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https://www.readbyqxmd.com/read/28647497/prediction-of-metastasis-in-advanced-colorectal-carcinomas-using-cgh-data
#1
Ehsan Saghapour, Mohammadreza Sehhati
Logistic Regression Model (LRM) and artificial neural networks (ANNs) as two nonlinear models have been used to establish a novel two-stage hybrid modeling procedure for prediction of metastasis in advanced colorectal carcinomas. Two different datasets were used in training and testing procedures. For the first stage of hybrid modeling procedure, LRM was used to evaluate the contribution of DNA sequence copy number aberrations detected by Comparative Genomic Hybridization in advanced colorectal carcinoma and its metastasis...
June 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28647368/identification-and-characterization-of-the-leaf-specific-networks-of-inner-and-rosette-leaves-in-brassica-rapa
#2
Man-Sun Kim, Seongmin Hong, Devaraj Sangeeth Prasath, Subin Im, Jeong-Rae Kim, Yong Pyo Lim
Inner and rosette leaves of Chinese cabbage (Brassica rapa) have different characteristics in terms of nutritional value, appearance, taste, color and texture. Many researchers have utilized differentially expressed genes for exploring the difference between inner and rosette leaves of Brassica rapa. The functional characteristics of a gene, however, is determined by complex interactions between genes. Hence, a noble network approach is required for elucidating such functional difference that is not captured by gene expression profiles alone...
June 21, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28646471/decoding-early-myelopoiesis-from-dynamics-of-core-endogenous-network
#3
Hang Su, Gaowei Wang, Ruoshi Yuan, Junqiang Wang, Ying Tang, Ping Ao, Xiaomei Zhu
A decade ago mainstream molecular biologists regarded it impossible or biologically ill-motivated to understand the dynamics of complex biological phenomena, such as cancer genesis and progression, from a network perspective. Indeed, there are numerical difficulties even for those who were determined to explore along this direction. Undeterred, seven years ago a group of Chinese scientists started a program aiming to obtain quantitative connections between tumors and network dynamics. Many interesting results have been obtained...
May 29, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28645956/exploring-the-components-of-physician-volunteer-engagement-a-qualitative-investigation-of-a-national-canadian-simulation-based-training-programme
#4
Aimee J Sarti, Stephanie Sutherland, Angele Landriault, Kirk DesRosier, Susan Brien, Pierre Cardinal
OBJECTIVES: Conceptual clarity on physician volunteer engagement is lacking in the medical literature. The aim of this study was to present a conceptual framework to describe the elements which influence physician volunteer engagement and to explore volunteer engagement within a national educational programme. SETTING: The context for this study was the Acute Critical Events Simulation (ACES) programme in Canada, which has successfully evolved into a national educational programme, driven by physician volunteers...
June 23, 2017: BMJ Open
https://www.readbyqxmd.com/read/28644851/comorbidities-in-the-diseasome-are-more-apparent-than-real-what-bayesian-filtering-reveals-about-the-comorbidities-of-depression
#5
Peter Marx, Peter Antal, Bence Bolgar, Gyorgy Bagdy, Bill Deakin, Gabriella Juhasz
Comorbidity patterns have become a major source of information to explore shared mechanisms of pathogenesis between disorders. In hypothesis-free exploration of comorbid conditions, disease-disease networks are usually identified by pairwise methods. However, interpretation of the results is hindered by several confounders. In particular a very large number of pairwise associations can arise indirectly through other comorbidity associations and they increase exponentially with the increasing breadth of the investigated diseases...
