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https://www.readbyqxmd.com/read/28107591/the-role-of-autonomic-dysfunction-in-predicting-one-year-mortality-after-liver-transplantation
#1
Kuang-Cheng Chan, Jia-Rong Yeh, Wei-Zen Sun
BACKGROUND & AIMS: Model for end-stage liver disease (MELD) score has been extensively used to prioritize patients for liver transplantation and determine their prognosis, but with limited predictive value. Autonomic dysfunction may correlate with increased mortality after liver transplant. In this study, two autonomic biomarkers, complexity and deceleration capacity, were added to the predicting model for one-year mortality after liver transplantation. METHODS: Thirty patients with end-stage liver diseases awaiting liver transplantation were included...
January 20, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28107510/effect-of-the-crystal-environment-on-side-chain-conformational-dynamics-in-cyanovirin-n-investigated-through-crystal-and-solution-molecular-dynamics-simulations
#2
Logan S Ahlstrom, Ivan I Vorontsov, Jun Shi, Osamu Miyashita
Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure...
2017: PloS One
https://www.readbyqxmd.com/read/28107341/complex-dynamics-of-virus-spread-from-low-infection-multiplicities-implications-for-the-spread-of-oncolytic-viruses
#3
Ignacio A Rodriguez-Brenes, Andrew Hofacre, Hung Fan, Dominik Wodarz
While virus growth dynamics have been well-characterized in several infections, data are typically collected once the virus population becomes easily detectable. Earlier dynamics, however, remain less understood. We recently reported unusual early dynamics in an experimental system using adenovirus infection of human embryonic kidney (293) cells. Under identical experimental conditions, inoculation at low infection multiplicities resulted in either robust spread, or in limited spread that eventually stalled, with both outcomes occurring with approximately equal frequencies...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28107053/diversity-and-coevolutionary-dynamics-in-high-dimensional-phenotype-spaces
#4
Michael Doebeli, Iaroslav Ispolatov
We study macroevolutionary dynamics by extending microevolutionary competition models to long timescales. It has been shown that for a general class of competition models, gradual evolutionary change in continuous phenotypes (evolutionary dynamics) can be nonstationary and even chaotic when the dimension of the phenotype space in which the evolutionary dynamics unfold is high. It has also been shown that evolutionary diversification can occur along nonequilibrium trajectories in phenotype space. We combine these lines of thinking by studying long-term coevolutionary dynamics of emerging lineages in multidimensional phenotype spaces...
February 2017: American Naturalist
https://www.readbyqxmd.com/read/28106441/loschmidt-echo-revivals-critical-and-noncritical
#5
R Jafari, Henrik Johannesson
A quantum phase transition is generally thought to imprint distinctive characteristics on the nonequilibrium dynamics of a closed quantum system. Specifically, the Loschmidt echo after a sudden quench to a quantum critical point-measuring the time dependence of the overlap between initial and time-evolved states-is expected to exhibit an accelerated relaxation followed by periodic revivals. We here introduce a new exactly solvable model, the extended Su-Schrieffer-Heeger model, the Loschmidt echo of which provides a counterexample...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106436/transient-casimir-forces-from-quenches-in-thermal-and-active-matter
#6
Christian M Rohwer, Mehran Kardar, Matthias Krüger
We compute fluctuation-induced (Casimir) forces for classical systems after a temperature quench. Using a generic coarse-grained model for fluctuations of a conserved density, we find that transient forces arise even if the initial and final states are force free. In setups reminiscent of Casimir (planar walls) and van der Waals (small inclusions) interactions, we find comparable exact universal expressions for the force. Dynamical details only scale the time axis of transient force curves. We propose that such quenches can be achieved, for instance, in experiments on active matter, employing tunable activity or interaction protocols...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106417/chaos-and-regularity-in-the-doubly-magic-nucleus-208-pb
#7
B Dietz, A Heusler, K H Maier, A Richter, B A Brown
High-resolution experiments have recently lead to a complete identification (energy, spin, and parity) of 151 nuclear levels up to an excitation energy of E_{x}=6.20  MeV in ^{208}Pb [Heusler et al., Phys. Rev. C 93, 054321 (2016)PRVCAN2469-998510.1103/PhysRevC.93.054321]. We present a thorough study of the fluctuation properties in the energy spectra of the unprecedented set of nuclear bound states. In a first approach, we group states with the same spin and parity into 14 subspectra, analyze standard statistical measures for short- and long-range correlations, i...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106223/next-generation-of-network-medicine-interdisciplinary-signaling-approaches
#8
REVIEW
Tamas Korcsmaros, Maria Victoria Schneider, Giulio Superti-Furga
In the last decade, network approaches have transformed our understanding of biological systems. Network analyses and visualizations have allowed us to identify essential molecules and modules in biological systems, and improved our understanding of how changes in cellular processes can lead to complex diseases, such as cancer, infectious and neurodegenerative diseases. "Network medicine" involves unbiased large-scale network-based analyses of diverse data describing interactions between genes, diseases, phenotypes, drug targets, drug transport, drug side-effects, disease trajectories and more...
