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Diffusion Models

Moises Hernandez-Fernandez, Istvan Reguly, Saad Jbabdi, Mike Giles, Stephen Smith, Stamatios N Sotiropoulos
The great potential of computational diffusion MRI (dMRI) relies on indirect inference of tissue microstructure and brain connections, since modelling and tractography frameworks map diffusion measurements to neuroanatomical features. This mapping however can be computationally highly expensive, particularly given the trend of increasing dataset sizes and the complexity in biophysical modelling. Limitations on computing resources can restrict data exploration and methodology development. A step forward is to take advantage of the computational power offered by recent parallel computing architectures, especially Graphics Processing Units (GPUs)...
December 8, 2018: NeuroImage
Pranas Katauskis, Feliksas Ivanauskas, Aidas Alaburda
Information in the brain is stored in a form of an altered synaptic strength between neurons. The long-term potentiation (LTP), a phenomenon when a short-term increase in neural activity is transformed into a long-lasting increase in strengths of synaptic connectivity, provides an experimental substrate of memory. Using reaction-diffusion equations, we established an LTP model, describing the dynamics of glutamate (Glu), calcium (Ca2+ ) and nitric oxide (NO) in response to the stimulus-a presynaptic action potential...
December 10, 2018: Bulletin of Mathematical Biology
Fabronia Murad, Ana J Garcia-Saez
The proteins of the Bcl-2 family regulate apoptosis by forming a complex interaction network whose output determines whether mitochondrial outer membrane permeabilization is executed. Quantification of complex formation between Bcl-2 proteins in solution and in membranes is therefore key to understand how the hierarchy of interactions controls cell death induction. Fluorescence correlation spectroscopy (FCS) is a noninvasive, nondestructive method to investigate the mobility and the association of fluorescently labeled biomolecules that has provided useful insight into the binding affinity of the Bcl-2 interactome...
2019: Methods in Molecular Biology
François Lucia, Dimitris Visvikis, Martin Vallières, Marie-Charlotte Desseroit, Omar Miranda, Philippe Robin, Pietro Andrea Bonaffini, Joanne Alfieri, Ingrid Masson, Augustin Mervoyer, Caroline Reinhold, Olivier Pradier, Mathieu Hatt, Ulrike Schick
PURPOSE: The aim of this study was to validate previously developed radiomics models relying on just two radiomics features from 18 F-fluorodeoxyglucose positron emission tomography (PET) and magnetic resonance imaging (MRI) images for prediction of disease free survival (DFS) and locoregional control (LRC) in locally advanced cervical cancer (LACC). METHODS: Patients with LACC receiving chemoradiotherapy were enrolled in two French and one Canadian center. Pre-treatment imaging was performed for each patient...
December 7, 2018: European Journal of Nuclear Medicine and Molecular Imaging
E Wenzler, M Lee, T J Wu, K A Meyer, R K Shields, M H Nguyen, C J Clancy, R M Humphries, A T Harrington
Objectives: To ensure the accuracy of susceptibility testing methods for ceftazidime/avibactam. Methods: The performances of the Etest (bioMérieux), 30/20 μg disc (Hardy diagnostics) and 10/4 μg disc (Mast Group) were evaluated against the reference broth microdilution (BMD) method for 102 clinically relevant Gram-negative organisms: 69 ceftazidime- and meropenem-resistant Klebsiella pneumoniae and 33 MDR non-K. pneumoniae. Essential and categorical agreement along with major and very major error rates were determined according to CLSI guidelines...
December 10, 2018: Journal of Antimicrobial Chemotherapy
Jacinta Edebeli, Markus Ammann, Thorsten Bartels-Rausch
The reaction of ozone with bromide is an initiation process in bromine activation resulting in the formation of reactive bromine species with impacts on the fate of compounds in the lower atmosphere. Environmental halide sources often contain organics, which are known to influence aqueous bulk reactivity. Here, we present a study investigating the temperature dependence of bromide oxidation by ozone using a coated wall flow tube reactor coated with an aqueous mixture of citric acid, as a proxy for oxidized secondary organic matter, and sodium bromide...
December 10, 2018: Environmental Science. Processes & Impacts
Krishnendu Kundu, Marie Ramirez Cohen, Akiva Feintuch, Daniella Goldfarb, Shimon Vega
Dynamic Nuclear Polarization (DNP) is an efficient technique for enhancing NMR signals by utilizing the large polarization of electron spins to polarize nuclei. The mechanistic details of the polarization transfer process involve the depolarization of the electrons resulting from microwave (MW) irradiation (saturation), as well as electron-electron cross-relaxation occurring during the DNP experiment. Recently, electron-electron double resonance (ELDOR) experiments have been performed under DNP conditions to map the depolarization profile along the EPR spectrum as a consequence of spectral diffusion...
