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https://www.readbyqxmd.com/read/29353313/general-solution-of-the-chemical-master-equation-and-modality-of-marginal-distributions-for-hierarchic-first-order-reaction-networks
#1
Matthias Reis, Justus A Kromer, Edda Klipp
Multimodality is a phenomenon which complicates the analysis of statistical data based exclusively on mean and variance. Here, we present criteria for multimodality in hierarchic first-order reaction networks, consisting of catalytic and splitting reactions. Those networks are characterized by independent and dependent subnetworks. First, we prove the general solvability of the Chemical Master Equation (CME) for this type of reaction network and thereby extend the class of solvable CME's. Our general solution is analytical in the sense that it allows for a detailed analysis of its statistical properties...
January 20, 2018: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/29353280/microstructure-of-strategic-white-matter-tracts-and-cognition-in-memory-clinic-patients-with-vascular-brain-injury
#2
J Matthijs Biesbroek, Alexander Leemans, Hanna den Bakker, Marco Duering, Benno Gesierich, Huiberdina L Koek, Esther van den Berg, Albert Postma, Geert Jan Biessels
BACKGROUND: White matter injury is an important factor for cognitive impairment in memory clinic patients. We determined the added value of diffusion tensor imaging (DTI) of strategic white matter tracts in explaining variance in cognition in memory clinic patients with vascular brain injury. METHODS: We included 159 patients. Conventional MRI markers (white matter hyperintensity volume, lacunes, nonlacunar infarcts, brain atrophy, and microbleeds), and fractional anisotropy and mean diffusivity (MD) of the whole brain white matter and of 18 white matter tracts were related to cognition using linear regression and Bayesian network analysis...
January 19, 2018: Dementia and Geriatric Cognitive Disorders
https://www.readbyqxmd.com/read/29353213/multiple-cortical-thickness-sub-networks-and-cognitive-impairments-in-first-episode-drug-na%C3%A3-ve-patients-with-late-life-depression-a-graph-theory-analysis
#3
Jeong-Hyeon Shin, Yu Hyun Um, Chang Uk Lee, Hyun Kook Lim, Joon-Kyung Seong
BACKGROUND: Coordinated and pattern-wise changes in large scale gray matter structural networks reflect neural circuitry dysfunction in late life depression (LLD), which in turn is associated with emotional dysregulation and cognitive impairments. However, due to methodological limitations, there have been few attempts made to identify individual-level structural network properties or sub-networks that are involved in important brain functions in LLD. METHODS: In this study, we sought to construct individual-level gray matter structural networks using average cortical thicknesses of several brain areas to investigate the characteristics of the gray matter structural networks in normal controls and LLD patients...
January 5, 2018: Journal of Affective Disorders
https://www.readbyqxmd.com/read/29352963/three-dimensional-visualization-of-extracellular-matrix-networks-during-murine-development
#4
Andrea Acuna, Michael A Drakopoulos, Yue Leng, Craig J Goergen, Sarah Calve
The extracellular matrix (ECM) plays a crucial role in embryogenesis, serving both as a substrate to which cells attach and as an active regulator of cell behavior. However, little is known about the spatiotemporal expression patterns and 3D structure of ECM proteins during embryonic development. The lack of suitable methods to visualize the embryonic ECM is largely responsible for this gap, posing a major technical challenge for biologists and tissue engineers. Here, we describe a method of viewing the 3D organization of the ECM using a polyacrylamide-based hydrogel to provide a 3D framework within developing murine embryos...
January 15, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29352808/frontal-dysconnectivity-in-22q11-2-deletion-syndrome-an-atlas-based-functional-connectivity-analysis
#5
Leah M Mattiaccio, Ioana L Coman, Carlie A Thompson, Wanda P Fremont, Kevin M Antshel, Wendy R Kates
BACKGROUND: 22q11.2 deletion syndrome (22q11DS) is a neurodevelopmental syndrome associated with deficits in cognitive and emotional processing. This syndrome represents one of the highest risk factors for the development of schizophrenia. Previous studies of functional connectivity (FC) in 22q11DS report aberrant connectivity patterns in large-scale networks that are associated with the development of psychotic symptoms. METHODS: In this study, we performed a functional connectivity analysis using the CONN toolbox to test for differential connectivity patterns between 54 individuals with 22q11DS and 30 healthy controls, between the ages of 17-25 years old...
