keyword
MENU ▼
Read by QxMD icon Read
search

network construction

keyword
https://www.readbyqxmd.com/read/28449558/in-silicomodel-driven-assessment-of-the-effects-of-brain-derived-neurotrophic-factor-deficiency-on-glutamate-and-gamma-aminobutyric-acid-implications-for-understanding-schizophrenia-pathophysiology
#1
Rimjhim Agrawal, Sunil Vasu Kalmady, Ganesan Venkatasubramanian
Objective: Deficient brain-derived neurotrophic factor (BDNF) is one of the important mechanisms underlying the neuroplasticity abnormalities in schizophrenia. Aberration in BDNF signaling pathways directly or circuitously influences neurotransmitters like glutamate and gamma-aminobutyric acid (GABA). For the first time, this study attempts to construct and simulate the BDNF-neurotransmitter network in order to assess the effects of BDNF deficiency on glutamate and GABA. Methods: Using CellDesigner, we modeled BDNF interactions with calcium influx via N-methyl-D-aspartate receptor (NMDAR)- Calmodulin activation; synthesis of GABA via cell cycle regulators protein kinase B, glycogen synthase kinase and β-catenin; transportation of glutamate and GABA...
May 31, 2017: Clinical Psychopharmacology and Neuroscience: the Official Scientific Journal of the Korean College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28448738/site-specific-recruitment-of-epigenetic-factors-with-a-modular-crispr-cas-system
#2
Tobias Anton, Sebastian Bultmann
Dissecting the complex network of epigenetic modifications requires tools that combine precise recognition of DNA sequences with the capability to modify epigenetic marks. The CRISPR/Cas system has been proven to be a valuable addition to existing methodologies that fulfill these tasks. So far, sequence-specific editing of epigenetic modifications such as DNA methylation and histone posttranslational modifications relied on direct fusions of enzymatically inactivated Cas9 (dCas9) with epigenetic effectors. Here, we report a novel, modular system that facilitates the recruitment of any GFP-tagged protein to desired genomic loci...
February 23, 2017: Nucleus
https://www.readbyqxmd.com/read/28448511/tracking-disease-progression-by-searching-paths-in-a-temporal-network-of-biological-processes
#3
Rajat Anand, Samrat Chatterjee
Metabolic disorders such as obesity and diabetes are diseases which develop gradually over time through the perturbations of biological processes. These perturbed biological processes usually work in an interdependent way. Systematic experiments tracking disease progression at gene level are usually conducted through a temporal microarray data. There is a need for developing methods to analyze such highly complex data to capture disease progression at the molecular level. In the present study, we have considered temporal microarray data from an experiment conducted to study development of obesity and diabetes in mice...
2017: PloS One
https://www.readbyqxmd.com/read/28448484/tissue-engineered-3d-human-lymphatic-microvascular-network-for-in-vitro-studies-of-lymphangiogenesis
#4
Laure Gibot, Todd Galbraith, Jennifer Bourland, Anita Rogic, Mihaela Skobe, François A Auger
This protocol describes a unique in vitro method for the generation of a 3D human lymphatic network within native connective tissue devoid of any exogenous material such as scaffolds or growth factors. In this five-stage protocol, human lymphatic endothelial cells (LECs) cocultured with dermal fibroblasts spontaneously organize into a stable 3D lymphatic capillary network. Stage 1 involves the isolation of primary fibroblasts and LECs from human skin. Fibroblasts are then cultured to produce connective tissue rich in extracellular matrix (stage 2), onto which LECs are seeded to form a network (stage 3)...
May 2017: Nature Protocols
https://www.readbyqxmd.com/read/28448124/bioinspired-engineering-of-poly-ethylene-glycol-hydrogels-and-natural-protein-fibers-for-layered-heart-valve-constructs
#5
Qian Li, Yun Bai, Tao Jin, Shuo Wang, Wei Cui, Ilinca Stanciulescu, Rui Yang, Hemin Nie, Linshan Wang, Xing Zhang
Layered constructs from poly(ethylene glycol) (PEG) hydrogels and chicken eggshell membranes (ESMs) are fabricated, which can be further crosslinked by glutaraldehyde (GA) to form GA-PEG-ESM composites. Our results indicate that ESMs composed of protein fibrous networks show elastic moduli ~3.3-5.0 MPa and elongation percentages ~47-56%, close to human heart valve leaflets. Finite element simulations reveal obvious stress concentration on a partial number of fibers in the GA-crosslinked ESM (GA-ESM) samples, which can be alleviated by efficient stress distribution among multiple layers of ESMs embedded in PEG hydrogels...