December 11, 2018: Physical Chemistry Chemical Physics: PCCP
Wei Song, Guiyun Song, Can Zhao, Xiaoguang Li, Xiaojiao Pei, Wen Zhao, Yudan Gao, Jia-Sheng Rao, Hongmei Duan, Zhaoyang Yang
The purpose of this study was to assess the pathological variation in white matter tracts in the adult severe thoracic contusion spinal cord injury (SCI) rat models combined with in vivo magnetic resonance imaging (MRI), as well as the effect of spared white matter (WM) quantity on hindlimb motor function recovery. 7.0T MRI was conducted for all experimental animals before SCI and 1, 3, 7, and 14 days after SCI. The variation in the white matter tract in different regions of the spinal cord after SCI was examined by luxol fast blue (LFB) staining, NF200 immunochemistry, and diffusion tensor imaging (DTI) parameters, including fraction anisotropy, mean diffusivity, axial diffusion, and radial diffusivity...
2018: BioMed Research International
Andrei Irimia, Xiaoyu Lei, Carinna M Torgerson, Zachary J Jacokes, Sumiko Abe, John D Van Horn
Despite substantial efforts, it remains difficult to identify reliable neuroanatomic biomarkers of autism spectrum disorder (ASD) based on magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI). Studies which use standard statistical methods to approach this task have been hampered by numerous challenges, many of which are innate to the mathematical formulation and assumptions of general linear models (GLM). Although the potential of alternative approaches such as machine learning (ML) to identify robust neuroanatomic correlates of psychiatric disease has long been acknowledged, few studies have attempted to evaluate the abilities of ML to identify structural brain abnormalities associated with ASD...
2018: Frontiers in Computational Neuroscience
Yang-Min Zheng, Bo Chen, Jian-Dong Jiang, Jing-Pu Zhang
Epilepsy is a neuronal dysfunction syndrome characterized by transient and diffusely abnormal discharges of neurons in the brain. Previous studies have shown that mutations in the syntaxin 1b ( stx1b ) gene cause a familial, fever-associated epilepsy syndrome. It is unclear as to whether the stx1b gene also correlates with other stimulations such as flashing and/or mediates the effects of antiepileptic drugs. In this study, we found that the expression of stx1b was present mainly in the brain and was negatively correlated with seizures in a pentylenetetrazole (PTZ)-induced seizure zebrafish model...
2018: Frontiers in Molecular Neuroscience
Rajamani Krishna
Molecular dynamics simulation data for a variety of binary guest mixtures (H2 /CO2 , Ne/CO2 , CH4 /CO2 , CO2 /N2 , H2 /CH4 , H2 /Ar, CH4 /Ar, Ar/Kr, Ne/Ar, CH4 /C2 H6 , CH4 /C3 H8 , C2 H6 C3 H8 , CH4 / n C4 H10 , and CH4 / n C5 H11 ) in zeolites (MFI, BEA, ISV, FAU (all-silica), NaY, NaX, LTA, CHA, DDR) and metal-organic frameworks (MOFs) (IRMOF-1, CuBTC, MgMOF-74) show that the Maxwell-Stefan (M-S) diffusivities, Đ 1 , Đ 2 , Đ 12 , are strongly dependent on the molar loadings. The main aim of this article is to develop a fundamental basis for describing the loading dependence of M-S diffusivities...
November 30, 2018: ACS Omega
Geneviève Richard, Knut Kolskår, Anne-Marthe Sanders, Tobias Kaufmann, Anders Petersen, Nhat Trung Doan, Jennifer Monereo Sánchez, Dag Alnæs, Kristine M Ulrichsen, Erlend S Dørum, Ole A Andreassen, Jan Egil Nordvik, Lars T Westlye
Multimodal imaging enables sensitive measures of the architecture and integrity of the human brain, but the high-dimensional nature of advanced brain imaging features poses inherent challenges for the analyses and interpretations. Multivariate age prediction reduces the dimensionality to one biologically informative summary measure with potential for assessing deviations from normal lifespan trajectories. A number of studies documented remarkably accurate age prediction, but the differential age trajectories and the cognitive sensitivity of distinct brain tissue classes have yet to be adequately characterized...
2018: PeerJ
Silvia Da Ros, Luca Aresu, Serena Ferraresso, Eleonora Zorzan, Eugenio Gaudio, Francesco Bertoni, Mauro Dacasto, Mery Giantin
Despite canine B-cell Lymphoma (BCL) representing the most common haematological tumour, epigenetic events driving development and progression are scarcely known. Recently, canine Diffuse Large BCL (DLBCL) DNA methylome by genome-wide CpG microarray has identified genes and pathways associated to pathogenesis. To validate data previously obtained by array analysis, the CLBL-1 cell line was used and the HOXD10, FGFR2, ITIH5 and RASAL3 genes were selected. CLBL-1 cells were treated with two hypomethylating drugs (HDs; IC50, 50% inhibitory concentration), i...
