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https://www.readbyqxmd.com/read/28636915/probing-the-structural-dynamics-of-the-nmda-receptor-activation-by-coarse-grained-modeling
#1
Wenjun Zheng, Han Wen, Gary J Iacobucci, Gabriela K Popescu
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636461/genice-a-novel-framework-for-gene-network-inference-by-clustering-exhaustive-search-and-multivariate-analysis
#2
Ricardo de Souza Jacomini, David Correa Martins-Jr, Felipe Leno da Silva, Anna Helena Reali Costa
Gene network (GN) inference from temporal gene expression data is a crucial and challenging problem in systems biology. Expression data sets usually consist of dozens of temporal samples, while networks consist of thousands of genes, thus rendering many inference methods unfeasible in practice. To improve the scalability of GN inference methods, we propose a novel framework called GeNICE, based on probabilistic GNs; the main novelty is the introduction of a clustering procedure to group genes with related expression profiles and to provide an approximate solution with reduced computational complexity...
June 21, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28635541/association-between-abnormal-brain-functional-connectivity-in-children-and-psychopathology-a-study-based-on-graph-theory-and-machine-learning
#3
João Ricardo Sato, Claudinei Eduardo Biazoli, Giovanni Abrahão Salum, Ary Gadelha, Nicolas Crossley, Gilson Vieira, André Zugman, Felipe Almeida Picon, Pedro Mario Pan, Marcelo Queiroz Hoexter, Edson Amaro, Mauricio Anés, Luciana Monteiro Moura, Marco Antonio Gomes Del'Aquilla, Philip Mcguire, Luis Augusto Rohde, Euripedes Constantino Miguel, Andrea Parolin Jackowski, Rodrigo Affonseca Bressan
OBJECTIVES: One of the major challenges facing psychiatry is how to incorporate biological measures in the classification of mental health disorders. Many of these disorders affect brain development and its connectivity. In this study, we propose a novel method for assessing brain networks based on the combination of a graph theory measure (eigenvector centrality) and a one-class support vector machine (OC-SVM). METHODS: We applied this approach to resting-state fMRI data from 622 children and adolescents...
February 8, 2017: World Journal of Biological Psychiatry
https://www.readbyqxmd.com/read/28633164/ann-prediction-of-ligament-stiffnesses-for-the-enhanced-predictive-ability-of-a-patient-specific-computational-foot-ankle-model
#4
Ruchi Chande, Jennifer S Wayne
Computational models of diarthrodial joints serve to inform the biomechanical function of these structures, and as such, must be supplied appropriate inputs for performance that is representative of actual joint function. Inputs for these models are sourced from both imaging modalities as well as literature. The latter is often the source of mechanical properties for soft tissues, like ligament stiffnesses; however, such data is not always available for all soft tissues nor is it known for patient specific work...
June 20, 2017: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/28629469/a-putative-molecular-network-associated-with-colon-cancer-metastasis-constructed-from-microarray-data
#5
Songtao Chu, Haipeng Wang, Miao Yu
BACKGROUND: This study aimed to identify the potential molecular network associated with colon cancer metastasis. METHODS: A gene expression profile dataset (GSE40367) downloaded from Gene Expression Omnibus was used to identify and compare differentially expressed genes (DEGs) between primary colon adenocarcinoma tissues and matched tissue samples of liver metastases of colon adenocarcinoma. After the functional analysis of the DEGs, their protein-protein interactions (PPIs) were analyzed, and the transcription factors (TFs) and microRNAs (miRNAs) that regulated these DEGs were predicted...
June 19, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28628834/functional-niti-grids-for-in-situ-straining-in-the-tem
#6
U Schürmann, C Chluba, N Wolff, D Smazna, R Lima de Miranda, P Junker, R Adelung, E Quandt, L Kienle
In situ measurements are a pivotal extension of conventional transmission electron microscopy (TEM). By means of the shape memory alloy NiTi thin film Functional Grids were produced for in situ straining as alternative or at least complement of expensive commercial holders. Due to the martensite-austenite transition temperature straining effects can be observed by use of customary heating holders in the range of 50 to 100°C. The grids can be produced in diversified designs to fit for different strain situations...
June 9, 2017: Ultramicroscopy
https://www.readbyqxmd.com/read/28628657/reported-family-burden-of-schizophrenia-patients-in-rural-china
#7
Yu Yu, Zi-Wei Liu, Bing-Wei Tang, Mei Zhao, Xi-Guang Liu, Shui-Yuan Xiao
We aim to assess the level of family burden of schizophrenia patients and identify its predicting factors in a rural community sample of China. A sample of 327 primary caregivers was recruited through a one-stage cluster sampling in Ningxiang County of Hunan province, China. Family burden was assessed using the Family Burden Interview Schedule (FBIS) of Pai and Kapur. Our results showed that the mean score of FBIS was 23.62±9.76 (range, 0-48), with over half (52%) caregivers reported their family burden being moderate and severe...
