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https://www.readbyqxmd.com/read/28636629/minimal-oscillating-subnetwork-in-the-huang-ferrell-model-of-the-mapk-cascade
#1
Otto Hadač, František Muzika, Vladislav Nevoral, Michal Přibyl, Igor Schreiber
Prompted by the recent growing evidence of oscillatory behavior involving MAPK cascades we present a systematic approach of analyzing models and elucidating the nature of biochemical oscillations based on reaction network theory. In particular, we formulate a minimal biochemically consistent mass action subnetwork of the Huang-Ferrell model of the MAPK signalling that provides an oscillatory response when a parameter controlling the activation of the top-tier kinase is varied. Such dynamics are either intertwined with or separated from the earlier found bistable/hysteretic behavior in this model...
2017: PloS One
https://www.readbyqxmd.com/read/28635674/exploring-wound-healing-genomic-machinery-with-a-network-based-approach
#2
Francesca Vitali, Simone Marini, Martina Balli, Hanne Grosemans, Maurilio Sampaolesi, Yves A Lussier, Maria Gabriella Cusella De Angelis, Riccardo Bellazzi
The molecular mechanisms underlying tissue regeneration and wound healing are still poorly understood despite their importance. In this paper we develop a bioinformatics approach, combining biology and network theory to drive experiments for better understanding the genetic underpinnings of wound healing mechanisms and for selecting potential drug targets. We start by selecting literature-relevant genes in murine wound healing, and inferring from them a Protein-Protein Interaction (PPI) network. Then, we analyze the network to rank wound healing-related genes according to their topological properties...
June 21, 2017: Pharmaceuticals
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/28633970/unified-neural-field-theory-of-brain-dynamics-underlying-oscillations-in-parkinson-s-disease-and-generalized-epilepsies
#4
E J Müller, S J van Albada, J W Kim, P A Robinson
The mechanisms underlying pathologically synchronized neural oscillations in Parkinson's disease (PD) and generalized epilepsies are explored in parallel via a physiologically-based neural field model of the corticothalamic-basal ganglia (CTBG) system. The basal ganglia (BG) are approximated as a single effective population and their roles in the modulation of oscillatory dynamics of the corticothalamic (CT) system and vice versa are analyzed. In addition to normal EEG rhythms, enhanced activity around 4 Hz and 20 Hz exists in the model, consistent with the characteristic frequencies observed in PD...
June 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28633689/the-relationship-between-community-nutritionists-use-of-policy-systems-and-environmental-strategies-to-prevent-obesity-and-its-determinants-depends-on-networking
#5
Angela H Lu, Katherine L Dickin, Mark A Constas, Jamie S Dollahite
OBJECTIVE: To apply the Theory of Planned Behaviour to examine the relationship between the constructs of background factors and beliefs towards using policy, systems and environmental (PSE) strategies and reported use of PSE strategies to prevent obesity by a group of professional nutrition educators. DESIGN: Cross-sectional study using self-reported survey. SETTING: Cooperative Extension in New York, USA. SUBJECTS: Nutrition educators (n 58); survey response rate 100 %...
June 21, 2017: Public Health Nutrition
https://www.readbyqxmd.com/read/28633299/structural-covariance-networks-in-children-with-autism-or-adhd
#6
R A I Bethlehem, R Romero-Garcia, E Mak, E T Bullmore, S Baron-Cohen
Background: While autism and attention-deficit/hyperactivity disorder (ADHD) are considered distinct conditions from a diagnostic perspective, clinically they share some phenotypic features and have high comorbidity. Regardless, most studies have focused on only one condition, with considerable heterogeneity in their results. Taking a dual-condition approach might help elucidate shared and distinct neural characteristics. Method: Graph theory was used to analyse topological properties of structural covariance networks across both conditions and relative to a neurotypical (NT; n = 87) group using data from the ABIDE (autism; n = 62) and ADHD-200 datasets (ADHD; n = 69)...
June 13, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28630968/designing-self-powered-materials-systems-that-perform-pattern-recognition
#7
Yan Fang, Victor V Yashin, Steven P Levitan, Anna C Balazs
Inspired by the advances in both materials and computer science, we describe efforts to design "materials that compute" where the material and the computer are the same entity. Using theory and simulation, we devise systems that integrate the behavior of self-oscillating gels and fundamental concepts from oscillator-based computing. We specifically focus on gels that undergo the Belousov-Zhabotinsky (BZ) reaction and thus exhibit self-sustained oscillations. In our models, we couple the BZ gel to an overlaying piezoelectric (PZ) cantilever to create a BZ-PZ unit...