June 23, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28643459/construction-of-competitive-endogenous-rna-network-reveals-regulatory-role-of-long-non-coding-rnas-in-type-2-diabetes-mellitus
#6
Zijing Lin, Xinyu Li, Xiaorong Zhan, Lijie Sun, Jie Gao, Yan Cao, Hui Qiu
Increasing epidemic of type 2 diabetes mellitus (T2DM) and its comorbidities makes it urgent to understand the pathogenesis and regulatory mechanism. However, little is known about the regulatory role of lncRNAs in diabetes. Here, we constructed a T2DM-related competitive endogenous RNA (ceRNA) network (DMCN) to explore biological function of lncRNAs during the development of diabetes mellitus. This network contained 351 nodes including 98 mRNAs, 86 microRNAs and 167 lncRNAs. Functional analysis showed that the mRNAs in DMCN were annotated into some diabetes-related pathways...
June 23, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28642938/correlation-weighted-sparse-group-representation-for-brain-network-construction-in-mci-classification
#7
Renping Yu, Han Zhang, Le An, Xiaobo Chen, Zhihui Wei, Dinggang Shen
Analysis of brain functional connectivity network (BFCN) has shown great potential in understanding brain functions and identifying biomarkers for neurological and psychiatric disorders, such as Alzheimer's disease and its early stage, mild cognitive impairment (MCI). In all these applications, the accurate construction of biologically meaningful brain network is critical. Due to the sparse nature of the brain network, sparse learning has been widely used for complex BFCN construction. However, the conventional l1-norm penalty in the sparse learning equally penalizes each edge (or link) of the brain network, which ignores the link strength and could remove strong links in the brain network...
October 2016: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/28642592/integrative-network-analysis-identifies-novel-drivers-of-pathogenesis-and-progression-in-newly-diagnosed-multiple-myeloma
#8
A Laganà, D Perumal, D Melnekoff, B Readhead, B A Kidd, V Leshchenko, P-Y Kuo, J Keats, M DeRome, J Yesil, D Auclair, S Lonial, A Chari, H J Cho, B Barlogie, S Jagannath, J T Dudley, S Parekh
Multiple Myeloma (MM) is an incurable malignancy of bone marrow plasma cells characterized by wide clinical and molecular heterogeneity. In this study we applied an integrative network biology approach to molecular and clinical data measured from 450 patients with newly diagnosed MM from the MMRF CoMMpass study. A novel network model of myeloma (MMNet) was constructed, revealing complex molecular disease patterns and novel associations between clinical traits and genomic markers. Genomic alterations and groups of co-expressed genes correlate with disease stage, tumor clonality, and early progression...
June 23, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28641502/ordering-theories-typologies-and-conceptual-frameworks-for-sociotechnical-change
#9
Benjamin K Sovacool, David J Hess
What theories or concepts are most useful at explaining socio technical change? How can - or cannot - these be integrated? To provide an answer, this study presents the results from 35 semi-structured research interviews with social science experts who also shared more than two hundred articles, reports and books on the topic of the acceptance, adoption, use, or diffusion of technology. This material led to the identification of 96 theories and conceptual approaches spanning 22 identified disciplines. The article begins by explaining its research terms and methods before honing in on a combination of fourteen theories deemed most relevant and useful by the material...
June 1, 2017: Social Studies of Science
https://www.readbyqxmd.com/read/28641312/impact-of-novel-mir-145-3p-regulatory-networks-on-survival-in-patients-with-castration-resistant-prostate-cancer
#10
Yusuke Goto, Akira Kurozumi, Takayuki Arai, Nijiro Nohata, Satoko Kojima, Atsushi Okato, Mayuko Kato, Kazuto Yamazaki, Yasuo Ishida, Yukio Naya, Tomohiko Ichikawa, Naohiko Seki
BACKGROUND: Despite recent advancements, metastatic castration-resistant prostate cancer (CRPC) is not considered curative. Novel approaches for identification of therapeutic targets of CRPC are needed. METHODS: Next-generation sequencing revealed 945-1248 miRNAs from each lethal mCRPC sample. We constructed miRNA expression signatures of CRPC by comparing the expression of miRNAs between CRPC and normal prostate tissue or hormone-sensitive prostate cancer (HSPC)...