2018: PloS One
Aaro Kasurinen, Taina Tervahartiala, Alli Laitinen, Arto Kokkola, Timo Sorsa, Camilla Böckelman, Caj Haglund
Matrix metalloproteinases (MMPs), endopeptidases with diverse biochemical functions, can promote cancer cell invasion and metastasis by degrading the extracellular matrix. A high matrix metalloproteinase-14 (MMP-14) expression in gastric cancer tissue has been associated with metastasis and poor prognosis. To further understand this association, we investigated serum MMP-14 as a biomarker in gastric cancer patients. The patient cohort consisted of 240 gastric adenocarcinoma patients who underwent surgery at Helsinki University Hospital, Finland, between 2000 and 2009...
2018: PloS One
Mengrou Shan, David Dai, Arunodai Vudem, Jeffrey D Varner, Abraham D Stroock
Cancer metabolism has received renewed interest as a potential target for cancer therapy. In this study, we use a multi-scale modeling approach to interrogate the implications of three metabolic scenarios of potential clinical relevance: the Warburg effect, the reverse Warburg effect and glutamine addiction. At the intracellular level, we construct a network of central metabolism and perform flux balance analysis (FBA) to estimate metabolic fluxes; at the cellular level, we exploit this metabolic network to calculate parameters for a coarse-grained description of cellular growth kinetics; and at the multicellular level, we incorporate these kinetic schemes into the cellular automata of an agent-based model (ABM), iDynoMiCS...
December 2018: PLoS Computational Biology
Aakash Kumar, Hagit Barda, Leonid Klinger, Michael W Finnis, Vincenzo Lordi, Eugen Rabkin, David J Srolovitz
Interface diffusion along a metal/ceramic interface present in numerous energy and electronic devices can critically affect their performance and stability. Hole formation in a polycrystalline Ni film on an α-Al2 O3 substrate coupled with a continuum diffusion analysis demonstrates that Ni diffusion along the Ni/α-Al2 O3 interface is surprisingly fast. Ab initio calculations demonstrate that both Ni vacancy formation and migration energies at the coherent Ni/α-Al2 O3 interface are much smaller than in bulk Ni, suggesting that the activation energy for diffusion along coherent Ni/α-Al2 O3 interfaces is comparable to that along (incoherent/high angle) grain boundaries...
December 7, 2018: Nature Communications
Heleen Demeyer, David Donaire-Gonzalez, Elena Gimeno-Santos, Maria A Ramon, Jordi de Batlle, Marta Benet, Ignasi Serra, Stefano Guerra, Eva Farrero, Esther Rodriguez, Jaume Ferrer, Jaume Sauleda, Eduard Monso, Joaquim Gea, Robert Rodriguez-Roisin, Alvar Agusti, Josep M Antó, Judith Garcia-Aymerich
INTRODUCTION: COPD progression is variable and affects several disease domains, including decline in lung function, exercise capacity, muscle strength and health status as well as changes in body composition. We aimed to assess the longitudinal association of physical activity (PA) with these a priori selected components of disease progression. METHOD: We studied 114 COPD patients from the PAC-COPD cohort [94% male, mean (SD) 70 (8) years of age, 54 (16) FEV1 % predicted] at baseline and 2...
December 7, 2018: Medicine and Science in Sports and Exercise
Sourajit M Mustafi, Jaroslaw Harezlak, Chandana Kodiweera, Jennifer S Randolph, James C Ford, Heather A Wishart, Yu-Chien Wu
Multiple sclerosis is a neurodegenerative and inflammatory disease, a hallmark of which is demyelinating lesions in the white matter. We hypothesized that alterations in white matter microstructures can be non-invasively characterized by advanced diffusion magnetic resonance imaging. Seven diffusion metrics were extracted from hybrid diffusion imaging acquisitions via classic diffusion tensor imaging, neurite orientation dispersion and density imaging, and q-space imaging. We investigated the sensitivity of the diffusion metrics in 36 sets of regions of interest in the brain white matter of six female patients (age 52...
January 2019: Neural Regeneration Research
Liu-Hong Zhu, Zhong-Ping Zhang, Fu-Nan Wang, Qi-Hua Cheng, Gang Guo
The location of an acute ischemic stroke is associated with its prognosis. The widely used Gaussian model-based parameter, apparent diffusion coefficient (ADC), cannot reveal microstructural changes in different locations or the degree of infarction. This prospective observational study was reviewed and approved by the Institutional Review Board of Xiamen Second Hospital, China (approval No. 2014002).Diffusion kurtosis imaging (DKI) was used to detect 199 lesions in 156 patients with acute ischemic stroke (61 males and 95 females), mean age 63...
February 2019: Neural Regeneration Research
Joana Wensing, Laura Carraresi, Stefanie Bröring
A transition towards a bio-based economy is accompanied by a growing demand for biomass resources as fossil fuels need to be replaced for the more sustainable production of consumer goods, chemicals and energy. To increase the supply of renewable biomass and avoid a conflict with food production, currently underutilized by-products (i.e. leaves, stems) from horticultural production could be valorised as feedstock. The success of this approach depends on farmers' willingness to adopt novel practices like the collection and treatment of plant leaves...
December 6, 2018: Journal of Environmental Management
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