June 20, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28630457/how-impaired-efficacy-happened-between-gancao-and-yuanhua-compounds-targets-and-pathways
#8
Jin-Gao Yu, Jianming Guo, Kevin Yue Zhu, Weiwei Tao, Yanyan Chen, Pei Liu, Yongqing Hua, Yuping Tang, Jin-Ao Duan
As recorded in Traditional Chinese Medicine (TCM) theory, Gancao (Glycyrrhizae Radix et Rhizoma) could weaken the pharmacological effect or increase the toxicity of Yuanhua (Genkwa Flos). However, the theory has been suspected due to lack of evidence. Here, we investigate whether Gancao could weaken Yuanhua's diuretic effect, if so, which chemicals and which targets may be involved. Results showed that Yuanhua exerted diuretic effect through down-regulating renal AQP 2, without electrolyte disturbances such as K(+) loss which has been observed as side-effect of most diuretics...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28625853/photoelicitation-a-useful-tool-to-investigate-management-of-the-vulnerability-of-homeless-women
#9
Cristina Oter-Quintana, Teresa González-Gil, Ángel Martín-García, María Teresa Alcolea-Cosín
AIMS: The proposal of the manuscript is to provide a methodological reflection on the use of photo-elicitation as a data gathering strategy to explore vulnerability management among homeless women. METHODS: A grounded theory study was carried out. Photo elicitation was one of the data gathering techniques used between February 2015 and February 2017. Five women were selected through intentional sampling. All of them were over 18 years old and residents in 4 shelters within the Madrid Care for the Homeless network...
June 15, 2017: Enfermería Clínica
https://www.readbyqxmd.com/read/28625209/involvement-of-the-left-supramarginal-gyrus-in-manipulation-judgment-tasks-contributions-to-theories-of-tool-use
#10
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/28623871/simple-computing-of-the-viscosity-of-water-dioxane-mixtures-according-to-a-fluctuating-spc-e-ih-interstitial-model
#11
Anis Ghazouani, Jalel M'halla
In this contribution, we propose a new simple and fast computing approach to model liquid water and water-1,4 dioxane mixture, which is intermediate between molecular dynamics calculation and lattice fluid H-bonding theory in which water molecules are arranged according to a fluctuating hexagonal Ih network. It generalizes the interstitial mixture models of Samoilov and Pauling by increasing the number of spatial configurations into the space of phases due to the addition of rotations and vibrations of the molecules around their equilibrium positions...
June 17, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28623705/counter-ion-transport-number-and-membrane-potential-in-working-membrane-systems
#12
Mette Birch Kristensen, Anders Bentien, Michele Tedesco, Jacopo Catalano
In this work we use the general space-charge (SC) theory for a combined transport model of fluid and ion through cylindrical nanopores to derive equations for the membrane potential and counter-ion transport numbers. We discuss this approach for ion exchange membranes assuming aqueous domains as interconnected network of cylindrical pores. The transport number calculations from the SC theory are compared with the corresponding ones from the uniform potential (UP) and Teorell-Meyer-Sievers (TMS) models in the case of both zero and non-zero concentration gradient across the membrane and with an applied current density...
June 8, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28623593/boolean-dynamic-modeling-approaches-to-study-plant-gene-regulatory-networks-integration-validation-and-prediction
#13
José Dávila Velderraín, Juan Carlos Martínez-García, Elena R Álvarez-Buylla
Mathematical models based on dynamical systems theory are well-suited tools for the integration of available molecular experimental data into coherent frameworks in order to propose hypotheses about the cooperative regulatory mechanisms driving developmental processes. Computational analysis of the proposed models using well-established methods enables testing the hypotheses by contrasting predictions with observations. Within such framework, Boolean gene regulatory network dynamical models have been extensively used in modeling plant development...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28622676/training-dcnn-by-combining-max-margin-max-correlation-objectives-and-correntropy-loss-for-multilabel-image-classification
#14
Weiwei Shi, Yihong Gong, Xiaoyu Tao, Nanning Zheng
In this paper, we build a multilabel image classifier using a general deep convolutional neural network (DCNN). We propose a novel objective function that consists of three parts, i.e., max-margin objective, max-correlation objective, and correntropy loss. The max-margin objective explicitly enforces that the minimum score of positive labels must be larger than the maximum score of negative labels by a predefined margin, which not only improves accuracies of the multilabel classifier, but also eases the threshold determination...
