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https://www.readbyqxmd.com/read/28101583/integrated-analysis-of-microrna-and-transcription-factor-reveals-important-regulators-and-regulatory-motifs-in-adult-b-cell-acute-lymphoblastic-leukemia
#1
Xiao-Cong Lin, Xin-Guang Liu, Yu-Ming Zhang, Ning Li, Zhi-Gang Yang, Wei-Yu Fu, Liu-Bo Lan, Hai-Tao Zhang, Yong Dai
B-cell acute lymphoblastic leukemia (B‑ALL) is an aggressive hematological malignancy and a leading cause of cancer-related mortality in children and young adults. The molecular mechanisms involved in the regulation of its gene expression has yet to be fully elucidated. In the present study, we performed large scale expression profiling of microRNA (miRNA) and transcription factor (TF) by Illumina deep‑sequencing and TF array technology, respectively, and identified 291 differentially expressed miRNAs and 201 differentially expressed TFs in adult B‑ALL samples relative to their controls...
February 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28101576/multiple-effects-of-ellagic-acid-on-human-colorectal-carcinoma-cells-identified-by-gene-expression-profile-analysis
#2
Jinlu Zhao, Guodong Li, Wanlan Bo, Yuhui Zhou, Shuwei Dang, Jiufeng Wei, Xinglong Li, Ming Liu
Colorectal carcinoma (CRC) is the third most commonly diagnosed cancer in the world. Phytochemicals have become a research hotspot in recent years as cancer prevention and treatment agents due to their low toxicity and limited side-effects. Ellagic acid (EA), a natural phenolic constituent, displays various biological activities, including anticancer effects. However, the detailed anticancer mechanisms of EA remain unclear. In the present study, we found that EA inhibited the growth of HCT-116 colon cancer cells...
February 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28101525/untangling-basal-ganglia-network-dynamics-and-function-role-of-dopamine-depletion-and-inhibition-investigated-in-a-spiking-network-model
#3
Mikael Lindahl, Jeanette Hellgren Kotaleski
The basal ganglia are a crucial brain system for behavioral selection, and their function is disturbed in Parkinson's disease (PD), where neurons exhibit inappropriate synchronization and oscillations. We present a spiking neural model of basal ganglia including plausible details on synaptic dynamics, connectivity patterns, neuron behavior, and dopamine effects. Recordings of neuronal activity in the subthalamic nucleus and Type A (TA; arkypallidal) and Type I (TI; prototypical) neurons in globus pallidus externa were used to validate the model...
November 2016: ENeuro
https://www.readbyqxmd.com/read/28100828/an-integrated-modelling-framework-for-neural-circuits-with-multiple-neuromodulators
#4
Alok Joshi, Vahab Youssofzadeh, Vinith Vemana, T M McGinnity, Girijesh Prasad, KongFatt Wong-Lin
Neuromodulators are endogenous neurochemicals that regulate biophysical and biochemical processes, which control brain function and behaviour, and are often the targets of neuropharmacological drugs. Neuromodulator effects are generally complex partly owing to the involvement of broad innervation, co-release of neuromodulators, complex intra- and extrasynaptic mechanism, existence of multiple receptor subtypes and high interconnectivity within the brain. In this work, we propose an efficient yet sufficiently realistic computational neural modelling framework to study some of these complex behaviours...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28100742/visual-sampling-predicts-hippocampal-activity
#5
Zhong-Xu Liu, Kelly Shen, Rosanna K Olsen, Jennifer D Ryan
: Eye movements serve to accumulate information from the visual world, contributing to the formation of coherent memory representations that support cognition and behavior. The hippocampus and the oculomotor network are well connected anatomically through an extensive set of polysynaptic pathways. However, the extent to which visual sampling behavior is related to functional responses in the hippocampus during encoding has not been studied directly in human neuroimaging. In the current study, participants engaged in a face processing task while brain responses were recorded with fMRI and eye movements were monitored simultaneously...
January 18, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28100246/genetic-effect-of-interleukin-1-beta-c-511t-polymorphism-on-the-structural-covariance-network-and-white-matter-integrity-in-alzheimer-s-disease
#6
Chi-Wei Huang, Shih-Wei Hsu, Shih-Jen Tsai, Nai-Ching Chen, Mu-En Liu, Chen-Chang Lee, Shu-Hua Huang, Weng-Neng Chang, Ya-Ting Chang, Wan-Chen Tsai, Chiung-Chih Chang
BACKGROUND: Inflammatory processes play a pivotal role in the degenerative process of Alzheimer's disease. In humans, a biallelic (C/T) polymorphism in the promoter region (position-511) (rs16944) of the interleukin-1 beta gene has been significantly associated with differences in the secretory capacity of interleukin-1 beta. In this study, we investigated whether this functional polymorphism mediates the brain networks in patients with Alzheimer's disease. METHODS: We enrolled a total of 135 patients with Alzheimer's disease (65 males, 70 females), and investigated their gray matter structural covariance networks using 3D T1 magnetic resonance imaging and their white matter macro-structural integrities using fractional anisotropy...