June 22, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28640939/global-transcriptome-and-co-expression-network-analyses-reveal-cultivar-specific-molecular-signatures-associated-with-seed-development-and-seed-size-weight-determination-in-chickpea
#11
Rohini Garg, Vikash K Singh, Mohan Singh Rajkumar, Vinay Kumar, Mukesh Jain
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes. About one-fourth of total genes exhibited significant differential expression in JGK 3 as compared to Himchana 1...
June 22, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28640883/an-artificial-emg-generation-model-based-on-signal-dependent-noise-and-related-application-to-motion-classification
#12
Akira Furui, Hideaki Hayashi, Go Nakamura, Takaaki Chin, Toshio Tsuji
This paper proposes an artificial electromyogram (EMG) signal generation model based on signal-dependent noise, which has been ignored in existing methods, by introducing the stochastic construction of the EMG signals. In the proposed model, an EMG signal variance value is first generated from a probability distribution with a shape determined by a commanded muscle force and signal-dependent noise. Artificial EMG signals are then generated from the associated Gaussian distribution with a zero mean and the generated variance...
2017: PloS One
https://www.readbyqxmd.com/read/28640829/an-exploration-of-collaborative-scientific-production-at-mit-through-spatial-organization-and-institutional-affiliation
#13
Matthew Claudel, Emanuele Massaro, Paolo Santi, Fiona Murray, Carlo Ratti
Academic research is increasingly cross-disciplinary and collaborative, between and within institutions. In this context, what is the role and relevance of an individual's spatial position on a campus? We examine the collaboration patterns of faculty at the Massachusetts Institute of Technology, through their academic output (papers and patents), and their organizational structures (institutional affiliation and spatial configuration) over a 10-year time span. An initial comparison of output types reveals: 1...
2017: PloS One
https://www.readbyqxmd.com/read/28640334/instruments-for-articulating-the-network-of-attention-to-women-in-situation-of-violence-collective-construction
#14
Laura Ferreira Cortes, Stela Maris de Mello Padoin, Daniela Dal Forno Kinalski
Objective: This paper aims at identifying all the necessary information to build instruments which are designed to facilitate the professional integration of services to women in situation of violence with a view to the establishment of a network of attention. Method: Qualitative study, convergent, whose information has been produced from February to August 2015 by 10 group meetings, with 32 participants from the Integrated Working Group to Confront Violence in Santa Maria-RS, located at the Universidade Federal de Santa Maria...
June 5, 2017: Revista Gaúcha de Enfermagem
https://www.readbyqxmd.com/read/28640074/bioinformatics-analysis-of-key-genes-and-pathways-for-hepatocellular-carcinoma-transformed-from-cirrhosis
#15
Bosheng He, Jianbing Yin, Shenchu Gong, Jinhua Gu, Jing Xiao, Weixiang Shi, Wenbin Ding, Ying He
OBJECTIVE: We aimed to identify some pivotal genes and pathways for hepatocellular carcinoma (HCC) transformation from cirrhosis and explore potential targets for treatment of the disease. METHODS: The GSE17548 microarray data were downloaded from Gene Expression Omnibus database, and 37 samples (20 cirrhosis and 17 HCC samples) were used for analysis. The differentially expressed genes (DEGs) in HCC tissues were compared with those in cirrhosis tissues and analyzed using the limma package...