June 13, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28622528/band-specific-atypical-functional-connectivity-pattern-in-childhood-autism-spectrum-disorder
#15
Tetsuya Takahashi, Teruya Yamanishi, Sou Nobukawa, Shinya Kasakawa, Yuko Yoshimura, Hirotoshi Hiraishi, Chiaki Hasegawa, Takashi Ikeda, Tetsu Hirosawa, Toshio Munesue, Haruhiro Higashida, Yoshio Minabe, Mitsuru Kikuchi
OBJECTIVE: Altered brain connectivity has been theorized as a key neural underpinning of autism spectrum disorder (ASD), but recent investigations have revealed conflicting patterns of connectivity, particularly hyper-connectivity and hypo-connectivity across age groups. The application of graph theory to neuroimaging data has become an effective approach for characterizing topographical patterns of large-scale functional networks. We used a graph approach to investigate alteration of functional networks in childhood ASD...
May 23, 2017: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/28622282/towards-a-neurobiological-understanding-of-alexithymia
#16
REVIEW
Nicolás Meza-Concha, Marcelo Arancibia, Felicia Salas, Rosa Behar, Germán Salas, Hernán Silva, Rocío Escobar
Although the specialized literature on the etiology of alexithymia is controversial, neurobiological research has shown relevant advances. The aim of this review is to analyze the available evidence regarding the neurophysiological bases of alexithymia. A comprehensive review of available articles from Medline/PubMed, EBSCO and SciELO was conducted. Previously, alexithymia was linked to a reduced interhemispheric brain connection. From a childhood traumatic perspective, the right prefrontal cortex and the default mode network would experience alterations, first hypermetabolic (dopaminergic and glutamatergic dysregulation) and then hypometabolic-dissociative (serotonergic and opioid dysregulation), resulting in a distorted interoceptive and emotional awareness...
May 29, 2017: Medwave
https://www.readbyqxmd.com/read/28620239/shared-and-specific-intrinsic-functional-connectivity-patterns-in-unmedicated-bipolar-disorder-and-major-depressive-disorder
#17
Ying Wang, Junjing Wang, Yanbin Jia, Shuming Zhong, Meiqi Niu, Yao Sun, Zhangzhang Qi, Ling Zhao, Li Huang, Ruiwang Huang
Identifying brain differences and similarities between bipolar disorder (BD) and major depressive disorder (MDD) is necessary for increasing our understanding of the pathophysiology and for developing more effective treatments. However, the features of whole-brain intrinsic functional connectivity underlying BD and MDD have not been directly compared. We collected resting-state fMRI data from 48 BD patients, 48 MDD patients, and 51 healthy subjects. We constructed voxel-wise whole-brain functional networks and computed regional functional connectivity strength (FCS) using graph-theory and further divided the regional FCS into long-range FCS (lFCS) and short-range FCS (sFCS)...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28620215/theta-band-transcranial-alternating-current-stimulations-modulates-network-behavior-of-dorsal-anterior-cingulate-cortex
#18
Keiichi Onoda, Toshikazu Kawagoe, Haixia Zheng, Shuhei Yamaguchi
Dorsal anterior cingulate cortex (dACC) is an important region in the processing of both cognition and affect. Recently, transcranial brain stimulation has been used to modulate cortical activity, but it is unclear whether this stimulation has a specific effect on dACC. Based on EEG evidence that frontal midline theta activity is generated in dACC, we hypothesized that transcranial alternating current stimulation (tACS) with theta band frequency would modulate neural networks including dACC. In this study, we examined the effects of theta band tACS on functional networks and emotional state...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28619656/the-large-scale-functional-connectivity-correlates-of-consciousness-and-arousal-during-the-healthy-and-pathological-human-sleep-cycle
#19
REVIEW
Enzo Tagliazucchi, Eus J W van Someren
Advances in neuroimaging have greatly improved our understanding of human sleep from a systems neuroscience perspective. However, cognition and awareness are reduced during sleep, hindering the applicability of standard task-based paradigms. Methods recently developed to study spontaneous brain activity fluctuations have proven useful to overcome this limitation. In this review, we focus on the concept of functional connectivity (FC, i.e. statistical covariance between brain activity signals) and its application to functional magnetic resonance imaging (fMRI) data acquired during sleep...
June 12, 2017: NeuroImage
https://www.readbyqxmd.com/read/28618829/detection-of-an-undersea-acoustic-communications-network-by-an-energy-detector
#20
Richard C Shockley, Paul J Gendron, J Mark Stevenson
A theory is presented for the upper bound on the mean time τ to the detection of an undersea acoustic communications network by an energy detector whose initial position and heading are uniformly distributed random variables. The network is an infinite square grid of omnidirectional transmit-receive nodes on a flat bottom. Each node transmits to one nearest neighbor at a bit-rate R equal to Shannon's capacity, maximizing τ. The network sets a signaling bandwidth W and node-spacing D. The detector sets a false-alarm rate, integration time, height above the bottom, and speed...
June 2017: Journal of the Acoustical Society of America
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