April 27, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28447701/structural-and-morphological-transitions-in-extension-induced-crystallization-of-poly-1-butene-melt
#6
Zhen Wang, Jianzhu Ju, Lingpu Meng, Nan Tian, Jiarui Chang, Haoran Yang, Youxin Ji, Fengmei Su, Liangbin Li
Structural and morphological transitions of flow-induced crystallization (FIC) in poly(1-butene) (PB-1) melt have been studied by combining extensional rheology and in situ synchrotron radiation ultrafast wide- and small-angle X-ray scattering (WAXD/SAXS) measurements. Unexpectedly, metastable Form III is crystallized directly from the PB-1 melt by high-speed extension, which has a short lifetime of several tens of milliseconds and manifests the thermodynamic and kinetic competition among Form III, Form II and melt under flow...
April 27, 2017: Soft Matter
https://www.readbyqxmd.com/read/28446914/constructing-integrated-networks-for-identifying-new-secondary-metabolic-pathway-regulators-in-grapevine-recent-applications-and-future-opportunities
#7
Darren C J Wong, José Tomás Matus
Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Whereas, some studies have used gene co-expression networks to find common pathways and putative targets for transcription factors related to development and metabolism, others have defined networks of primary and secondary metabolites for characterizing the main metabolic differences between cultivars throughout fruit ripening...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28446913/de-novo-transcriptome-analysis-of-miscanthus-lutarioriparius-identifies-candidate-genes-in-rhizome-development
#8
Ruibo Hu, Changjiang Yu, Xiaoyu Wang, Chunlin Jia, Shengqiang Pei, Kang He, Guo He, Yingzhen Kong, Gongke Zhou
HIGHLIGHTDe novo transcriptome profiling of five tissues reveals candidate genes putatively involved in rhizome development in M. lutarioriparius. Miscanthus lutarioriparius is a promising lignocellulosic feedstock for second-generation bioethanol production. However, the genomic resource for this species is relatively limited thus hampers our understanding of the molecular mechanisms underlying many important biological processes. In this study, we performed the first de novo transcriptome analysis of five tissues (leaf, stem, root, lateral bud and rhizome bud) of M...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28446747/a-systems-pharmacology-approach-to-determine-active-compounds-and-action-mechanisms-of-xipayi-kuijie-an-enema-for-treatment-of-ulcerative-colitis
#9
Wei Yu, Zhihong Li, Fei Long, Wen Chen, Yurong Geng, Zhiyong Xie, Meicun Yao, Bo Han, Teigang Liu
Xipayi Kui Jie'an (KJA), a type of traditional Uygur medicine (TUM), has shown promising therapeutic effects in Ulcerative colitis (UC). Owing to the complexity of TUM, the pharmacological mechanism of KJA remains vague. Therefore, the identification of complex molecular mechanisms is a major challenge and a new method is urgently needed to address this problem. In this study, we established a feasible pharmacological model based on systems pharmacology to identify potential compounds and targets. We also applied compound-target and target-diseases network analysis to evaluate the action mechanisms...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28445748/directional-force-originating-from-atp-hydrolysis-drives-the-groel-conformational-change
#10
Jie Liu, Kannan Sankar, Yuan Wang, Kejue Jia, Robert L Jernigan
Protein functional mechanisms usually require conformational changes, and often there are known structures for the different conformational states. However, usually neither the origin of the driving force nor the underlying pathways for these conformational transitions is known. Exothermic chemical reactions may be an important source of forces that drive conformational changes. Here we investigate this type of force originating from ATP hydrolysis in the chaperonin GroEL, by applying forces originating from the chemical reaction...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445550/classifying-patents-based-on-their-semantic-content
#11
Antonin Bergeaud, Yoann Potiron, Juste Raimbault
In this paper, we extend some usual techniques of classification resulting from a large-scale data-mining and network approach. This new technology, which in particular is designed to be suitable to big data, is used to construct an open consolidated database from raw data on 4 million patents taken from the US patent office from 1976 onward. To build the pattern network, not only do we look at each patent title, but we also examine their full abstract and extract the relevant keywords accordingly. We refer to this classification as semantic approach in contrast with the more common technological approach which consists in taking the topology when considering US Patent office technological classes...