January 20, 2018: Behavioral and Brain Functions: BBF
https://www.readbyqxmd.com/read/29352721/hyperconnective-and-hypoconnective-cortical-and-subcortical-functional-networks-in-multiple-system-atrophy
#6
Johannes Rosskopf, Martin Gorges, Hans-Peter Müller, Elmar H Pinkhardt, Albert C Ludolph, Jan Kassubek
INTRODUCTION: In multiple system atrophy (MSA), the organization of the functional brain connectivity within cortical and subcortical networks and its clinical correlates remains to be investigated. METHODS: Whole-brain based 'resting-state' fMRI data were obtained from 22 MSA patients (11 MSA-C, 11 MSA-P) and 22 matched healthy controls, together with standardized clinical assessment and video-oculographic recordings (EyeLink®). RESULTS: MSA patients vs...
January 12, 2018: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/29352651/catheter-injected-bone-marrow-mesenchymal-stem-cells-induce-efficacious-occlusion-of-arteriovenous-nidus-in-a-swine-model
#7
Joseph Touma, Jianping Dai, Andre Gaston, Marianne Gervais, Eric Allaire
OBJECTIVES: Arteriovenous malformations (AVMs) are complex vascular lesions. Surgical excision is the treatment of choice, but is often not achievable. Embolo-sclerotherapy alone is associated with high recurrence rates. This study tested the hypothesis that seeding hydrogel conditioned bone marrow derived mesenchymatous stem cells (BM-MSCs) in an AVM nidus model induces solid microvascular occlusion through endoluminal tissue growth. METHODS: AVMs were modelled as arteriovenous microvascular nidus, using swine rete mirabile, a plexiform intracranial structure composed of arterial microvessels that extensively anastomose...
January 15, 2018: European Journal of Vascular and Endovascular Surgery
https://www.readbyqxmd.com/read/29352311/decreased-%C3%AE-cell-mass-and-early-structural-alterations-of-the-exocrine-pancreas-in-patients-with-type-1-diabetes-an-analysis-based-on-the-npod-repository
#8
Fidéline Bonnet-Serrano, Marc Diedisheim, Roberto Mallone, Etienne Larger
BACKGROUND AND AIMS: Abnormal glucagon secretion and functional alterations of the exocrine pancreas have been described in patients with type 1 diabetes (T1D), but their respective anatomical substrata have seldom been investigated. Our aim was to develop an automated morphometric analysis process to characterize the anatomy of α-cell and exocrine pancreas in patients with T1D, using the publicly available slides of the Network for Pancreatic Organ Donors (nPOD). MATERIALS AND METHODS: The ratio of β- and α-cell area to total tissue area were quantified in 75 patients with T1D (thereafter patients) and 66 control subjects (thereafter controls), on 2 insulin-stained and 4 glucagon-stained slides from both the head and the tail of the pancreas...
2018: PloS One
https://www.readbyqxmd.com/read/29352154/resting-state-brain-networks-in-the-prairie-vole
#9
Juan J Ortiz, Wendy Portillo, Raul G Paredes, Larry J Young, Sarael Alcauter
Resting state functional magnetic resonance imaging (rsfMRI) has shown the hierarchical organization of the human brain into large-scale complex networks, referred as resting state networks. This technique has turned into a promising translational research tool after the finding of similar resting state networks in non-human primates, rodents and other animal models of great value for neuroscience. Here, we demonstrate and characterize the presence of resting states networks in Microtus ochrogaster, the prairie vole, an extraordinary animal model to study complex human-like social behavior, with potential implications for the research of normal social development, addiction and neuropsychiatric disorders...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352082/clostridial-strain-specific-characteristics-associated-with-necrotizing-enterocolitis
#10
Sophia Schönherr-Hellec, Geraldine L Klein, Johanne Delannoy, Laurent Ferraris, Jean Christophe Rozé, Marie José Butel, Julio Aires
We aimed at identifying potential clostridial factors linking these bacteria with necrotizing enterocolitis (NEC). We compared the phenotypic traits, stress responses, cellular cytotoxicity and inflammatory capabilities of the largest collection of Clostridium butyricum and Clostridium neonatale strains isolated from fecal samples of NEC and control preterm neonates (PN). When strains characteristics were used as explanatory variables, a statistical discriminant analysis allowed the separation of NEC and control strains into separate groups...