2017: PloS One
https://www.readbyqxmd.com/read/28627811/energy-based-neural-networks-as-a-tool-for-harmony-based-virtual-screening
#8
Nelly I Zhokhova, Igor I Baskin
In Energy-Based Neural Networks (EBNNs), relationships between variables are captured by means of a scalar function conventionally called "energy". In this article, we introduce a procedure of "harmony search", which looks for compounds providing the lowest energies for the EBNNs trained on active compounds. It can be considered as a special kind of similarity search that takes into account regularities in the structures of active compounds. In this paper, we show that harmony search can be used for performing virtual screening...
June 19, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28627690/data-mining-and-pathway-analysis-of-glucose-6-phosphate-dehydrogenase-with-natural-language-processing
#9
Long Chen, Chunhua Zhang, Yanling Wang, Yuqian Li, Qiaoqiao Han, Huixin Yang, Yuechun Zhu
Human glucose-6-phosphate dehydrogenase (G6PD) is a crucial enzyme in the pentose phosphate pathway, and serves an important role in biosynthesis and the redox balance. G6PD deficiency is a major cause of neonatal jaundice and acute hemolyticanemia, and recently, G6PD has been associated with diseases including inflammation and cancer. The aim of the present study was to conduct a search of the National Center for Biotechnology Information PubMed library for articles discussing G6PD. Genes that were identified to be associated with G6PD were recorded, and the frequency at which each gene appeared was calculated...
June 15, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28626845/temporally-factorized-network-modeling-for-evolutionary-network-analysis
#10
Wenchao Yu, Charu C Aggarwal, Wei Wang
The problem of evolutionary network analysis has gained increasing attention in recent years, because of an increasing number of networks, which are encountered in temporal settings. For example, social networks, communication networks, and information networks continuously evolve over time, and it is desirable to learn interesting trends about how the network structure evolves over time, and in terms of other interesting trends. One challenging aspect of networks is that they are inherently resistant to parametric modeling, which allows us to truly express the edges in the network as functions of time...
February 2017: Proceedings of the ... International Conference on Web Search & Data Mining. International Conference on Web Search & Data Mining
https://www.readbyqxmd.com/read/28626165/identification-and-functional-profiling-of-differentially-expressed-long-non-coding-rnas-in-nasal-mucosa-with-allergic-rhinitis
#11
Zhiqi Ma, Yaoshu Teng, Xiang Liu, Jing Li, Jiangwei Mo, Min Sha, Yong Li
Long non-coding RNAs (lncRNAs) have been proved to play important roles in a variety of human immune diseases. However, their pathological effects on the development of allergic rhinitis (AR) have not been clearly understood. The aim of this study was to determine the expression profile of lncRNAs in nasal mucosa of AR patients by lncRNA microarray and to predict potential roles of specific lncRNAs in the pathogenic mechanisms of AR by analysis of lncRNA-mRNA co-expression network, Gene Ontology (GO) and pathway...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28625914/prioritizing-disease-causing-microbes-based-on-random-walking-on-the-heterogeneous-network
#12
Xianjun Shen, Yao Chen, Xingpeng Jiang, Xiaohua Hu, Tingting He, Jincai Yang
As we all know, the microbiota show remarkable variability within individuals. At the same time, those microorganisms living in the human body play a very important role in our health and disease, so the identification of the relationships between microbes and diseases will contribute to better understanding of microbes interactions, mechanism of functions. However, the microbial data which are obtained through the related technical sequencing is too much, but the known associations between the diseases and microbes are very less...
June 15, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28625209/involvement-of-the-left-supramarginal-gyrus-in-manipulation-judgment-tasks-contributions-to-theories-of-tool-use
#13
Mathieu Lesourd, François Osiurak, Jordan Navarro, Emanuelle Reynaud
OBJECTIVES: Two theories of tool use, namely the gesture engram and the technical reasoning theories, make distinct predictions about the involvement of the left inferior parietal lobe (IPL) in manipulation judgement tasks. The objective here is to test these alternative predictions based on previous studies on manipulation judgment tasks using transcranial magnetic stimulations (TMS) targeting the left supramarginal gyrus (SMG). METHODS: We review recent TMS studies on manipulation judgement tasks and confront these data with predictions made by both tool use theories...
June 19, 2017: Journal of the International Neuropsychological Society: JINS
https://www.readbyqxmd.com/read/28624521/semanticized-autobiographical-memory-and-the-default-executive-coupling-hypothesis-of-aging
#14
R Nathan Spreng, Amber W Lockrow, Elizabeth DuPre, Roni Setton, Karen A P Spreng, Gary R Turner
As we age, the architecture of cognition undergoes a fundamental transition. Fluid intellectual abilities decline while crystalized abilities remain stable or increase. This shift has a profound impact across myriad cognitive and functional domains, yet the neural mechanisms remain under-specified. We have proposed that greater connectivity between the default network and executive control regions in lateral prefrontal cortex may underlie this shift, as older adults increasingly rely upon accumulated knowledge to support goal-directed behavior...
