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https://www.readbyqxmd.com/read/29342229/a-rapid-epistatic-mixed-model-association-analysis-by-linear-retransformations-of-genomic-estimated-values
#1
Chao Ning, Dan Wang, Huimin Kang, Raphael Mrode, Lei Zhou, Shizhong Xu, Jian-Feng Liu
Motivation: Epistasis provides a feasible way for probing potential genetic mechanism of complex traits. However, time-consuming computation challenges successful detection of interaction in practice, especially when linear mixed model (LMM) is used to control type I error in the presence of population structure and cryptic relatedness. Results: A rapid epistatic mixed-model association analysis (REMMA) method was developed to overcome computational limitation. This method first estimates individuals' epistatic effects by an extended genomic best linear unbiased prediction (EG-BLUP) model with additive and epistatic kinship matrix, then pairwise interaction effects are obtained by linear retransformations of individuals' epistatic effects...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29341685/intermittent-granular-dynamics-at-a-seismogenic-plate-boundary
#2
Yasmine Meroz, Brendan J Meade
Earthquakes at seismogenic plate boundaries are a response to the differential motions of tectonic blocks embedded within a geometrically complex network of branching and coalescing faults. Elastic strain is accumulated at a slow strain rate on the order of 10^{-15}  s^{-1}, and released intermittently at intervals >100  yr, in the form of rapid (seconds to minutes) coseismic ruptures. The development of macroscopic models of quasistatic planar tectonic dynamics at these plate boundaries has remained challenging due to uncertainty with regard to the spatial and kinematic complexity of fault system behaviors...
September 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29341386/at-the-core-of-reasoning-dissociating-deductive-and-non-deductive-load
#3
John P Coetzee, Martin M Monti
In recent years, neuroimaging methods have been used to investigate how the human mind carries out deductive reasoning. According to some, the neural substrate of language is integral to deductive reasoning. According to others, deductive reasoning is supported by a language-independent distributed network including left frontopolar and frontomedial cortices. However, it has been suggested that activity in these frontal regions might instead reflect non-deductive factors such as working memory load and general cognitive difficulty...
January 16, 2018: Human Brain Mapping
https://www.readbyqxmd.com/read/29339553/engineering-abiotic-stress-response-in-plants-for-biomass-production
#4
Sneh Lata Singla-Pareek, Rohit Joshi, Ashwani Pareek
One of the major challenges in today's agriculture is to achieve enhanced plant growth and biomass even under adverse environmental conditions. Recent advancements in genetics and molecular biology have enabled identification of a complex signaling network contributing towards plant growth and development on the one hand and abiotic stress response on the other. As an outcome of these studies, three major approaches have been identified having a potential to improve biomass production in plants under abiotic stress conditions...
January 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29339429/the-biochemistry-of-sensing-enteric-pathogens-regulate-type-iii-secretion-in-response-to-environmental-and-host-cues
#5
REVIEW
Nicole J De Nisco, Giomar Rivera-Cancel, Kim Orth
Enteric pathogens employ sophisticated strategies to colonize and infect mammalian hosts. Gram-negative bacteria, such as Escherichia coli, Salmonella, and Campylobacter jejuni, are among the leading causes of gastrointestinal tract infections worldwide. The virulence strategies of many of these Gram-negative pathogens rely on type III secretion systems (T3SSs), which are macromolecular syringes that translocate bacterial effector proteins directly into the host cytosol. However, synthesis of T3SS proteins comes at a cost to the bacterium in terms of growth rate and fitness, both in the environment and within the host...
January 16, 2018: MBio
https://www.readbyqxmd.com/read/29339311/general-crystallized-and-fluid-intelligence-are-not-associated-with-functional-global-network-efficiency-a-replication-study-with-the-human-connectome-project-1200-data-set
#6
J D Kruschwitz, L Waller, L S Daedelow, H Walter, I M Veer
One hallmark example of a link between global topological network properties of complex functional brain connectivity and cognitive performance is the finding that general intelligence may depend on the efficiency of the brain's intrinsic functional network architecture. However, although this association has been featured prominently over the course of the last decade, the empirical basis for this broad association of general intelligence and global functional network efficiency is quite limited. In the current study, we set out to replicate the previously reported association between general intelligence and global functional network efficiency using the large sample size and high quality data of the Human Connectome Project, and extended the original study by testing for separate association of crystallized and fluid intelligence with global efficiency, characteristic path length, and global clustering coefficient...