January 20, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28106047/scale-dependent-diffusion-anisotropy-in-nanoporous-silicon
#9
Daria Kondrashova, Alexander Lauerer, Dirk Mehlhorn, Hervé Jobic, Armin Feldhoff, Matthias Thommes, Dipanjan Chakraborty, Cedric Gommes, Jovana Zecevic, Petra de Jongh, Armin Bunde, Jörg Kärger, Rustem Valiullin
Nanoporous silicon produced by electrochemical etching of highly B-doped p-type silicon wafers can be prepared with tubular pores imbedded in a silicon matrix. Such materials have found many technological applications and provide a useful model system for studying phase transitions under confinement. This paper reports a joint experimental and simulation study of diffusion in such materials, covering displacements from molecular dimensions up to tens of micrometers with carefully selected probe molecules. In addition to mass transfer through the channels, diffusion (at much smaller rates) is also found to occur in directions perpendicular to the channels, thus providing clear evidence of connectivity...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28106010/models-of-life-epigenetics-diversity-cycles
#10
Kim Sneppen
This review emphasize aspects of biology that can be understood through repeated applications of simple causal rules. The selected topics include perspectives on gene regulation, phage lambda development, epigenetics, microbial ecology, as well as model approaches to diversity and punctuated equilibrium in evolution. Two outstanding features are repeatedly described. One is minimal rules to sustain specific states of a complex systems for a long time. The other is the collapse of such states and the subsequent dynamical cycle of situations that later return to new metastable states...
January 20, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28105914/homology-modeling-and-molecular-dynamics-provide-structural-insights-into-tospovirus-nucleoprotein
#11
Rayane Nunes Lima, Muhammad Faheem, João Alexandre Ribeiro Gonçalves Barbosa, Marcelo Depólo Polêto, Hugo Verli, Fernando Lucas Melo, Renato Oliveira Resende
BACKGROUND: Tospovirus is a plant-infecting genus within the family Bunyaviridae, which also includes four animal-infecting genera: Hantavirus, Nairovirus, Phlebovirus and Orthobunyavirus. Compared to these members, the structures of Tospovirus proteins still are poorly understood. Despite multiple studies have attempted to identify candidate N protein regions involved in RNA binding and protein multimerization for tospovirus using yeast two-hybrid systems (Y2HS) and site-directed mutagenesis, the tospovirus ribonucleocapsids (RNPs) remains largely uncharacterized at the molecular level and the lack of structural information prevents detailed insight into these interactions...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105525/characterization-of-the-cell-polarity-gene-crumbs-during-the-early-development-and-maintenance-of-the-squid-vibrio-light-organ-symbiosis
#12
Suzanne M Peyer, Elizabeth A C Heath-Heckman, Margaret J McFall-Ngai
The protein Crumbs is a determinant of apical-basal cell polarity and plays a role in apoptosis of epithelial cells and their protection against photodamage. Using the squid-vibrio system, a model for development of symbiotic partnerships, we examined the modulation of the crumbs gene in host epithelial tissues during initiation and maintenance of the association. The extracellular luminous symbiont Vibrio fischeri colonizes the apical surfaces of polarized epithelia in deep crypts of the Euprymna scolopes light organ...
January 20, 2017: Development Genes and Evolution
https://www.readbyqxmd.com/read/28103436/directional-charge-carrier-transport-in-oriented-benzodithiophene-covalent-organic-framework-thin-films
#13
Dana D Medina, Michiel L Petrus, Askhat N Jumabekov, Johannes T Margraf, Simon Weinberger, Julian M Rotter, Timothy Clark, Thomas Bein
Charge carrier transport in oriented COF thin films is an important factor for realizing COF-based optoelectronic devices. We describe how highly oriented electron-donating BDT-COF thin films serve as a model system for a directed charge transport study. Oriented BDT-COF films were deposited on different electrodes with excellent control over film roughness and topology, allowing for high quality electrode-COF interfaces suitable for device fabrication. Hole-only devices were constructed to study the columnar hole-mobility of the BDT-COF films...