January 19, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29352028/the-mysteries-of-remote-memory
#11
REVIEW
Zimbul Albo, Johannes Gräff
Long-lasting memories form the basis of our identity as individuals and lie central in shaping future behaviours that guide survival. Surprisingly, however, our current knowledge of how such memories are stored in the brain and retrieved, as well as the dynamics of the circuits involved, remains scarce despite seminal technical and experimental breakthroughs in recent years. Traditionally, it has been proposed that, over time, information initially learnt in the hippocampus is stored in distributed cortical networks...
March 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29351844/interactome-screening-identifies-the-er-luminal-chaperone-hsp47-as-a-regulator-of-the-unfolded-protein-response-transducer-ire1%C3%AE
#12
Denisse Sepulveda, Diego Rojas-Rivera, Diego A Rodríguez, Jody Groenendyk, Andres Köhler, Cynthia Lebeaupin, Shinya Ito, Hery Urra, Amado Carreras-Sureda, Younis Hazari, Mireille Vasseur-Cognet, Maruf M U Ali, Eric Chevet, Gisela Campos, Patricio Godoy, Tomas Vaisar, Béatrice Bailly-Maitre, Kazuhiro Nagata, Marek Michalak, Jimena Sierralta, Claudio Hetz
Maintenance of endoplasmic reticulum (ER) proteostasis is controlled by a dynamic signaling network known as the unfolded protein response (UPR). IRE1α is a major UPR transducer, determining cell fate under ER stress. We used an interactome screening to unveil several regulators of the UPR, highlighting the ER chaperone Hsp47 as the major hit. Cellular and biochemical analysis indicated that Hsp47 instigates IRE1α signaling through a physical interaction. Hsp47 directly binds to the ER luminal domain of IRE1α with high affinity, displacing the negative regulator BiP from the complex to facilitate IRE1α oligomerization...
January 18, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29351810/identify-down-syndrome-transcriptome-associations-using-integrative-analysis-of-microarray-database-and-correlation-interaction-network
#13
Min Chen, Jiayan Wang, Yingjun Luo, Kailing Huang, Xiaoshun Shi, Yanhui Liu, Jin Li, Zhengfei Lai, Shuya Xue, Haimei Gao, Allen Chen, Dunjin Chen
BACKGROUND: Long non-coding RNAs (lncRNAs) have previously been emerged as key players in a series of biological processes. Dysregulation of lncRNA is correlated to human diseases including neurological disorders. Here, we developed a multi-step bioinformatics analysis to study the functions of a particular Down syndrome-associated gene DSCR9 including the lncRNAs. The method is named correlation-interaction-network (COIN), based on which a pipeline is implemented. Co-expression gene network analysis and biological network analysis results are presented...
January 19, 2018: Human Genomics
https://www.readbyqxmd.com/read/29351798/comparative-salivary-proteomics-analysis-of-children-with-and-without-dental-caries-using-the-itraq-mrm-approach
#14
Kun Wang, Yufei Wang, Xiuqing Wang, Qian Ren, Sili Han, Longjiang Ding, Zhongcheng Li, Xuedong Zhou, Wei Li, Linglin Zhang
BACKGROUND: Dental caries is a major worldwide oral disease afflicting a large proportion of children. As an important host factor of caries susceptibility, saliva plays a significant role in the occurrence and development of caries. The aim of the present study was to characterize the healthy and cariogenic salivary proteome and determine the changes in salivary protein expression of children with varying degrees of active caries, also to establish salivary proteome profiles with a potential therapeutic use against dental caries...