2017: PloS One
https://www.readbyqxmd.com/read/28445293/possible-pathways-used-to-predict-different-stages-of-lung-adenocarcinoma
#12
Xiaodong Chen, Qiongyu Duan, Ying Xuan, Yunan Sun, Rong Wu
We aimed to find some specific pathways that can be used to predict the stage of lung adenocarcinoma.RNA-Seq expression profile data and clinical data of lung adenocarcinoma (stage I [37], stage II 161], stage III [75], and stage IV [45]) were obtained from the TCGA dataset. The differentially expressed genes were merged, correlation coefficient matrix between genes was constructed with correlation analysis, and unsupervised clustering was carried out with hierarchical clustering method. The specific coexpression network in every stage was constructed with cytoscape software...
April 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28444934/dynamic-iminoboronate-based-boroxine-chemistry-for-the-design-of-ambient-humidity-sensitive-self-healing-polymers
#13
Sébastien Delpierre, Bertrand Willocq, Julien De Winter, Philippe Dubois, Pascal Gerbaux, Jean-Marie Raquez
Developing intrinsic self-healing polymeric materials is of great interest nowadays to extend material lifetime and/or prevent the replacement of damaged pieces. Spontaneously humidity-sensitive healable polymer network built around dynamic covalent B-O bonds was templated by using iminoboronate-based boroxine derivatives. Taking advantage of the dynamic boroxine/boronic acid equilibrium and iminoboronate chemistry, it is possible to construct polymeric materials able to self-heal without requiring any energy-demanding external activation...
April 26, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28444041/primary-health-care-and-the-coordination-of-care-in-health-regions-managers-and-users-perspective
#14
Aylene Bousquat, Ligia Giovanella, Estela Márcia Saraiva Campos, Patty Fidelis de Almeida, Cleide Lavieri Martins, Paulo Henrique Dos Santos Mota, Maria Helena Magalhães de Mendonça, Maria Guadalupe Medina, Ana Luiza d'Ávila Viana, Márcia Cristina Rodrigues Fausto, Daniel Baffini de Paula
This paper aims to analyze the healthcare coordination by Primary Health Care (PHC), with the backdrop of building a Health Care Network (RAS) in a region in the state of São Paulo, Brazil. We conducted a case study with qualitative and quantitative approaches, proceeding to the triangulation of data between the perception of managers and experience of users. We drew analysis realms and variables from the three pillars of healthcare coordination - informational, clinical and administrative/organizational. Stroke was the tracer event chosen and therapeutic itineraries were conducted with users and questionnaires applied to the managers...
April 2017: Ciência & Saúde Coletiva
https://www.readbyqxmd.com/read/28444032/thoughts-on-the-development-of-active-regional-public-health-systems
#15
Ademar Arthur Chioro Dos Reis, Ana Paula Menezes Sóter, Lumena Almeida Castro Furtado, Silvana Souza da Silva Pereira
Decentralization and regionalization are strategic themes for reforms in the health system. This paper analyzes the complex process of health regionalization being developed in Brazil. This paper identifies that the normative framework from the Brazilian National Health System, SUS has made advances with respect to its institutionalization and overcoming the initial centrality involved in municipalization. This has strengthened the development of regionalization and the intergovernmental agreement on health but the evidence points to the need to promote a revision...
