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Spatial modeling

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https://www.readbyqxmd.com/read/28212525/ablation-of-ferroptosis-regulator-glutathione-peroxidase-4-in-forebrain-neurons-promotes-cognitive-impairment-and-neurodegeneration
#1
William Sealy Hambright, Rene Solano Fonseca, Liuji Chen, Ren Na, Qitao Ran
Synaptic loss and neuron death are the underlying cause of neurodegenerative diseases such as Alzheimer's disease (AD); however, the modalities of cell death in those diseases remain unclear. Ferroptosis, a newly identified oxidative cell death mechanism triggered by massive lipid peroxidation, is implicated in the degeneration of neurons populations such as spinal motor neurons and midbrain neurons. Here, we investigated whether neurons in forebrain regions (cerebral cortex and hippocampus) that are severely afflicted in AD patients might be vulnerable to ferroptosis...
February 1, 2017: Redox Biology
https://www.readbyqxmd.com/read/28212416/the-variability-of-multisensory-processes-of-natural-stimuli-in-human-and-non-human-primates-in-a-detection-task
#2
Cécile Juan, Céline Cappe, Baptiste Alric, Benoit Roby, Sophie Gilardeau, Pascal Barone, Pascal Girard
BACKGROUND: Behavioral studies in both human and animals generally converge to the dogma that multisensory integration improves reaction times (RTs) in comparison to unimodal stimulation. These multisensory effects depend on diverse conditions among which the most studied were the spatial and temporal congruences. Further, most of the studies are using relatively simple stimuli while in everyday life, we are confronted to a large variety of complex stimulations constantly changing our attentional focus over time, a modality switch that can impact on stimuli detection...
2017: PloS One
https://www.readbyqxmd.com/read/28212385/the-effect-of-tumour-size-on-drug-transport-and-uptake-in-3-d-tumour-models-reconstructed-from-magnetic-resonance-images
#3
Wenbo Zhan, Wladyslaw Gedroyc, Xiao Yun Xu
Drug transport and its uptake by tumour cells are strongly dependent on tumour properties, which vary in different types of solid tumours. By simulating the key physical and biochemical processes, a numerical study has been carried out to investigate the transport of anti-cancer drugs in 3-D tumour models of different sizes. The therapeutic efficacy for each tumour is evaluated by using a pharmacodynamics model based on the predicted intracellular drug concentration. Simulation results demonstrate that interstitial fluid pressure and interstitial fluid loss vary non-linearly with tumour size...
2017: PloS One
https://www.readbyqxmd.com/read/28212305/epigenetic-landscape-during-coronavirus-infection
#4
Alexandra Schäfer, Ralph S Baric
Coronaviruses (CoV) comprise a large group of emerging human and animal pathogens, including the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) strains. The molecular mechanisms regulating emerging coronavirus pathogenesis are complex and include virus-host interactions associated with entry, replication, egress and innate immune control. Epigenetics research investigates the genetic and non-genetic factors that regulate phenotypic variation, usually caused by external and environmental factors that alter host expression patterns and performance without any change in the underlying genotype...
February 15, 2017: Pathogens
https://www.readbyqxmd.com/read/28212025/advances-in-tip-enhanced-near-field-raman-microscopy-using-nanoantennas
#5
Xian Shi, Nicolás Coca-López, Julia Janik, Achim Hartschuh
Tip-enhanced near-field Raman microscopy spectroscopy is a scanning probe technique that is capable of providing vibrational spectroscopic information on single nanoobjects and surfaces at (sub-) nanometer spatial resolution and high detection sensitivity. In this review, we first illustrate the physical principle of optical nanoantennas used in tip-enhanced near-field Raman microscopy and tip-enhanced Raman scattering (TERS) to efficiently couple light to Raman excitations on nanometer length scales. Although the antennas' electric near-field distributions are commonly understood to determine the spatial resolution, recent experiments showing subnanometer-resolved optical images put this understanding into question...