January 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28103280/formulation-general-features-and-global-calibration-of-a-bioenergetically-constrained-fishery-model
#14
David A Carozza, Daniele Bianchi, Eric D Galbraith
Human exploitation of marine resources is profoundly altering marine ecosystems, while climate change is expected to further impact commercially-harvested fish and other species. Although the global fishery is a highly complex system with many unpredictable aspects, the bioenergetic limits on fish production and the response of fishing effort to profit are both relatively tractable, and are sure to play important roles. Here we describe a generalized, coupled biological-economic model of the global marine fishery that represents both of these aspects in a unified framework, the BiOeconomic mArine Trophic Size-spectrum (BOATS) model...
2017: PloS One
https://www.readbyqxmd.com/read/28102956/experimental-verification-of-4d-monte-carlo-simulations-of-dose-delivery-to-a-moving-anatomy
#15
Sara Gholampourkashi, Miro Vujicic, Jason Belec, Joanna E Cygler, Emily Heath
PURPOSE: To evaluate a novel 4D Monte Carlo simulation tool by comparing calculations to physical measurements using a respiratory motion phantom. METHODS: We used a dynamic Quasar phantom in both stationary and breathing states (sinusoidal motion of amplitude of 1.8 cm and period of 3.3 s) for dose measurements on an Elekta Agility linear accelerator. Gafchromic EBT3 film and the RADPOS 4D dosimetry system were placed inside the lung insert of the phantom to measure dose profiles and point-dose values at the center of the spherical tumor inside the insert...
January 2017: Medical Physics
https://www.readbyqxmd.com/read/28102531/a-systems-dynamics-approach-to-the-efficacy-of-oxime-therapy-for-mild-exposure-to-sarin-gas
#16
Daniel J Droste, Michael L Shelley, Jeffery M Gearhart, David M Kempisty
The use of nerve agents such as sarin is as much a threat today as any other time in our history. The events in Syria in 2013 are proof of this. "The Obama administration asserted Sunday for the first time that the Syrian government used the nerve gas sarin to kill more than 1,400 people (August 21, 2013) in the world's gravest chemical weapons attack in 25 years." With these recent events clear in our mind, we must focus on the horrific nature of these chemical agents to devise a strategy that will enable first responders to counteract these insidious chemicals...
April 2016: American Journal of Disaster Medicine
https://www.readbyqxmd.com/read/28102344/predicting-drug-combination-index-and-simulating-the-network-regulation-dynamics-by-mathematical-modeling-of-drug-targeted-egfr-erk-signaling-pathway
#17
Lu Huang, Yuyang Jiang, Yuzong Chen
Synergistic drug combinations enable enhanced therapeutics. Their discovery typically involves the measurement and assessment of drug combination index (CI), which can be facilitated by the development and applications of in-silico CI predictive tools. In this work, we developed and tested the ability of a mathematical model of drug-targeted EGFR-ERK pathway in predicting CIs and in analyzing multiple synergistic drug combinations against observations. Our mathematical model was validated against the literature reported signaling, drug response dynamics, and EGFR-MEK drug combination effect...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102267/a-theoretical-foundation-for-multi-scale-regular-vegetation-patterns
#18
Corina E Tarnita, Juan A Bonachela, Efrat Sheffer, Jennifer A Guyton, Tyler C Coverdale, Ryan A Long, Robert M Pringle
Self-organized regular vegetation patterns are widespread and thought to mediate ecosystem functions such as productivity and robustness, but the mechanisms underlying their origin and maintenance remain disputed. Particularly controversial are landscapes of overdispersed (evenly spaced) elements, such as North American Mima mounds, Brazilian murundus, South African heuweltjies, and, famously, Namibian fairy circles. Two competing hypotheses are currently debated. On the one hand, models of scale-dependent feedbacks, whereby plants facilitate neighbours while competing with distant individuals, can reproduce various regular patterns identified in satellite imagery...
January 18, 2017: Nature
https://www.readbyqxmd.com/read/28102262/scaling-single-cell-genomics-from-phenomenology-to-mechanism
#19
Amos Tanay, Aviv Regev
Three of the most fundamental questions in biology are how individual cells differentiate to form tissues, how tissues function in a coordinated and flexible fashion and which gene regulatory mechanisms support these processes. Single-cell genomics is opening up new ways to tackle these questions by combining the comprehensive nature of genomics with the microscopic resolution that is required to describe complex multicellular systems. Initial single-cell genomic studies provided a remarkably rich phenomenology of heterogeneous cellular states, but transforming observational studies into models of dynamics and causal mechanisms in tissues poses fresh challenges and requires stronger integration of theoretical, computational and experimental frameworks...
January 18, 2017: Nature
https://www.readbyqxmd.com/read/28102001/evaluation-of-the-hybrid-resolution-pace-model-for-the-study-of-folding-insertion-and-pore-formation-of-membrane-associated-peptides
#20
Michael D Ward, Shivangi Nangia, Eric R May
The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp)...
January 19, 2017: Journal of Computational Chemistry
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