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Complex Network

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https://www.readbyqxmd.com/read/29031098/stepwise-construction-of-a-metabolic-network-in-event-b-the-heat-shock-response
#1
Usman Sanwal, Luigia Petre, Ion Petre
There is a high interest in constructing large, detailed computational models for biological processes. This is often done by putting together existing submodels and adding to them extra details/knowledge. The result of such approaches is usually a model that can only answer questions on a very specific level of detail, and thus, ultimately, is of limited use. We focus instead on an approach to systematically add details to a model, with formal verification of its consistency at each step. In this way, one obtains a set of reusable models, at different levels of abstraction, to be used for different purposes depending on the question to address...
September 30, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29031031/riceanthernet-a-gene-co-expression-network-for-identifying-anther-and-pollen-development-genes
#2
Hong Lin, Jing Yu, Simon Pearce, Dabing Zhang, Zoe Wilson
In plants, normal anther and pollen development involves many important biological events and complex molecular regulatory coordination. Understanding gene regulatory relationships during male reproductive development is essential for fundamental biology and crop breeding. In this work, we developed a rice gene co-expression network for anther development (RiceAntherNet) that allows prediction of gene regulatory relationships during pollen development. RiceAntherNet was generated from 57 rice anther tissue microarrays across all developmental stages...
October 14, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29029246/the-epidermal-growth-factor-network-role-in-oocyte-growth-maturation-and-developmental-competence
#3
Dulama Richani, Robert B Gilchrist
BACKGROUND: The LH surge induces great physiological changes within the preovulatory follicle, which culminate in the ovulation of a mature oocyte that is capable of supporting embryo and foetal development. However, unlike mural granulosa cells, the oocyte and its surrounding cumulus cells are not directly responsive to LH, indicating that the LH signal is mediated by secondary factors produced by the granulosa cells. The mechanisms by which the oocyte senses the ovulatory LH signal and hence prepares for ovulation has been a subject of considerable controversy for the past four decades...
September 20, 2017: Human Reproduction Update
https://www.readbyqxmd.com/read/29028982/trove-a-user-friendly-tool-for-visualizing-and-analyzing-cancer-hallmarks-in-signaling-networks
#4
Huey Eng Chua, Sourav S Bhowmick, Jie Zheng
Summary: Cancer hallmarks, a concept that seeks to explain the complexity of cancer initiation and development, provide a new perspective of studying cancer signaling which could lead to a greater understanding of this complex disease. However, to the best of our knowledge, there is currently a lack of tools that support such hallmark-based study of the cancer signaling network, thereby impeding the gain of knowledge in this area. We present TROVE, a user-friendly software that facilitates hallmark annotation, visualization and analysis in cancer signaling networks...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028941/dysregulation-of-cortical-neuron-dna-methylation-profile-in-autism-spectrum-disorder
#5
Stefano Nardone, Dev Sharan Sams, Antonino Zito, Eli Reuveni, Evan Elliott
Autism Spectrum Disorder (ASD) is a complex neuropsychiatric syndrome whose etiology includes genetic and environmental components. Since epigenetic marks are sensitive to environmental insult, they may be involved in the development of ASD. Initial brain studies have suggested a dysregulation of epigenetic marks in ASD. However, due to cellular heterogeneity in the brain, these studies have not determined if there is a true change in the neuronal epigenetic signature. Here, we report a genome-wide methylation study on fluorescence-activated cell sorting-sorted neuronal nuclei from the frontal cortex of 16 male ASD and 15 male control subjects...
September 28, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/29028906/critical-assessment-and-performance-improvement-of-plant-pathogen-protein-protein-interaction-prediction-methods
#6
Shiping Yang, Hong Li, Huaqin He, Yuan Zhou, Ziding Zhang
The identification of plant-pathogen protein-protein interactions (PPIs) is an attractive and challenging research topic for deciphering the complex molecular mechanism of plant immunity and pathogen infection. Considering that the experimental identification of plant-pathogen PPIs is time-consuming and labor-intensive, computational methods are emerging as an important strategy to complement the experimental methods. In this work, we first evaluated the performance of traditional computational methods such as interolog, domain-domain interaction and domain-motif interaction in predicting known plant-pathogen PPIs...
September 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29028356/aggregation-of-a-cationic-gemini-surfactant-with-a-chelating-molecule-and-effects-from-calcium-ion
#7
Weiwei Zhao, Kai Song, Yao Chen, Hua Wang, Zhang Liu, Qiang Shi, Jianbin Huang, Yilin Wang
The aggregation behavior of a cationic ammonium gemini surfactant hexamethylene-1,6-bis(dodecyldimethylammonium bromide) (12-6-12) with a chelating molecule ethylenediaminetetraacetic acid (EDTA) and the effects of calcium bromide (CaBr2) on the structure and morphology of the aggregates in the mixture have been investigated by surface tension, isothermal titration microcalorimetry, electrical conductivity, ζ potential, dynamic light scattering, cryogenic transmission electron microscopy, freeze-fracture transmission electron microscopy and 1H NMR techniques...