January 18, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28100212/the-effects-of-breakfast-on-short-term-cognitive-function-among-chinese-white-collar-workers-protocol-for-a-three-phase-crossover-study
#7
Zhenchuang Tang, Na Zhang, Ailing Liu, Dechun Luan, Yong Zhao, Chao Song, Guansheng Ma
BACKGROUND: As the first meal of the day, breakfast plays an important role in supplying energy and nutrients, which are critical to working and learning activities. A three-phase crossover study was designed to investigate the effects of breakfast on cognitive function among Chinese white-collar workers. The planned study protocol is presented. METHODS: A total of 264 participants aged 25-45 years will be recruited from Shenyang and Chongqing. Self-administered questionnaires will be used to collect information on age, gender, marital status, education level, occupation, smoking habits, drinking habits, and breakfast behaviours...
January 18, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28099009/thickness-controlled-quasi-two-dimensional-colloidal-pbse-nanoplatelets
#8
Weon-Kyu Koh, Naveen Kumar Dandu, Andrew F Fidler, Victor I Klimov, Jeffrey M Pietryga, Svetlana V Kilina
We demonstrate controlled synthesis of discrete two-dimensional (2D) PbSe nanoplatelets (NPLs), with measureable photoluminescence, via oriented attachment directed by quantum dot (QD) surface chemistry. Halide passivation is critical to the growth of these (100) face-dominated NPLs, as corroborated by density functional theory studies. PbCl2 moieties attached to the (111) and (110) of small nanocrystals form interparticle bridges, aligning the QDs and leading to attachment. We find that a 2D bridging network is energetically favored over a 3D network, driving the formation of NPLs...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28097908/common-and-specific-genes-and-peripheral-biomarkers-in-children-and-adults-with-attention-deficit-hyperactivity-disorder
#9
Cristian Bonvicini, Stephen V Faraone, Catia Scassellati
OBJECTIVES: Elucidating the biological mechanisms involved in Attention-deficit/hyperactivity disorder (ADHD) has been challenging. Relatively unexplored is the fact that these mechanisms can differ with age. METHODS: We present an overview on the major differences between children and adults with ADHD, describing several studies from genomics to metabolomics performed in ADHD children and in adults. A systematic search (up until February, 2016) was conducted. RESULTS: From a PRISMA flow-chart, a total of eligibility 350 studies from genomics and metabolomics were found for cADHD and 91 for aADHD...
January 18, 2017: World Journal of Biological Psychiatry
https://www.readbyqxmd.com/read/28095197/solving-nonlinearly-separable-classifications-in-a-single-layer-neural-network
#10
Nolan Conaway, Kenneth J Kurtz
Since the work of Minsky and Papert (1969), it has been understood that single-layer neural networks cannot solve nonlinearly separable classifications (i.e., XOR). We describe and test a novel divergent autoassociative architecture capable of solving nonlinearly separable classifications with a single layer of weights. The proposed network consists of class-specific linear autoassociators. The power of the model comes from treating classification problems as within-class feature prediction rather than directly optimizing a discriminant function...
January 17, 2017: Neural Computation
https://www.readbyqxmd.com/read/28094815/drd2-co-expression-network-and-a-related-polygenic-index-predict-imaging-behavioral-and-clinical-phenotypes-linked-to-schizophrenia
#11
G Pergola, P Di Carlo, E D'Ambrosio, B Gelao, L Fazio, M Papalino, A Monda, G Scozia, B Pietrangelo, M Attrotto, J A Apud, Q Chen, V S Mattay, A Rampino, G Caforio, D R Weinberger, G Blasi, A Bertolino
Genetic risk for schizophrenia (SCZ) is determined by many genetic loci whose compound biological effects are difficult to determine. We hypothesized that co-expression pathways of SCZ risk genes are associated with system-level brain function and clinical phenotypes of SCZ. We examined genetic variants related to the dopamine D2 receptor gene DRD2 co-expression pathway and associated them with working memory (WM) behavior, the related brain activity and treatment response. Using two independent post-mortem prefrontal messenger RNA (mRNA) data sets (total N=249), we identified a DRD2 co-expression pathway enriched for SCZ risk genes...
January 17, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28093558/glutamatergic-synapses-are-structurally-and-biochemically-complex-because-of-multiple-plasticity-processes-long-term-potentiation-long-term-depression-short-term-potentiation-and-scaling
#12
REVIEW
John Lisman
Synapses are complex because they perform multiple functions, including at least six mechanistically different forms of plasticity. Here, I comment on recent developments regarding these processes. (i) Short-term potentiation (STP), a Hebbian process that requires small amounts of synaptic input, appears to make strong contributions to some forms of working memory. (ii) The rules for long-term potentiation (LTP) induction in CA3 have been clarified: induction does not depend obligatorily on backpropagating sodium spikes but, rather, on dendritic branch-specific N-methyl-d-aspartate (NMDA) spikes...