January 12, 2018: NeuroImage
https://www.readbyqxmd.com/read/29339310/distant-from-input-evidence-of-regions-within-the-default-mode-network-supporting-perceptually-decoupled-and-conceptually-guided-cognition
#7
Charlotte Murphy, Elizabeth Jefferies, Shirley-Ann Rueschemeyer, Mladen Sormaz, Hao-Ting Wang, Daniel S Margulies, Jonathan Smallwood
The default mode network supports a variety of mental operations such as semantic processing, episodic memory retrieval, mental time travel and mind-wandering, yet the commonalities between these functions remains unclear. One possibility is that this system supports cognition that is independent of the immediate environment; alternatively or additionally, it might support higher-order conceptual representations that draw together multiple features. We tested these accounts using a novel paradigm that separately manipulated the availability of perceptual information to guide decision-making and the representational complexity of this information...
January 12, 2018: NeuroImage
https://www.readbyqxmd.com/read/29338773/chemokine-ligand-receptor-interactions-critically-regulate-cutaneous-wound-healing
#8
Erich Bünemann, Norman-Philipp Hoff, Bettina Alexandra Buhren, Ulrike Wiesner, Stephan Meller, Edwin Bölke, Anja Müller-Homey, Robert Kubitza, Thomas Ruzicka, Albert Zlotnik, Bernhard Homey, Peter Arne Gerber
BACKGROUND: Wound healing represents a dynamic process involving directional migration of different cell types. Chemokines, a family of chemoattractive proteins, have been suggested to be key players in cell-to-cell communication and essential for directed migration of structural cells. Today, the role of the chemokine network in cutaneous wound healing is not fully understood. Unraveling the chemokine-driven communication pathways in this complex process could possibly lead to new therapeutic strategies in wound healing disorders...
January 16, 2018: European Journal of Medical Research
https://www.readbyqxmd.com/read/29338545/identification-of-g2-m-phase-transitionby-sequential-nuclear-and-cytoplasmic-changes-and-molecular-markers-in-mice-intestinal-epithelial-cells
#9
Jiong Ren, Cai-Zhi Tang, Xu-Dong Li, Zhi-Bin Niu, Bo-Yang Zhang, Tao Zhang, Mei-Jiao Gao, Xin-Ze Ran, Yong-Ping Su, Feng-Chao Wang
Although the regulatory network of G2/M phase transition has been intensively studied in mammalian cell lines, the identification of morphological and molecular markers to identify G2/M phase transition in vivo remains elusive. In this study, we found no obvious morphological changes between the S phase and G2 phase in mice intestinal epithelial cells. The G2 phase could be identified by Brdu incorporation resistance, marginal and scattered foci of histone H3 phosphorylated at Ser10 (pHH3), and relatively intact Golgi ribbon...
January 17, 2018: Cell Cycle
https://www.readbyqxmd.com/read/29338461/mtor-dysregulation-and-tuberous-sclerosis-related-epilepsy
#10
Paolo Curatolo, Romina Moavero, Jackelien van Scheppingen, Eleonora Aronica
The mammalian target of rapamycin (mTOR) pathway has emerged as a key player for proper neural network development, and it is involved in epileptogenesis triggered by both genetic or acquired factors. Areas covered. The robust mTOR signaling deregulation observed in a large spectrum of epileptogenic developmental pathologies, such as focal cortical dysplasias and tuberous sclerosis complex (TSC), has been linked to germline and somatic mutations in mTOR pathway regulatory genes, increasing the spectrum of "mTORopathies"...