June 14, 2017: Neuropsychologia
https://www.readbyqxmd.com/read/28624483/biomarker-profiles-of-acute%C3%A2-heart%C3%A2-failure%C3%A2-patients-with-a%C3%A2-mid-range-ejection%C3%A2-fraction
#15
Jasper Tromp, Mohsin A F Khan, Robert J Mentz, Christopher M O'Connor, Marco Metra, Howard C Dittrich, Piotr Ponikowski, John R Teerlink, Gad Cotter, Beth Davison, John G F Cleland, Michael M Givertz, Daniel M Bloomfield, Dirk J van Veldhuisen, Hans L Hillege, Adriaan A Voors, Peter van der Meer
OBJECTIVES: In this study, the authors used biomarker profiles to characterize differences between patients with acute heart failure with a midrange ejection fraction (HFmrEF) and compare them with patients with a reduced (heart failure with a reduced ejection fraction [HFrEF]) and preserved (heart failure with a preserved ejection fraction [HFpEF]) ejection fraction. BACKGROUND: Limited data are available on biomarker profiles in acute HFmrEF. METHODS: A panel of 37 biomarkers from different pathophysiological domains (e...
May 31, 2017: JACC. Heart Failure
https://www.readbyqxmd.com/read/28623591/predicting-transcription-factor-binding-sites-and-their-cognate-transcription-factors-using-gene-expression-data
#16
Chun-Ping Yu, Wen-Hsiung Li
A transcription factor (TF) is a DNA binding protein that targets specific binding-sites (TFBSs) to regulate the transcript levels of its downstream genes. Thus, identifying the TF-TFBS pairs is a pivotal step in understanding the function of TFs and the regulatory network in an organism. Here, we describe two methods for predicting the TFBS of a given TF and for predicting the cognate TF of a given TFBS from a set of strongly co-expressed genes, using time-course transcriptome data of maize developing leaves...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623589/aranet-a-network-biology-server-for-arabidopsis-thaliana-and-other-non-model-plant-species
#17
Tak Lee, Insuk Lee
Functional gene networks link genes based on their functional relatedness, which is inferred from various complementary biological datasets. Gene networks comprising vast amounts of data can be used to predict which genes are associated with complex traits. Decades of studies in plant biology using the model organism Arabidopsis thaliana have generated large amounts of information, enabling the development of a system-level molecular network. AraNet (currently version 2) is a genome-scale functional gene network for Arabidopsis thaliana, constructed by integrating 19 types of genomics data and can be explored through a web-server (http://www...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623581/analysis-of-a-plant-transcriptional-regulatory-network-using-transient-expression-systems
#18
Sara Díaz-Triviño, Yuchen Long, Ben Scheres, Ikram Blilou
In plant biology, transient expression systems have become valuable approaches used routinely to rapidly study protein expression, subcellular localization, protein-protein interactions, and transcriptional activity prior to in vivo studies. When studying transcriptional regulation, luciferase reporter assays offer a sensitive readout for assaying promoter behavior in response to different regulators or environmental contexts and to confirm and assess the functional relevance of predicted binding sites in target promoters...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623335/complex-neuroanatomy-in-the-rostrum-of-the-isle-of-wight-theropod-neovenator-salerii
#19
Chris Tijani Barker, Darren Naish, Elis Newham, Orestis L Katsamenis, Gareth Dyke
The discovery of large, complex, internal canals within the rostra of fossil reptiles has been linked with an enhanced tactile function utilised in an aquatic context, so far in pliosaurids, the Cretaceous theropod Spinosaurus, and the related spinosaurid Baryonyx. Here, we report the presence of a complex network of large, laterally situated, anastomosing channels, discovered via micro-focus computed tomography (μCT), in the premaxilla and maxilla of Neovenator, a mid-sized allosauroid theropod from the Early Cretaceous of the UK...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28620443/pattern-recognition-for-predictive-preventive-and-personalized-medicine-in-cancer
#20
REVIEW
Tingting Cheng, Xianquan Zhan
Predictive, preventive, and personalized medicine (PPPM) is the hot spot and future direction in the field of cancer. Cancer is a complex, whole-body disease that involved multi-factors, multi-processes, and multi-consequences. A series of molecular alterations at different levels of genes (genome), RNAs (transcriptome), proteins (proteome), peptides (peptidome), metabolites (metabolome), and imaging characteristics (radiome) that resulted from exogenous and endogenous carcinogens are involved in tumorigenesis and mutually associate and function in a network system, thus determines the difficulty in the use of a single molecule as biomarker for personalized prediction, prevention, diagnosis, and treatment for cancer...
March 2017: EPMA Journal
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