January 19, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29351669/how-pairwise-coevolutionary-models-capture-the-collective-residue-variability-in-proteins
#15
Matteo Figliuzzi, Pierre Barrat-Charlaix, Martin Weigt
Global coevolutionary models of homologous protein families, as constructed by direct coupling analysis (DCA), have recently gained popularity in particular due to their capacity to accurately predict residueresidue contacts from sequence information alone, and thereby to facilitate tertiary and quaternary protein structure prediction. More recently, they have also been used to predict fitness effects of aminoacid substitutions in proteins, and to predict evolutionary conserved protein-protein interactions...
January 17, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29351588/sorghum-root-system-classification-in-contrasting-p-environments-reveals-three-main-rooting-types-and-root-architecture-related-marker-trait-associations
#16
Sebastian Parra-Londono, Mareike Kavka, Birgit Samans, Rod Snowdon, Silke Wieckhorst, Ralf Uptmoor
Background and Aims: Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions...
January 17, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29351350/visualized-analysis-of-developing-trends-and-hot-topics-in-natural-disaster-research
#17
Shi Shen, Changxiu Cheng, Jing Yang, Shanli Yang
This study visualized and analyzed the developing trends and hot topics in natural disaster research. 19694 natural disaster-related articles (January 1900 to June 2015) are indexed in the Web of Science database. The first step in this study is using complex networks to visualize and analyze these articles. CiteSpace and Gephi were employed to generate a countries collaboration network and a disciplines collaboration network, and then attached hot topics to countries and disciplines, respectively. The results show that USA, China, and Italy are the three major contributors to natural disaster research...
2018: PloS One
https://www.readbyqxmd.com/read/29351331/the-association-between-previous-and-future-severe-exacerbations-of-chronic-obstructive-pulmonary-disease-updating-the-literature-using-robust-statistical-methodology
#18
Mohsen Sadatsafavi, Hui Xie, Mahyar Etminan, Kate Johnson, J Mark FitzGerald
BACKGROUND: There is minimal evidence on the extent to which the occurrence of a severe acute exacerbation of COPD that results in hospitalization affects the subsequent disease course. Previous studies on this topic did not generate causally-interpretable estimates. Our aim was to use corrected methodology to update previously reported estimates of the associations between previous and future exacerbations in these patients. METHODS: Using administrative health data in British Columbia, Canada (1997-2012), we constructed a cohort of patients with at least one severe exacerbation, defined as an episode of inpatient care with the main diagnosis of COPD based on international classification of diseases (ICD) codes...
2018: PloS One
https://www.readbyqxmd.com/read/29351281/automatic-labeling-of-molecular-biomarkers-of-immunohistochemistry-images-using-fully-convolutional-networks
#19
Fahime Sheikhzadeh, Rabab K Ward, Dirk van Niekerk, Martial Guillaud
This paper addresses the problem of quantifying biomarkers in multi-stained tissues based on the color and spatial information of microscopy images of the tissue. A deep learning-based method that can automatically localize and quantify the regions expressing biomarker(s) in any selected area on a whole slide image is proposed. The deep learning network, which we refer to as Whole Image (WI)-Net, is a fully convolutional network whose input is the true RGB color image of a tissue and output is a map showing the locations of each biomarker...
2018: PloS One
https://www.readbyqxmd.com/read/29351262/imu-to-segment-assignment-and-orientation-alignment-for-the-lower-body-using-deep-learning
#20
Tobias Zimmermann, Bertram Taetz, Gabriele Bleser
Human body motion analysis based on wearable inertial measurement units (IMUs) receives a lot of attention from both the research community and the and industrial community. This is due to the significant role in, for instance, mobile health systems, sports and human computer interaction. In sensor based activity recognition, one of the major issues for obtaining reliable results is the sensor placement/assignment on the body. For inertial motion capture (joint kinematics estimation) and analysis, the IMU-to-segment (I2S) assignment and alignment are central issues to obtain biomechanical joint angles...
January 19, 2018: Sensors
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