February 17, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28211815/generation-and-characterization-of-knock-in-mouse-models-expressing-versions-of-huntingtin-with-either-an-n17-or-a-combined-polyq-and-proline-rich-region-deletion
#6
Emily A André, Elise M Braatz, Jeh-Ping Liu, Scott O Zeitlin
BACKGROUND: The polyglutamine (polyQ) stretch of the Huntingtin protein (HTT) in mammals is flanked by a highly conserved 17 amino acid N-terminal domain (N17), and a proline-rich region (PRR). The PRR is a binding site for many HTT-interacting proteins, and the N17 domain regulates several normal HTT functions, including HTT's ability to associate with membranes and organelles. OBJECTIVE: This study investigates the consequence of deleting mouse Huntingtin's (Htt's) N17 domain or a combination of its polyQ stretch and PRR (QP) on normal Htt function in mice...
February 16, 2017: Journal of Huntington's Disease
https://www.readbyqxmd.com/read/28211736/short-time-behavior-and-criticality-of-driven-lattice-gases
#7
Urna Basu, Valerio Volpati, Sergio Caracciolo, Andrea Gambassi
The nonequilibrium short-time critical behaviors of driven and undriven lattice gases are investigated via Monte Carlo simulations in two spatial dimensions starting from a fully disordered initial configuration. In particular, we study the time evolution of suitably defined order parameters, which account for the strong anisotropy introduced by the homogeneous drive. We demonstrate that, at short times, the dynamics of all these models is unexpectedly described by an effective continuum theory in which transverse fluctuations, i...
February 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28211463/ecological-and-genetic-basis-of-metapopulation-persistence-of-the-glanville-fritillary-butterfly-in-fragmented-landscapes
#8
Ilkka Hanski, Torsti Schulz, Swee Chong Wong, Virpi Ahola, Annukka Ruokolainen, Sami P Ojanen
Ecologists are challenged to construct models of the biological consequences of habitat loss and fragmentation. Here, we use a metapopulation model to predict the distribution of the Glanville fritillary butterfly during 22 years across a large heterogeneous landscape with 4,415 small dry meadows. The majority (74%) of the 125 networks into which the meadows were clustered are below the extinction threshold for long-term persistence. Among the 33 networks above the threshold, spatial configuration and habitat quality rather than the pooled habitat area predict metapopulation size and persistence, but additionally allelic variation in a SNP in the gene Phosphoglucose isomerase (Pgi) explains 30% of variation in metapopulation size...
February 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28210980/molecular-mechanisms-of-ire1%C3%AE-ask1-pathway-reactions-to-unfolded-protein-response-in-drn-neurons-of-post-traumatic-stress-disorder-rats
#9
Fanzhen Kong, Fang Han, Yanhao Xu, Yuxiu Shi
The goal of this study was to further elucidate the molecular mechanisms of post-traumatic stress disorder (PTSD) pathogenesis and to provide experimental evidence for new drug targets for effective PTSD treatment. Expression changes of IRE1α, ASK1, and other downstream molecules of the IRE1α-ASK1 endoplasmic reticulum stress (ERS) signaling pathway were investigated. JNK, P38, CHOP, Bcl-2, and Bax were analyzed at both protein and mRNA levels of dorsal raphe nucleus (DRN) neurons of PTSD rats. The rat PTSD model was established via the single-prolonged stress (SPS) method...
February 16, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/28210970/a-suspended-carbon-fiber-culture-to-model-myelination-by-human-schwann-cells
#10
Antonio Merolli, Yong Mao, Joachim Kohn
Understanding of myelination/remyelination process is essential to guide tissue engineering for nerve regeneration. In vitro models currently used are limited to cell population studies and cannot easily identify individual cell contribution to the process. We established a novel model to study the contribution of human Schwann cells to the myelination process. The model avoids the presence of neurons in culture; Schwann cells respond solely to the biophysical properties of an artificial axon. The model uses a single carbon fiber suspended in culture media far from the floor of the well...