January 17, 2018: Expert Review of Neurotherapeutics
https://www.readbyqxmd.com/read/29338122/no-co-and-h2-s-what-about-gasotransmitters-in-fish-and-amphibian-hearts
#11
REVIEW
Sandra Imbrogno, Mariacristina Filice, Maria Carmela Cerra, Alfonsina Gattuso
The gasotransmitters nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2 S), long considered only toxicant, are produced in vivo during the catabolism of common biological molecules, and are crucial for a large variety of physiological processes. Mounting evidence is emerging that in poikilotherm vertebrates, as in mammals, they modulate the basal performance of the heart and the response to stress challenges. In this review, we will focus on teleost fish and amphibians to highlight the evolutionary importance in vertebrates of the cardiac control elicited by NO, CO and H2 S, and the conservation of the intracellular cascades they activate...
January 16, 2018: Acta Physiologica
https://www.readbyqxmd.com/read/29338012/using-geospatial-techniques-to-develop-an-emergency-referral-transport-system-for-suspected-sepsis-patients-in-bangladesh
#12
Atique Iqbal Chowdhury, Rafiqul Haider, Abu Yousuf Md Abdullah, Aliki Christou, Nabeel Ashraf Ali, Ahmed Ehsnaur Rahman, Afrin Iqbal, Sanwarul Bari, D M Emdadul Hoque, Shams El Arifeen, Niranjan Kissoon, Charles P Larson
BACKGROUND: A geographic information system (GIS)-based transport network within an emergency referral system can be the key to reducing health system delays and increasing the chances of survival, especially during an emergency. We employed a GIS to design an emergency transport system for the rapid transfer of pregnant or early post-partum women, newborns, and children under 5 years of age with suspected sepsis under the Interrupting Pathways to Sepsis Initiative (IPSI) project. METHODS: A GIS database was developed by mapping the villages, roads, and relevant physical features of the study area...
2018: PloS One
https://www.readbyqxmd.com/read/29337576/impact-of-nanoporosity-on-hydrocarbon-transport-in-shales-organic-matter
#13
Amaël Obliger, Franz-Josef Ulm, Roland J-M Pellenq
In a context of growing attention for shale gas, the precise impact of organic matter (kerogen) on hydrocarbon recovery from unconventional reservoirs still has to be assessed. Kerogen's microstructure is characterized by a very disordered pore network that greatly affects hydrocarbon transport. The specific structure and texture of this organic matter at the nanoscale is highly dependent on its origin. In this study, by the use of statistical physics and molecular dynamics, we shed some new lights on hydrocarbon transport through realistic molecular models of kerogen at different level of maturity [Bousige et al...
January 16, 2018: Nano Letters
https://www.readbyqxmd.com/read/29337412/metallic-nanodot-patterns-with-unique-symmetries-templated-from-abc-triblock-terpolymer-networks
#14
Karim Aissou, Muhammad Mumtaz, Alberto Alvarez-Fernandez, Jean Mercat, Ségolène Antoine, Gilles Pécastaings, Virginie Ponsinet, Cécile Dobrzynski, Guillaume Fleury, Georges Hadziioannou
Nanotemplates derived from the self-assembly of AB-type block copolymers provide an elegant route to achieve well-defined metallic dot arrays, even if the variety of pattern symmetries is restricted due to the limited number of structures offered by microphase separated diblock copolymers. A strategy that relies on the use of complex network structures accessible through the self-assembly of linear ABC-type terpolymers is presented for the formation of metallic nanodots arrays with "outside-the-box" symmetries...
January 16, 2018: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/29337282/comparative-proteome-analysis-of-monolayer-and-spheroid-culture-of-canine-osteosarcoma-cells
#15
Christiane Gebhard, Ingrid Miller, Karin Hummel, Martina Neschi Née Ondrovics, Sarah Schlosser, Ingrid Walter
Osteosarcoma is an aggressive bone tumor with high metastasis rate in the lungs and affects both humans and dogs in a similar way. Three-dimensional tumor cell cultures mimic the in vivo situation of micro-tumors and metastases and are therefore better experimental in vitro models than the often applied two-dimensional monolayer cultures. The aim of the present study was to perform comparative proteomics of standard monolayer cultures of canine osteosarcoma cells (D17) and three-dimensional spheroid cultures, to better characterize the 3D model before starting with experiments like migration assays...
