuyuan Wang, Xuexin Yu, Dianming Liu, Qian Yang, Hong Dai, Wei Jiang, Hong Ling
Selecting the available treatment for each cancer patient from genomic context is a core goal of precision medicine, but innovative approaches with mechanism interpretation and improved performance are still highly needed. Through utilizing in vitro chemotherapy response data coupled with gene and miRNA expression profiles, we applied a network-based approach that identified markers not as individual molecules but as functional groups extracted from the integrated transcription factor and miRNA regulatory network...
November 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29143172/identification-of-key-genes-and-construction-of-microrna-mrna-regulatory-networks-in-bladder-smooth-muscle-cell-response-to-mechanical-stimuli-using-microarray-expression-profiles-and-bioinformatics-analysis
#13
Liao Peng, De-Yi Luo
PURPOSE: To identify keys genes and elucidate miRNA-mRNA regulatory networks in Bladder smooth muscle cell (BSMC) response to mechanical stimuli. METHODS: Human BSMCs, seeded on a silicone membrane, were subjected to mechanical stretch or without stretch. Microarray was used to analyze the differential expression of mRNAs and miRNAs between human BSMCs under mechanical stretch and control static control group. Differentially expressed genes(DEGs) and miRNAs (DEMs) in these two groups were identified...
November 15, 2017: World Journal of Urology
https://www.readbyqxmd.com/read/29140500/the-persuasion-network-is-modulated-by-drug-use-risk-and-predicts-anti-drug-message-effectiveness
#14
Richard Huskey, J Michael Mangus, Benjamin O Turner, René Weber
While a persuasion network has been proposed, little is known about how network connections between brain regions contribute to attitude change. Two possible mechanisms have been advanced. One hypothesis predicts that attitude change results from increased connectivity between structures implicated in affective and executive processing in response to increases in argument strength. A second functional perspective suggests that highly arousing messages reduce connectivity between structures implicated in the encoding of sensory information, which disrupts message processing and thereby inhibits attitude change...
November 11, 2017: Social Cognitive and Affective Neuroscience
https://www.readbyqxmd.com/read/29140274/an-efficient-approach-for-lipase-catalyzed-synthesis-of-retinyl-laurate-nutraceutical-by-combining-ultrasound-assistance-and-artificial-neural-network-optimization
#15
Shang-Ming Huang, Hsin-Ju Li, Yung-Chuan Liu, Chia-Hung Kuo, Chwen-Jen Shieh
Although retinol is an important nutrient, retinol is highly sensitive to oxidation. At present, some ester forms of retinol are generally used in nutritional supplements because of its stability and bioavailability. However, such esters are commonly synthesized by chemical procedures which are harmful to the environment. Thus, this study utilized a green method using lipase as a catalyst with sonication assistance to produce a retinol derivative named retinyl laurate. Moreover, the process was optimized by an artificial neural network (ANN)...
November 15, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29139548/prospects-from-systems-serology-research
#16
REVIEW
Kelly B Arnold, Amy W Chung
Antibodies are highly functional glycoproteins capable of providing immune protection through multiple mechanisms, including direct pathogen neutralization and the engagement of their Fc-portions with surrounding effector immune cells and immune components that induce anti-pathogenic responses. Small modifications to multiple antibody biophysical features induced by vaccines and other therapeutic regimens can significantly alter functional immune outcomes, though it is difficult to predict which combinations confer protective immunity...
November 15, 2017: Immunology
https://www.readbyqxmd.com/read/29139050/modeling-mesoscopic-cortical-dynamics-using-a-mean-field-model-of-conductance-based-networks-of-adaptive-exponential-integrate-and-fire-neurons
#17
Yann Zerlaut, Sandrine Chemla, Frederic Chavane, Alain Destexhe
Voltage-sensitive dye imaging (VSDi) has revealed fundamental properties of neocortical processing at macroscopic scales. Since for each pixel VSDi signals report the average membrane potential over hundreds of neurons, it seems natural to use a mean-field formalism to model such signals. Here, we present a mean-field model of networks of Adaptive Exponential (AdEx) integrate-and-fire neurons, with conductance-based synaptic interactions. We study a network of regular-spiking (RS) excitatory neurons and fast-spiking (FS) inhibitory neurons...
November 15, 2017: Journal of Computational Neuroscience
https://www.readbyqxmd.com/read/29138682/mir-128-is-implicated-in-stress-responses-by-targeting-mafg-in-skeletal-muscle-cells
#18
Rocco Caggiano, Fabio Cattaneo, Ornella Moltedo, Giovanni Esposito, Cinzia Perrino, Bruno Trimarco, Rosario Ammendola, Raffaella Faraonio
MAFG (v-Maf avian musculoaponeurotic fibrosarcoma oncogene homolog G) is a bZIP-type transcriptional regulator that belongs to the small MAF (sMAFs) protein family. By interacting with other bZIP transcription factors, sMAFs can form homo- and heterodimers governing either repressive or activating transcriptional functions. As heterodimeric partner of Nrf2, MAFG positively influences the ARE-dependent antioxidant/xenobiotic pathways, at least in condition of a correct MAFG:Nrf2 balance. MicroRNAs (miRs) participate to different regulatory networks being involved as fine-tuning regulators of gene expression...
2017: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/29138518/predicted-molecular-targets-and-pathways-for-germacrone-curdione-and-furanodiene-in-the-treatment-of-breast-cancer-using-a-bioinformatics-approach
#19
Qi Kong, Yong Ma, Jie Yu, Xiuping Chen
Germacrone, curdione, and furanodiene have been shown to be useful in the treatment of breast cancer but the pharmacological mechanism of action is unclear. In this paper, we explored a new method to study the molecular network and function of Traditional Chinese Medicine (TCM) herbs and their corresponding ingredients with bioinformatics tools, including PubChem Compound Database, BATMAN-TCM, SystemsDock, Coremine Medical, Gene ontology, and KEGG. Eleven targeted genes/proteins, 4 key pathways, and 10 biological processes were identified to participate in the mechanism of action in treating breast cancer with germacrone, curdione, and furanodiene...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138116/in-silico-identification-of-genes-involved-in-chronic-metabolic-acidosis
#20
Ishfaq A Sheikh, Adeel Malik, Sameera F M AlBasri, Mohd A Beg
AIMS: Chronic metabolic acidosis (CMA) refers to increased plasma acidity due to disturbed acid-base equilibrium in human body. CMA leads to many dysfunctions including disorders of intestinal metabolism and barrier functions. The human body responds to these intestinal dysfunctions by creating a compensatory mechanism at genomic level in intestinal epithelial cells. This study was to identify the molecular pathways involved in metabolic dysfunction and compensatory adaptations in intestinal epithelium during CMA...
November 11, 2017: Life Sciences
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