April 2017: Journal of Materials Science. Materials in Medicine
https://www.readbyqxmd.com/read/28210739/retinal-oxidative-stress-at-the-onset-of-diabetes-determined-by-synchrotron-ftir-widefield-imaging-towards-diabetes-pathogenesis
#11
Ebrahim Aboualizadeh, Mahsa Ranji, Christine M Sorenson, Reyhaneh Sepehr, Nader Sheibani, Carol J Hirschmugl
Diabetic retinopathy is a microvascular complication of diabetes that can lead to blindness. In the present study, we aimed to determine the nature of diabetes-induced, highly localized biochemical changes in the neuroretina at the onset of diabetes. High-resolution synchrotron Fourier transform infrared (s-FTIR) wide field microscopy coupled with multivariate analysis (PCA-LDA) was employed to identify biomarkers of diabetic retinopathy with spatial resolution at the cellular level. We compared the retinal tissue prepared from 6-week-old Ins2(Akita/+) heterozygous (Akita/+, N = 6; a model of diabetes) male mice with the wild-type (control, N = 6) mice...
February 17, 2017: Analyst
https://www.readbyqxmd.com/read/28209969/solution-of-the-spatial-neutral-model-yields-new-bounds-on-the-amazonian-species-richness
#12
Yahav Shem-Tov, Matan Danino, Nadav M Shnerb
Neutral models, in which individual agents with equal fitness undergo a birth-death-mutation process, are very popular in population genetics and community ecology. Usually these models are applied to populations and communities with spatial structure, but the analytic results presented so far are limited to well-mixed or mainland-island scenarios. Here we combine analytic results and numerics to obtain an approximate solution for the species abundance distribution and the species richness for the neutral model on continuous landscape...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209776/distance-dependent-gradient-in-nmdar-driven-spine-calcium-signals-along-tapering-dendrites
#13
Alison S Walker, Guilherme Neves, Federico Grillo, Rachel E Jackson, Mark Rigby, Cian O'Donnell, Andrew S Lowe, Gema Vizcay-Barrena, Roland A Fleck, Juan Burrone
Neurons receive a multitude of synaptic inputs along their dendritic arbor, but how this highly heterogeneous population of synaptic compartments is spatially organized remains unclear. By measuring N-methyl-d-aspartic acid receptor (NMDAR)-driven calcium responses in single spines, we provide a spatial map of synaptic calcium signals along dendritic arbors of hippocampal neurons and relate this to measures of synapse structure. We find that quantal NMDAR calcium signals increase in amplitude as they approach a thinning dendritic tip end...
February 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28209283/community-audit-of-social-civil-and-activity-domains-in-diverse-environments-cascadde
#14
Emily A Knapp, Claudia Nau, Sy Brandau, Joseph DeWalle, Annemarie G Hirsch, Lisa Bailey-Davis, Brian S Schwartz, Thomas A Glass
There are currently no direct observation environmental audit tools that measure diverse aspects of the obesity-related environment efficiently and reliably in a variety of geographic settings. The goal was to develop a new instrument to reliably characterize the overall properties and features of rural, suburban, and urban settings along multiple dimensions. The Community Audit of Social, Civil, and Activity Domains in Diverse Environments (CASCADDE) is an iPad-based instrument that incorporates GPS coordinates and photography and comprises 214 items yielding seven summary indices...
February 10, 2017: American Journal of Preventive Medicine
https://www.readbyqxmd.com/read/28209171/integrated-strategy-for-in-vitro-characterization-of-a-bileaflet-mechanical-aortic-valve
#15
Francesca Maria Susin, Stefania Espa, Riccardo Toninato, Stefania Fortini, Giorgio Querzoli
BACKGROUND: Haemodynamic performance of heart valve prosthesis can be defined as its ability to fully open and completely close during the cardiac cycle, neither overloading heart work nor damaging blood particles when passing through the valve. In this perspective, global and local flow parameters, valve dynamics and blood damage safety of the prosthesis, as well as their mutual interactions, have all to be accounted for when assessing the device functionality. Even though all these issues have been and continue to be widely investigated, they are not usually studied through an integrated approach yet, i...