April 2017: Ciência & Saúde Coletiva
https://www.readbyqxmd.com/read/28443668/tungsten-vi-copper-i-sulfur-cluster-supported-metal-organic-frameworks-bridged-by-in-situ-click-formed-tetrazolate-ligands
#16
Qiu-Fang Chen, Xin Zhao, Quan Liu, Ji-Dong Jia, Xiao-Ting Qiu, Ying-Lin Song, David James Young, Wen-Hua Zhang, Jian-Ping Lang
Six analogous two-dimensional (2D) [Tp*WS3Cu3]-based (Tp* = hydridotris(3,5-dimethylpyrazol-1-yl)borate) networks, namely, {[(Tp*WS3Cu3)2L3](μ3-N3)}n (2: L = 5-methyltetrazolate (Mtta); 3a: L = 5-ethyltetrazolate (Etta)) and {[(Tp*WS3Cu3)2L3]BF4}n (3b: L = Etta; 4: L = 5-propyltetrazolate (Ptta); 5: L = 5-butyltetrazolate (Btta); 6: L = 5-pentyltetrazolate (Petta)) were synthesized by reactions of [Et4N][Tp*WS3] (1), [Cu(CH3CN)4]BF4, NaN3, and NH4BF4 in different nitrile solvents (CH3(CH2)nCN, n = 0, 1, 2, 3, and 4) under solvothermal conditions...
April 26, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28443230/prediction-of-optimal-gene-functions-for-osteosarcoma-using-network-based-guilt-by-association-method-based-on-gene-oncology-and-microarray-profile
#17
Xinrang Chen
In the current study, we planned to predict the optimal gene functions for osteosarcoma (OS) by integrating network-based method with guilt by association (GBA) principle (called as network-based gene function inference approach) based on gene oncology (GO) data and gene expression profile. To begin with, differentially expressed genes (DEGs) were extracted using linear models for microarray data (LIMMA) package. Then, construction of differential co-expression network (DCN) relying on DEGs was implemented, and sub-DCN was identified using Spearman correlation coefficient (SCC)...
June 2017: Journal of Bone Oncology
https://www.readbyqxmd.com/read/28442703/controllable-and-fast-quantum-information-transfer-between-distant-nodes-in-two-dimensional-networks
#18
Zhi-Rong Zhong
We construct shortcuts to adiabatic passage to achieve controllable and fast quantum-information transfer (QIT) between arbitrary two distant nodes in a two-dimensional (2D) quantum network. Through suitable designing of time-dependent Rabi frequencies, we show that perfect QIT between arbitrary two distant nodes can be rapidly achieved. Numerical simulations demonstrate that the proposal is robust to the decoherence caused by atomic spontaneous emission and cavity photon leakage. Additionally, the proposed scheme is also insensitive to the variations of the experimental parameters...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28442363/the-global-expression-profiling-in-esophageal-squamous-cell-carcinoma
#19
Fuqiang Dai, Longyong Mei, Shenglan Meng, Zheng Ma, Wei Guo, Jinghai Zhou, Jingge Zhang
Esophageal squamous cell carcinoma (ESCC) is the dominant subtype of esophageal cancer worldwide. This study aimed to explore the aberrant global expression profiling and construct regulatory network in ESCC for understanding tumorigenesis of ESCC. The expression pattern of long non-coding RNA (lncRNA), microRNA (miRNA) and mRNA was measured by RNA-sequencing in ESCC. Differentially expressed lncRNAs/miRNAs/mRNAs (DELs/DEMs/DEMIs) were identified in ESCC. DEMIs-DEMs network was constructed; hsa-miR-424-5p and hsa-miR-450b-5p were the hub miRNAs in the network, which negatively regulated 19 and 17 DEMs...
April 22, 2017: Genomics
https://www.readbyqxmd.com/read/28442194/a-child-abuse-research-network-now-what
#20
Daniel M Lindberg, Philip V Scribano
As foundational work in preparation for a sustainable, multi-center network devoted to child abuse medical research, we recently used a combination of survey and modified Delphi methodologies to determine research priorities for future multi-center studies. Avoiding missed diagnoses, and improving selected/indicated prevention were the topics rated most highly in terms of research priority. Several constructive commentaries in this issue identify the key challenges which must be overcome to ensure a successful network...
April 22, 2017: Child Abuse & Neglect
keyword
keyword
21322
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"