October 13, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29028348/directed-organization-of-platinum-nanocrystals-through-organic-supramolecular-nanoporous-templates
#8
Farid Kameche, Alice Six, Fabrice Charra, Anh Tu Ngo, Fabrice Mathevet, Caroline Salzemann, David Kreher, Imad Arfaoui, André-Jean Attias, Christophe Petit
We propose a novel approach to trap 2 nm Pt nanocrystals using nanoporous two-dimensional supramolecular networks for cavity-confined host-guest recognition process. This will be achieved by taking advantage of two features of supramolecular self-assembly at surfaces. First, its capability to allow to the formation of complex 2D architectures, more particularly nanoporous networks, through non-covalent interactions between organic molecular building-blocks. Second, the ability of the nanopores to selectively host and immobilize a large variety of guest species...
October 13, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29028334/dynamic-control-of-aptamer-ligand-activity-using-strand-displacement-reactions
#9
Jonathan Lloyd, Claire H Tran, Krishen Wadhwani, Christian Cuba Samaniego, Hari K K Subramanian, Elisa Franco
Nucleic acid aptamers are an expandable toolkit of sensors and regulators. To employ aptamer regulators within non-equilibrium molecular networks, the aptamer-ligand interactions should be tunable over time, so that functions within a given system can be activated or suppressed on demand. This is accomplished through complementary sequences to aptamers, which achieve programmable aptamer-ligand dissociation by displacing the aptamer from the ligand. We demonstrate the effectiveness of our simple approach on light-up aptamers as well as on aptamers inhibiting viral RNA polymerases, dynamically controlling the functionality of the aptamer-ligand complex...
October 13, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29028235/how-to-include-public-health-practice-and-practitioners-in-a-european-network
#10
Silvio Brusaferro, Pierfrancesco Tricarico
There is a wide range of different Public Health (PH) activities and programs running in Europe. Besides the richness of national traditions, differences exist in numbers of programs, methods adopted, types of engaged professionals, available resources (including public investments), awareness to the problem and finally in health indicators among and within countries. Promoting networks of PH practices and practitioners strengthens the possibility to share knowledge across organizational, sectorial and geographic boundaries, promotes adaptation and local implementation, fosters innovation in the form of knowledge creation by developing more efficient new services and by sharing effective practices within and between organizations and sectors...
October 1, 2017: European Journal of Public Health
https://www.readbyqxmd.com/read/29028232/towards-an-overarching-european-health-information-system
#11
Marieke Verschuuren, Annemiek van Bolhuis, Nicole Rosenkötter, Mariken Tijhuis, Hans van Oers
A European health information system (HIS) supports mutual learning between member states through international comparisons. In addition, it informs international policy agendas. Collaboration between the major stakeholders, most importantly the World Health Organization Regional Office for Europe (WHO-Euro), the European Commission and OECD, is important for member states, as this will contribute to better and more efficiently produced health intelligence. This paper focuses on this 'supra-international' collaboration...
October 1, 2017: European Journal of Public Health
https://www.readbyqxmd.com/read/29028218/activity-recognition-using-complex-network-analysis
#12
Nahed Jalloul, Fabienne Poree, Geoffrey Viardot, Phillipe L'Hostis, Guy Carrault
In this paper, we perform complex network analysis on a connectivity dataset retrieved from a monitoring system in order to classify simple daily activities. The monitoring system is composed of a set of wearable sensing modules positioned on the subject's body and the connectivity data consists of the correlation between each pair of modules. A number of network measures are then computed followed by the application of statistical significance and feature selection methods. These methods were implemented for the purpose of reducing the total number of modules in the monitoring system required to provide accurate activity classification...
October 12, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/29028000/influence-of-resistance-breeding-in-common-bean-on-rhizosphere-microbiome-composition-and-function
#13
Lucas William Mendes, Jos M Raaijmakers, Mattias de Hollander, Rodrigo Mendes, Siu Mui Tsai
The rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027948/comparing-the-performance-of-indoor-localization-systems-through-the-evaal-framework
#14
Francesco Potortì, Sangjoon Park, Antonio Ramón Jiménez Ruiz, Paolo Barsocchi, Michele Girolami, Antonino Crivello, So Yeon Lee, Jae Hyun Lim, Joaquín Torres-Sospedra, Fernando Seco, Raul Montoliu, Germán Martin Mendoza-Silva, Maria Del Carmen Pérez Rubio, Cristina Losada-Gutiérrez, Felipe Espinosa, Javier Macias-Guarasa
In recent years, indoor localization systems have been the object of significant research activity and of growing interest for their great expected social impact and their impressive business potential. Application areas include tracking and navigation, activity monitoring, personalized advertising, Active and Assisted Living (AAL), traceability, Internet of Things (IoT) networks, and Home-land Security. In spite of the numerous research advances and the great industrial interest, no canned solutions have yet been defined...