March 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28093547/functional-consequences-of-pre-and-postsynaptic-expression-of-synaptic-plasticity
#13
REVIEW
Rui Ponte Costa, Beatriz E P Mizusaki, P Jesper Sjöström, Mark C W van Rossum
Growing experimental evidence shows that both homeostatic and Hebbian synaptic plasticity can be expressed presynaptically as well as postsynaptically. In this review, we start by discussing this evidence and methods used to determine expression loci. Next, we discuss the functional consequences of this diversity in pre- and postsynaptic expression of both homeostatic and Hebbian synaptic plasticity. In particular, we explore the functional consequences of a biologically tuned model of pre- and postsynaptically expressed spike-timing-dependent plasticity complemented with postsynaptic homeostatic control...
March 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28093455/genomewide-landscape-of-gene-metabolome-associations-in-escherichia-coli
#14
Tobias Fuhrer, Mattia Zampieri, Daniel C Sévin, Uwe Sauer, Nicola Zamboni
Metabolism is one of the best-understood cellular processes whose network topology of enzymatic reactions is determined by an organism's genome. The influence of genes on metabolite levels, however, remains largely unknown, particularly for the many genes encoding non-enzymatic proteins. Serendipitously, genomewide association studies explore the relationship between genetic variants and metabolite levels, but a comprehensive interaction network has remained elusive even for the simplest single-celled organisms...
January 16, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28092580/determination-of-the-edge-of-criticality-in-echo-state-networks-through-fisher-information-maximization
#15
Lorenzo Livi, Filippo Maria Bianchi, Cesare Alippi
It is a widely accepted fact that the computational capability of recurrent neural networks (RNNs) is maximized on the so-called "edge of criticality." Once the network operates in this configuration, it performs efficiently on a specific application both in terms of: 1) low prediction error and 2) high short-term memory capacity. Since the behavior of recurrent networks is strongly influenced by the particular input signal driving the dynamics, a universal, application-independent method for determining the edge of criticality is still missing...
January 16, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28092154/correlating-the-network-topology-of-oxide-glasses-with-their-chemical-durability
#16
Nerea Mascaraque, Mathieu Bauchy, Morten M Smedskjaer
Glasses gradually dissolve and corrode when they are exposed to aqueous solutions and for many applications it is necessary to understand and predict the kinetics of the glass dissolution. Despite the recent progress in understanding the impact of chemical composition on the dissolution rate, a detailed understanding of the structural and topological origin of chemical durability in solutions of different pH is still largely lacking. Such knowledge would enable the tailoring of glass dissolution kinetics as a function of chemical composition...
January 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28087642/stxbp4-drives-tumor-growth-and-is-associated-with-poor-prognosis-through-pdgf-receptor-signaling-in-lung-squamous-cell-carcinoma
#17
Yukihiro Otaka, Susumu Rokudai, Kyoichi Kaira, Michiru Fujieda, Ikuko Horikoshi, Reika Kawabata, Shinji Yoshiyama, Takehiko Yokobori, Yoichi Ohtaki, Kimihiro Shimizu, Tetsunari Oyama, Jun'ichi Tamura, Carol Prives, Masahiko Nishiyama
PURPOSE: Expression of the ΔN isoform of p63 (ΔNp63) is a diagnostic marker highly specific for lung squamous cell carcinoma (SCC). We previously found that Syntaxin Binding Protein 4 (STXBP4) regulates ΔNp63 ubiquitination, suggesting that STXBP4 may also be a SCC biomarker. To address this issue, we investigated the role of STXBP4 expression in SCC biology and the impact of STXBP4 expression on SCC prognosis. EXPERIMENTAL DESIGN: We carried out a clinicopathological analysis of STXBP4 expression in 87 lung SCC patients...
January 13, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#18
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28086790/rna-sequencing-for-global-gene-expression-associated-with-muscle-growth-in-a-single-male-modern-broiler-line-compared-to-a-foundational-barred-plymouth-rock-chicken-line
#19
Byung-Whi Kong, Nicholas Hudson, Dongwon Seo, Seok Lee, Bhuwan Khatri, Kentu Lassiter, Devin Cook, Alissa Piekarski, Sami Dridi, Nicholas Anthony, Walter Bottje
BACKGROUND: Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive genetic selection for meat production. This study was designed to investigate the genetic alterations accumulated in modern broiler breeder lines during selective breeding conducted over several decades. METHODS: To identify genes important in determining muscle growth and feed efficiency in broilers, RNA sequencing (RNAseq) was conducted with breast muscle in modern pedigree male (PeM) broilers (n = 6 per group), and with an unselected foundation broiler line (Barred Plymouth Rock; BPR)...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28086788/comprehensive-circrna-expression-profile-and-selection-of-key-circrnas-during-priming-phase-of-rat-liver-regeneration
#20
Lifei Li, Jianlin Guo, Yanhui Chen, Cuifang Chang, Cunshuan Xu
BACKGROUND: Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play important roles. The molecular mechanism of hepatocyte proliferation, energy metabolism and substance metabolism during rat LR had been elucidated. Further, the correlation of circular RNA (circRNA) abundance with proliferation has recently been clarified. However, the regulatory capacity of circRNA in rat LR remains a fascinating topic...
January 13, 2017: BMC Genomics
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