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https://www.readbyqxmd.com/read/28732056/inferring-microbial-interactions-in-thermophilic-and-mesophilic-anaerobic-digestion-of-hog-waste
#1
Grace Tzun-Wen Shaw, An-Chi Liu, Chieh-Yin Weng, Chu-Yang Chou, Daryi Wang
Anaerobic digestion (AnD) is a microbiological process that converts organic waste materials into biogas. Because of its high methane content, biogas is a combustible energy source and serves as an important environmental technology commonly used in the management of animal waste generated on large animal farms. Much work has been done on hardware design and process engineering for the generation of biogas. However, little is known about the complexity of the microbiology in this process. In particular, how microbes interact in the digester and eventually breakdown and convert organic matter into biogas is still regarded as a "black box...
2017: PloS One
https://www.readbyqxmd.com/read/28732007/a-data-driven-modeling-approach-to-identify-disease-specific-multi-organ-networks-driving-physiological-dysregulation
#2
Warren D Anderson, Danielle DeCicco, James S Schwaber, Rajanikanth Vadigepalli
Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension). We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28731695/how-rhodopsin-tunes-the-equilibrium-between-protonated-and-deprotonated-forms-of-the-retinal-chromophore
#3
Siri Camee van Keulen, Alicia Solano, Ursula Rothlisberger
Rhodopsin is a photoactive G-protein-coupled receptor (GPCR) that converts dim light into a signal for the brain, leading to eyesight. Full activation of this GPCR is achieved after passing through several steps of the protein's photoactivation pathway. Key events of rhodopsin activation are the initial cis-trans photoisomerisation of the covalently bound retinal moiety followed by conformational rearrangements and deprotonation of the chromophore's protonated Schiff base (PSB), which ultimately lead to full activation in the meta II state...
July 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28731639/exploring-family-home-food-environments-household-resources-needed-to-utilise-weekly-deliveries-of-free-fruits-and-vegetables
#4
Sophie A Carty, Louise A Mainvil, John D Coveney
AIM: An adapted ethnographic approach was used to explore household factors that influence family fruit and vegetable consumption when access and cost barriers are removed. 'Structural' barriers, such as food affordability and accessibility, are likely to influence fruit and vegetable consumption in disadvantaged households, but households may require additional resources (human and social) to increase consumption. METHODS: Five low-income and five high-income households with children (N = 39 individuals) were observed in their home environment for three months...
April 2017: Nutrition & Dietetics: the Journal of the Dietitians Association of Australia
https://www.readbyqxmd.com/read/28731479/marine-archaeal-dynamics-and-interactions-with-the-microbial-community-over-5-years-from-surface-to-seafloor
#5
Alma E Parada, Jed A Fuhrman
Marine archaea are critical contributors to global carbon and nitrogen redox cycles, but their temporal variability and microbial associations across the water column are poorly known. We evaluated seasonal variability of free living (0.2-1 μm size fraction) Thaumarchaea Marine Group I (MGI) and Euryarchaea Marine Group II (MGII) communities and their associations with the microbial community from surface to seafloor (890 m) over 5 years by 16S rRNA V4-V5 gene sequencing. MGI and MGII communities demonstrated distinct compositions at different depths, and seasonality at all depths...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731098/a-reaction-model-on-the-self-assembly-process-of-octahedron-shaped-coordination-capsules
#6
Yoshihiro Matsumura, Shuichi Hiraoka, Hirofumi Sato
Herein, the self-assembly process of an octahedron-shaped coordination capsule was analyzed based on a master equation approach using a reaction network model. This model was found to adequately reproduce the overall experimentally observed time evolutions and enabled us to trace the real-time evolution of transient intermediates, ranging from milli-second to hours. The time evolution of the distribution of individual intermediates species was obtained; a few linear-oligomers located near the reactant were produced at first, followed by an explosive increase in several types of intermediates...