February 16, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28208764/spatial-impairment-and-memory-in-genetic-disorders-insights-from-mouse-models
#16
Sang Ah Lee, Valter Tucci, Giorgio Vallortigara
Research across the cognitive and brain sciences has begun to elucidate some of the processes that guide navigation and spatial memory. Boundary geometry and featural landmarks are two distinct classes of environmental cues that have dissociable neural correlates in spatial representation and follow different patterns of learning. Consequently, spatial navigation depends both on the type of cue available and on the type of learning provided. We investigated this interaction between spatial representation and memory by administering two different tasks (working memory, reference memory) using two different environmental cues (rectangular geometry, striped landmark) in mouse models of human genetic disorders: Prader-Willi syndrome (PWScr(m+/p-) mice, n = 12) and Beta-catenin mutation (Thr653Lys-substituted mice, n = 12)...
February 9, 2017: Brain Sciences
https://www.readbyqxmd.com/read/28208441/local-average-height-distribution-of-fluctuating-interfaces
#17
Naftali R Smith, Baruch Meerson, Pavel V Sasorov
Height fluctuations of growing surfaces can be characterized by the probability distribution of height in a spatial point at a finite time. Recently there has been spectacular progress in the studies of this quantity for the Kardar-Parisi-Zhang (KPZ) equation in 1+1 dimensions. Here we notice that, at or above a critical dimension, the finite-time one-point height distribution is ill defined in a broad class of linear surface growth models unless the model is regularized at small scales. The regularization via a system-dependent small-scale cutoff leads to a partial loss of universality...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208424/geometric-approach-to-optimal-nonequilibrium-control-minimizing-dissipation-in-nanomagnetic-spin-systems
#18
Grant M Rotskoff, Gavin E Crooks, Eric Vanden-Eijnden
Optimal control of nanomagnets has become an urgent problem for the field of spintronics as technological tools approach thermodynamically determined limits of efficiency. In complex, fluctuating systems, such as nanomagnetic bits, finding optimal protocols is challenging, requiring detailed information about the dynamical fluctuations of the controlled system. We provide a physically transparent derivation of a metric tensor for which the length of a protocol is proportional to its dissipation. This perspective simplifies nonequilibrium optimization problems by recasting them in a geometric language...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208398/driven-tracers-in-narrow-channels
#19
J Cividini, D Mukamel, H A Posch
Steady-state properties of a driven tracer moving in a narrow two-dimensional (2D) channel of quiescent medium are studied. The tracer drives the system out of equilibrium, perturbs the density and pressure fields, and gives the bath particles a nonzero average velocity, creating a current in the channel. Three models in which the confining effect of the channel is probed are analyzed and compared in this study: the first is the simple symmetric exclusion process (SSEP), for which the stationary density profile and the pressure on the walls in the frame of the tracer are computed...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208379/prediction-of-the-moments-in-advection-diffusion-lattice-boltzmann-method-i-truncation-dispersion-skewness-and-kurtosis
#20
Irina Ginzburg
The effect of the heterogeneity in the soil structure or the nonuniformity of the velocity field on the modeled resident time distribution (RTD) and breakthrough curves is quantified by their moments. While the first moment provides the effective velocity, the second moment is related to the longitudinal dispersion coefficient (k_{T}) in the developed Taylor regime; the third and fourth moments are characterized by their normalized values skewness (Sk) and kurtosis (Ku), respectively. The purpose of this investigation is to examine the role of the truncation corrections of the numerical scheme in k_{T}, Sk, and Ku because of their interference with the second moment, in the form of the numerical dispersion, and in the higher-order moments, by their definition...
January 2017: Physical Review. E
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