October 13, 2017: Sensors
https://www.readbyqxmd.com/read/29027943/low-grade-dysplastic-nodules-revealed-as-the-tipping-point-during-multistep-hepatocarcinogenesis-by-dynamic-network-biomarkers
#15
Lina Lu, Zhonglin Jiang, Yulin Dai, Luonan Chen
Hepatocellular carcinoma (HCC) is a complex disease with a multi-step carcinogenic process from preneoplastic lesions, including cirrhosis, low-grade dysplastic nodules (LGDNs), and high-grade dysplastic nodules (HGDNs) to HCC. There is only an elemental understanding of its molecular pathogenesis, for which a key problem is to identify when and how the critical transition happens during the HCC initiation period at a molecular level. In this work, for the first time, we revealed that LGDNs is the tipping point (i...
October 13, 2017: Genes
https://www.readbyqxmd.com/read/29027238/a-deep-convolutional-neural-network-using-directional-wavelets-for-low-dose-x-ray-ct-reconstruction
#16
Eunhee Kang, Junhong Min, Jong Chul Ye
PURPOSE: Due to the potential risk of inducing cancer, radiation exposure by X-ray CT devices should be reduced for routine patient scanning. However, in low-dose X-ray CT, severe artifacts typically occur due to photon starvation, beam hardening, and other causes, all of which decrease the reliability of the diagnosis. Thus, a high-quality reconstruction method from low-dose X-ray CT data has become a major research topic in the CT community. Conventional model-based de-noising approaches are, however, computationally very expensive, and image-domain de-noising approaches cannot readily remove CT-specific noise patterns...
October 2017: Medical Physics
https://www.readbyqxmd.com/read/29026903/the-effect-of-cognitive-demand-on-performance-of-an-executive-function-task-following-wild-blueberry-supplementation-in-7-to-10-years-old-children
#17
A R Whyte, G Schafer, C M Williams
The cognitive benefits of acute flavonoid interventions have been well documented, however, research to date has found that, depending on developmental stage, these benefits manifest themselves in different cognitive domains. It is argued that the lack of global cognitive effects following flavonoid intervention may be a result of insufficient task sensitivity for those domains where no benefits are found. In children, executive function is a cognitive domain which has shown little apparent benefit following flavonoid intervention...
October 13, 2017: Food & Function
https://www.readbyqxmd.com/read/29026837/binding-site-analysis-of-the-caenorhabditis-elegans-nr4a-nuclear-receptor-nhr-6-during-development
#18
Brandon Praslicka, Jeremy S Harmson, Joohyun Kim, Vittobai Rashika Rangaraj, Aikseng Ooi, Chris R Gissendanner
Members of the NR4A subfamily of nuclear receptors make up a highly conserved, functionally diverse group of transcription factors implicated in a multitude of cellular processes such as proliferation, differentiation, apoptosis, metabolism and DNA repair. The gene nhr-6, which encodes the sole C. elegans NR4A nuclear receptor homolog, has a critical role in organogenesis and regulates the development of the spermatheca organ system. Our previous work revealed that nhr-6 is required for spermatheca cell divisions in late L3 and early L4 and spermatheca cell differentiation during the mid L4 stage...
2017: Nuclear Receptor Research
https://www.readbyqxmd.com/read/29026654/population-genetic-structuring-of-methicillin-resistant-staphylococcus-aureus-clone-emrsa-15-within-uk-reflects-patient-referral-patterns
#19
Tjibbe Donker, Sandra Reuter, James Scriberras, Rosy Reynolds, Nicholas M Brown, M Estée Török, Richard James, East Of England Microbiology Research Network, David M Aanensen, Stephen D Bentley, Matthew T G Holden, Julian Parkhill, Brian G Spratt, Sharon J Peacock, Edward J Feil, Hajo Grundmann
Antibiotic resistance forms a serious threat to the health of hospitalised patients, rendering otherwise treatable bacterial infections potentially life-threatening. A thorough understanding of the mechanisms by which resistance spreads between patients in different hospitals is required in order to design effective control strategies. We measured the differences between bacterial populations of 52 hospitals in the United Kingdom and Ireland, using whole-genome sequences from 1085 MRSA clonal complex 22 isolates collected between 1998 and 2012...
July 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29025971/role-of-connexin-43-in-different-forms-of-intercellular-communication-gap-junctions-extracellular-vesicles-and-tunnelling-nanotubes
#20
REVIEW
Teresa M Ribeiro-Rodrigues, Tânia Martins-Marques, Sandrine Morel, Brenda R Kwak, Henrique Girão
Communication is important to ensure the correct and efficient flow of information, which is required to sustain active social networks. A fine-tuned communication between cells is vital to maintain the homeostasis and function of multicellular or unicellular organisms in a community environment. Although there are different levels of complexity, intercellular communication, in prokaryotes to mammalians, can occur through secreted molecules (either soluble or encapsulated in vesicles), tubular structures connecting close cells or intercellular channels that link the cytoplasm of adjacent cells...
October 12, 2017: Journal of Cell Science
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