July 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28730495/modeling-of-receptor-tyrosine-kinase-signaling-computational-and-experimental-protocols
#7
Dirk Fey, Edita Aksamitiene, Anatoly Kiyatkin, Boris N Kholodenko
The advent of systems biology has convincingly demonstrated that the integration of experiments and dynamic modelling is a powerful approach to understand the cellular network biology. Here we present experimental and computational protocols that are necessary for applying this integrative approach to the quantitative studies of receptor tyrosine kinase (RTK) signaling networks. Signaling by RTKs controls multiple cellular processes, including the regulation of cell survival, motility, proliferation, differentiation, glucose metabolism, and apoptosis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730491/development-of-selected-reaction-monitoring-methods-to-systematically-quantify-kinase-abundance-and-phosphorylation-stoichiometry-in-human-samples
#8
Kirsten Beck, Nathan Camp, Michael Bereman, James Bollinger, Jarrett Egertson, Michael MacCoss, Alejandro Wolf-Yadlin
Protein phosphorylation, one of the most common types of post-translational modifications, is the central regulatory mechanism of cellular signaling networks. In human cells, thousands of proteins are continuously and dynamically phosphorylated and dephosphorylated at specific sites and times in response to external and internal stimuli. Reversible phosphorylation is facilitated by the action of two protein superfamilies: kinases and phosphatases. Kinases play an essential role in almost every relevant physiological process in human cells and their deregulation is linked to pathologies ranging from cancer to autoimmune diseases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730490/mass-spectrometry-analysis-of-spatial-protein-networks-by-colocalization-analysis-cola
#9
Faraz K Mardakheh
A major challenge in systems biology is comprehensive mapping of protein interaction networks. Crucially, such interactions are often dynamic in nature, necessitating methods that can rapidly mine the interactome across varied conditions and treatments to reveal change in the interaction networks. Recently, we described a fast mass spectrometry-based method to reveal functional interactions in mammalian cells on a global scale, by revealing spatial colocalizations between proteins (COLA) (Mardakheh et al., Mol Biosyst 13:92-105, 2017)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729938/abnormal-resting-state-effective-connectivity-within-the-default-mode-network-in-major-depressive-disorder-a-spectral-dynamic-causal-modeling-study
#10
Liang Li, Baojuan Li, Yuanhan Bai, Wenlei Liu, Huaning Wang, Hoi-Chung Leung, Ping Tian, Linchuan Zhang, Fan Guo, Long-Biao Cui, Hong Yin, Hongbing Lu, Qingrong Tan
INTRODUCTION: Understanding the neural basis underlying major depressive disorder (MDD) is essential for the diagnosis and treatment of this mental disorder. Aberrant activation and functional connectivity of the default mode network (DMN) have been consistently found in patients with MDD. It is not known whether effective connectivity within the DMN is altered in MDD. OBJECTS: The primary object of this study is to investigate the effective connectivity within the DMN during resting state in MDD patients before and after eight weeks of antidepressant treatment...
July 2017: Brain and Behavior
https://www.readbyqxmd.com/read/28729711/an-ecological-and-digital-epidemiology-analysis-on-the-role-of-human-behavior-on-the-2014-chikungunya-outbreak-in-martinique
#11
Benjamin Roche, Béatrice Gaillard, Lucas Léger, Renélise Pélagie-Moutenda, Thomas Sochacki, Bernard Cazelles, Martine Ledrans, Alain Blateau, Didier Fontenille, Manuel Etienne, Frédéric Simard, Marcel Salathé, André Yébakima
Understanding the spatio-temporal dynamics of endemic infections is of critical importance for a deeper understanding of pathogen transmission, and for the design of more efficient public health strategies. However, very few studies in this domain have focused on emerging infections, generating a gap of knowledge that hampers epidemiological response planning. Here, we analyze the case of a Chikungunya outbreak that occurred in Martinique in 2014. Using time series estimates from a network of sentinel practitioners covering the entire island, we first analyze the spatio-temporal dynamics and show that the largest city has served as the epicenter of this epidemic...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729647/neural-determinants-of-human-goal-directed-vs-habitual-action-control-and-their-relation-to-trait-motivation
#12
Hamdi Eryilmaz, Anais Rodriguez-Thompson, Alexandra S Tanner, Madeline Giegold, Franklin C Huntington, Joshua L Roffman
Instrumental learning is mediated by goal-directed and habit systems in the brain. While rodent studies implicate distinct prefrontal/striatal regions in goal-directed and habit learning, neural systems underpinning these two processes in humans remain poorly understood. Here, using a validated discrimination learning task that distinguishes goal-directed learning from habit learning in 72 subjects in fMRI, we investigated the corticostriatal correlates of goal-directed learning and tested whether brain activation during learning is associated with trait motivation and behavioral performance in the post-learning test phase...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729607/effective-methods-of-restraining-diffusion-in-terms-of-epidemic-dynamics
#13
Fei Xiong, Zhao-Yi Li
Removing influential nodes or shortcuts in a network restrains epidemic or information diffusion, but this method destroys the connectivity of the network and changes the topological structure. As an alternative, an additional field can be imposed in the network to affect node behaviors and slow down diffusion dynamics. However, little research has been performed systematically to analyze and compare these methods. This paper investigates epidemic dynamics and proposes the following four methods to restrain the diffusion process: blocking nodes, blocking edges, distracting node attention, and propagating opposite information...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729309/the-role-of-a-decision-support-smartphone-application-in-enhancing-community-health-volunteers-effectiveness-to-improve-maternal-and-newborn-outcomes-in-nairobi-kenya-quasi-experimental-research-protocol
#14
Pauline Bakibinga, Eva Kamande, Milka Omuya, Abdhalah K Ziraba, Catherine Kyobutungi
INTRODUCTION: Improving maternal and newborn survival remains major aspirations for many countries in the Global South. Slum settlements, a result of rapid urbanisation in many developing countries including Kenya, exhibit high levels of maternal and neonatal mortality. There are limited referral mechanisms for sick neonates and their mothers from the community to healthcare facilities with ability to provide adequate care. In this study, we specifically plan to develop and assess the added value of having community health volunteers (CHVs) use smartphones to identify and track mothers and children in a bid to reduce pregnancy-related complications and newborn deaths in the urban slums of Kamukunji subcounty in Nairobi, Kenya...