June 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28639886/a-competing-endogenous-rna-network-identifies-novel-mrna-mirna-and-lncrna-markers-for-the-prognosis-of-diabetic-pancreatic-cancer
#16
Kanyu Yao, Qi Wang, Jianhua Jia, Haiping Zhao
Pancreatic cancer (PaC) is highly associated with diabetes mellitus (DM). However, the mechanisms are insufficient. The study aimed to uncover the underlying regulatory mechanism on diabetic PaC and find novel biomarkers for the disease prognosis. Two RNA-sequencing (RNA-seq) datasets, GSE74629 and GSE15932, as well as relevant data in TCGA were utilized. After pretreatment, differentially expressed genes (DEGs) or miRNAs (DEMs) or lncRNAs (DELs) between diabetic PaC and non-diabetic PaC patients were identified, and further examined for their correlations with clinical information...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28638648/an-infinite-two-dimensional-hybrid-water-chloride-network-in-a-4-furan-2-yl-2-2-6-2-terpyridine-nickel-ii-matrix
#17
Wei-Wei Fu, Ya-Qian Li, Yang Liu, Man-Sheng Chen, Wei Li, Ying-Qun Yang
A new complex, namely bis-[4'-(furan-2-yl)-2,2':6',2''-terpyridine]-nickel(II) dichloride deca-hydrate, [Ni(C19H13N3O)2]Cl2·10H2O, has been crystallized by solvent evaporation and characterized by single-crystal X-ray diffraction. The coordination environment of the Ni(II) cation is distorted octa-hedral with slight deviations from an idealized geometry. The most intriguing structural feature is an infinite two-dimensional hybrid water-chloride network parallel to (011) constructed by O-H⋯O and O-H⋯Cl hydrogen bonds involving two independent chloride ions and ten independent solvent water mol-ecules with an l-shaped pattern...
June 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/28638386/weighted-gene-co-expression-network-analysis-of-the-dioscin-rich-medicinal-plant-dioscorea-nipponica
#18
Wei Sun, Bo Wang, Jun Yang, Weihao Wang, An Liu, Liang Leng, Li Xiang, Chi Song, Shilin Chen
Dioscorea contains critically important species which can be used as staple foods or sources of bioactive substances, including Dioscorea nipponica, which has been used to develop highly successful drugs to treat cardiovascular disease. Its major active ingredients are thought to be sterol compounds such as diosgenin, which has been called "medicinal gold" because of its valuable properties. However, reliance on naturally growing plants as a production system limits the potential use of D. nipponica, raising interest in engineering metabolic pathways to enhance the production of secondary metabolites...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28636943/opa1-isoforms-in-the-hierarchical-organization-of-mitochondrial-functions
#19
Valentina Del Dotto, Prashant Mishra, Sara Vidoni, Mario Fogazza, Alessandra Maresca, Leonardo Caporali, J Michael McCaffery, Martina Cappelletti, Enrico Baruffini, Guy Lenaers, David Chan, Michela Rugolo, Valerio Carelli, Claudia Zanna
OPA1 is a GTPase that controls mitochondrial fusion, cristae integrity, and mtDNA maintenance. In humans, eight isoforms are expressed as combinations of long and short forms, but it is unclear whether OPA1 functions are associated with specific isoforms and/or domains. To address this, we expressed each of the eight isoforms or different constructs of isoform 1 in Opa1(-/-) MEFs. We observed that any isoform could restore cristae structure, mtDNA abundance, and energetic efficiency independently of mitochondrial network morphology...
June 20, 2017: Cell Reports
https://www.readbyqxmd.com/read/28636542/niaoduqing-granules-relieve-chronic-kidney-disease-symptoms-by-decreasing-renal-fibrosis-and-anemia
#20
Xu Wang, Suyun Yu, Qi Jia, Lichuan Chen, Jinqiu Zhong, Yanhong Pan, Peiliang Shen, Yin Shen, Siliang Wang, Zhonghong Wei, Yuzhu Cao, Yin Lu
NiaoDuQing (NDQ) granules, a traditional Chinese medicine, has been clinically used in China for over fourteen years to treat chronic kidney disease (CKD). To elucidate the mechanisms underlying the therapeutic benefits of NDQ, we designed an approach incorporating chemoinformatics, bioinformatics, network biology methods, and cellular and molecular biology experiments. A total of 182 active compounds were identified in NDQ granules, and 397 putative targets associated with different diseases were derived through ADME modelling and target prediction tools...
June 14, 2017: Oncotarget
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