January 11, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29337084/a-graph-based-approach-to-analyze-flux-balanced-pathways-in-metabolic-networks
#16
Mona Arabzadeh, Morteza Saheb Zamani, Mehdi Sedighi, Sayed-Amir Marashi
An Elementary Flux Mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find these flux-balanced pathways. In this paper, an approach to find a subset of EFMs is proposed based on a graph data model. The given metabolic network is mapped to the graph model and decisions for reaction inclusion can be made based on metabolites and their associated reactions...
January 11, 2018: Bio Systems
https://www.readbyqxmd.com/read/29336158/chromosome-gene-orientations-inversion-networks-goins-of-plasmodium-proteome
#17
Viviana F Quevedo-Tumailli, Bernabe Ortega-Tenezaca, Humbert Gonzalez-Diaz
The spatial distribution of genes in chromosomes seems not to be random. For instance, only 10% of genes are transcribed from bidirectional promoters in humans and many more are organised in larger clusters. This raises intriguing questions asked by different authors before. We would like to add a few more questions in this context, related to gene orientation inversions. Does gene orientation (inversion) follow a random pattern? Is it relevant to biological activity somehow? In this paper, we define a new kind of network coined as the Gene Orientation Inversion Network (GOIN)...
January 16, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29336157/glycerol-hydrogen-bonding-network-dominates-structure-and-collective-dynamics-in-a-deep-eutectic-solvent
#18
A Faraone, D V Wagle, G A Baker, E C Novak, M Ohl, D Reuter, P Lunkenheimer, A Loidl, E Mamontov
The deep eutectic solvent glyceline formed by choline chloride and glycerol in 1:2 molar ratio is much less viscous compared to glycerol, which facilitates its use in many applications where high viscosity is undesirable. Despite the large difference in viscosity, we have found that the structural network of glyceline is completely defined by its glycerol constituent, which exhibits complex microscopic dynamic behavior, as expected from a highly correlated hydrogen-bonding network. Choline ions occupy interstitial voids in the glycerol network and show little structural or dynamic correlations with glycerol molecules...
January 16, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29336068/isatin-an-endogenous-nonpeptide-biofactor-a-review-of-its-molecular-targets-mechanisms-of-actions-and-their-biomedical-implications
#19
REVIEW
Alexei Medvedev, Olga Buneeva, Oksana Gnedenko, Pavel Ershov, Alexis Ivanov
Isatin (indole-2,3-dione) is an oxidized indole. It is widely distributed in mammalian tissues and body fluids, where isatin concentrations vary significantly from <0.1 to > 10 µM. Isatin output is increased under conditions of stress. Exogenously administered isatin is characterized by low toxicity, mutagenicity, and genotoxicity in vivo. Cytotoxic effects of isatin on various cell cultures are usually observed at concentrations exceeding 100 µM. Binding of [3 H]isatin to rat brain sections is consistent with its physiological concentrations...
January 16, 2018: BioFactors
https://www.readbyqxmd.com/read/29335872/disruptor-of-telomeric-silencing-1-like-dot1l-disclosing-a-new-class-of-non-nucleoside-inhibitors-by-means-of-ligand-based-and-structure-based-approaches
#20
Manuela Sabatino, Dante Rotili, Alexandros Patsilinakos, Mariantonietta Forgione, Daniela Tomaselli, Fréderic Alby, Paola B Arimondo, Antonello Mai, Rino Ragno
Chemical inhibition of chromatin-mediated signaling involved proteins is an established strategy to drive expression networks and alter disease progression. Protein methyltransferases are among the most studied proteins in epigenetics and, in particular, disruptor of telomeric silencing 1-like (DOT1L) lysine methyltransferase plays a key role in MLL-rearranged acute leukemia Selective inhibition of DOT1L is an established attractive strategy to breakdown aberrant H3K79 methylation and thus overexpression of leukemia genes, and leukemogenesis...
January 15, 2018: Journal of Computer-aided Molecular Design
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