July 20, 2017: BMJ Open
https://www.readbyqxmd.com/read/28728968/hybrid-time-space-dynamical-systems-of-growth-bacteria-with-applications-in-segmentation
#15
Rabha W Ibrahim, Hemant K Nashine, Norshaliza Kamaruddin
A biological dynamic system carries engineering properties such as control systems and signal processing (or image processing) addicted to molecular biology at the level of bio-molecular communication networks. Dynamical system features and signal reply functions of cellular signaling pathways are some of the main topics in biological dynamic systems (for example the biological segmentation). In the present paper, we introduce new generalized hybrid time-space dynamical systems of growing bacteria. We impose the approximate analytic solution for the system...
July 17, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28728677/dynamically-timed-stimulation-of-corticolimbic-circuitry-activates-a-stress-compensatory-pathway
#16
David Carlson, Lisa K David, Neil M Gallagher, Mai-Anh T Vu, Matthew Shirley, Rainbo Hultman, Joyce Wang, Caley Burrus, Colleen A McClung, Sunil Kumar, Lawrence Carin, Stephen D Mague, Kafui Dzirasa
BACKGROUND: The prefrontal cortex plays a critical role in regulating emotional behaviors, and dysfunction of prefrontal cortex-dependent networks has been broadly implicated in mediating stress-induced behavioral disorders including major depressive disorder. METHODS: Here we acquired multicircuit in vivo activity from eight cortical and limbic brain regions as mice were subjected to the tail suspension test (TST) and an open field test. We used a linear decoder to determine whether cellular responses across each of the cortical and limbic areas signal movement during the TST and open field test...
June 15, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/28728423/changing-antibiotic-prescribing-in-a-primary-care-network-the-role-of-readiness-to-change-and-group-dynamics-in-success
#17
Suratha Elango, Julia E Szymczak, Ian M Bennett, Rinad S Beidas, Rachel M Werner
Overuse of broad-spectrum antibiotics in outpatient pediatrics remains a significant issue and there is limited evidence on how to effectively implement outpatient stewardship interventions. This study examines the relationship between readiness to change and modifiable factors affecting success of a primary care network antibiotic stewardship intervention. A survey designed to measure readiness to accept a health care innovation was administered to 209 clinicians. Practices were split in half into "high" versus "low" readiness to change...
July 1, 2017: American Journal of Medical Quality: the Official Journal of the American College of Medical Quality
https://www.readbyqxmd.com/read/28727829/functional-differentiation-and-spatial-temporal-co-expression-networks-of-the-nbs-encoding-gene-family-in-jilin-ginseng-panax-ginseng-c-a-meyer
#18
Rui Yin, Mingzhu Zhao, Kangyu Wang, Yanping Lin, Yanfang Wang, Chunyu Sun, Yi Wang, Meiping Zhang
Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal plants for human health and medicine. It has been documented that over 80% of genes conferring resistance to bacteria, viruses, fungi and nematodes are contributed by the nucleotide binding site (NBS)-encoding gene family. Therefore, identification and characterization of NBS genes expressed in ginseng are paramount to its genetic improvement and breeding. However, little is known about the NBS-encoding genes in ginseng. Here we report genome-wide identification and systems analysis of the NBS genes actively expressed in ginseng (PgNBS genes)...
2017: PloS One
https://www.readbyqxmd.com/read/28727566/model-free-adaptive-control-for-unknown-nonlinear-zero-sum-differential-game
#19
Xiangnan Zhong, Haibo He, Ding Wang, Zhen Ni
In this paper, we present a new model-free globalized dual heuristic dynamic programming (GDHP) approach for the discrete-time nonlinear zero-sum game problems. First, the online learning algorithm is proposed based on the GDHP method to solve the Hamilton-Jacobi-Isaacs equation associated with H∞ optimal regulation control problem. By setting backward one step of the definition of performance index, the requirement of system dynamics, or an identifier is relaxed in the proposed method. Then, three neural networks are established to approximate the optimal saddle point feedback control law, the disturbance law, and the performance index, respectively...
July 17, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28727558/understanding-robust-adaptation-dynamics-of-gene-regulatory-network
#20
Xiao-Na Huang, Hai-Peng Ren
Robust adaptation is a critical attribute for gene regulatory network (GRN), understanding the relationship between adaptation and the GRN topology, and corresponding parameters is a challenging issue. The work in this paper includes: first, seven constraint multiobjective optimization algorithms are used to find sufficient solutions to get more reliable statistic rules. Meanwhile, the algorithms are compared to facilitate the future algorithm selection; second, a fuzzy c-mean algorithm is used to analyze solutions and to classify the solutions into different groups; third, the histogram analysis for all satisfactory solutions shows the preferred parameter range, i...
July 18, 2017: IEEE Transactions on Biomedical Circuits and Systems
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