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Spatial modeling

Malgorzata A Gazda, Pedro Andrade, Sandra Afonso, Jolita Dilyte, John P Archer, Ricardo J Lopes, Rui Faria, Miguel Carneiro
Racing pigeons have been selectively bred to find their way home quickly over what are often extremely long distances. This breed is of substantial commercial value and is also an excellent avian model to gain empirical insights into the evolution of traits associated with flying performance and spatial orientation. Here, we investigate the molecular basis of the superior athletic and navigational capabilities of racing pigeons using whole-genome and RNA sequencing data. We inferred multiple signatures of positive selection distributed across the genome of racing pigeons...
March 13, 2018: Molecular Biology and Evolution
Cheng Jin, Jianjiang Feng, Lei Wang, Heng Yu, Jiang Liu, Jiwen Lu, Jie Zhou
In this paper, we present an approach for left atrial appendage (LAA) multi-phase fast segmentation and quantitative assisted diagnosis of atrial fibrillation (AF) based on 4D-CT data. We take full advantage of the temporal dimension information to segment the living, flailed LAA based on a parametric max-flow method and graph-cut approach to build 3-D model of each phase. To assist the diagnosis of AF, we calculate the volumes of 3-D models, and then generate a "volume-phase" curve to calculate the important dynamic metrics: ejection fraction, filling flux, and emptying flux of the LAA's blood by volume...
March 9, 2018: Computers in Biology and Medicine
Caroline Oakland, Jaymie R Meliker
BACKGROUND: Few studies have investigated the association between radon and thyroid cancer despite the sensitivity of the thyroid gland to radiation. Our goal is to investigate the association between county-level radon and incidence of female thyroid cancer in the US States of Iowa, New Jersey, and Wisconsin. METHODS: Thyroid cancer incidence data were provided by individual state cancer registries and span 1990-2013. Radon data come from a publicly available third-party database, AirChek, accessed in 2017...
March 16, 2018: Toxics
G Satta, N Mascia, T Serra, A Salis, L Saba, S Sanna, M G Zucca, E Angelucci, A Gabbas, F Culurgioni, P Pili, E Mura, M Cappai, M G Ennas, P Cocco
We investigated the association between environmental exposure to radiofrequency electromagnetic fields (RF-EMF) and risk of lymphoma subtypes in a case-control study comprised of 322 patients and 444 individuals serving as controls in Sardinia, Italy in 1998-2004. Questionnaire information included the self-reported distance of the three longest held residential addresses from fixed radio-television transmitters and mobile phone base stations. We georeferenced the residential addresses of all study subjects and obtained the spatial coordinates of mobile phone base stations...
March 16, 2018: Radiation Research
Hirofumi Akamatsu, Yakun Yuan, Vladimir A Stoica, Greg Stone, Tiannan Yang, Zijian Hong, Shiming Lei, Yi Zhu, Ryan C Haislmaier, John W Freeland, Long-Qing Chen, Haidan Wen, Venkatraman Gopalan
Using time- and spatially resolved hard x-ray diffraction microscopy, the striking structural and electrical dynamics upon optical excitation of a single crystal of BaTiO_{3} are simultaneously captured on subnanoseconds and nanoscale within individual ferroelectric domains and across walls. A large emergent photoinduced electric field of up to 20×10^{6}  V/m is discovered in a surface layer of the crystal, which then drives polarization and lattice dynamics that are dramatically distinct in a surface layer versus bulk regions...
March 2, 2018: Physical Review Letters
Thomas Lilienkamp, Ulrich Parlitz
Transient chaos in spatially extended systems can be characterized by the length of the transient phase, which typically grows quickly with the system size (supertransients). For a large class of these systems, the chaotic phase terminates abruptly, without any obvious precursors in commonly used observables. Here we investigate transient spatiotemporal chaos in two different models of this class. By probing the state space using perturbed trajectories we show the existence of a "terminal transient phase," which occurs prior to the abrupt collapse of chaotic dynamics...
March 2, 2018: Physical Review Letters
Brendan Dyett, Hao Hao, Detlef Lohse, Xuehua Zhang
The coalescence between growing droplets is important for the surface coverage and spatial arrangements of droplets on surfaces. In this work, total internal reflection fluorescence (TIRF) microscopy is utilized to in situ investigate the formation of nanodroplets around the rim of a polymer microcap, with sub-micron spatial and millisecond temporal resolution. We observe that the coalescence among droplets occurs frequently during their growth by solvent exchange. Our experimental results show that the position of the droplet from two merged droplets is related to the size of the parent droplets...
March 16, 2018: Soft Matter
Laura E Erban, Stephen B Balogh, Daniel E Campbell, Henry A Walker
Urban water systems consist of natural and engineered flows of water interacting in complex ways. System complexity can be understood via mass conservative models that account for the interrelationships among all major flows and storages. We have developed a generic urban water system model in the R package CityWaterBalance . CityWaterBalance provides a reproducible workflow for studying urban water systems by facilitating automated retrievals of open data and post-processing with open source R functions. It allows the user to 1) rapidly assemble a quantitative, comprehensive assessment of flows thorough an urban area, and 2) easily change the spatial and temporal boundaries of analysis...
February 1, 2018: Open Water
Sophie Meuret, Toon Coenen, Steffi Woo, Yong-Ho Ra, Zetian Mi, Albert Polman
Cathodoluminescence (CL) imaging spectroscopy provides two-dimensional optical excitation images of photonic nanostructures with deep-subwavelength spatial resolution. So far, CL imaging was unable to provide a direct measurement of the excitation and emission probabilities of photonic nanostructures in a spatially resolved manner. Here, we demonstrate that by mapping the cathodoluminescence autocorrelation function g(2) together with the CL spectral distribution the excitation and emission rates can be disentangled at every excitation position...
March 16, 2018: Nano Letters
Ilhem Bouderbala, Nadjia El Saadi, Alassane Bah, Pierre Auger
In this paper, we develop a 3D-individual-based model (IBM) to understand effect of various small-scale mechanisms in phytoplankton cells, on the cellular aggregation process. These mechanisms are: spatial interactions between cells due to their chemosensory abilities (chemotaxis), a molecular diffusion and a demographical process. The latter is considered as a branching process with a density-dependent death rate to take into account the local competition on resources. We implement the IBM and simulate various scenarios under real parameter values for phytoplankton cells...
March 15, 2018: Acta Biotheoretica
Jyoti Singh Kirar, R K Agrawal
This paper presents a novel algorithm (CVSTSCSP) for determining discriminative features from an optimal combination of temporal, spectral and spatial information for motor imagery brain computer interfaces. The proposed method involves four phases. In the first phase, EEG signal is segmented into overlapping time segments and bandpass filtered through frequency filter bank of variable size subbands. In the next phase, features are extracted from the segmented and filtered data using stationary common spatial pattern technique (SCSP) that can handle the non- stationarity and artifacts of EEG signal...
March 16, 2018: Journal of Medical Systems
Nikhil Krishnan, Daniel B Poll, Zachary P Kilpatrick
Working memory (WM) is limited in its temporal length and capacity. Classic conceptions of WM capacity assume the system possesses a finite number of slots, but recent evidence suggests WM may be a continuous resource. Resource models typically assume there is no hard upper bound on the number of items that can be stored, but WM fidelity decreases with the number of items. We analyze a neural field model of multi-item WM that associates each item with the location of a bump in a finite spatial domain, considering items that span a one-dimensional continuous feature space...
March 15, 2018: Journal of Computational Neuroscience
Michael J R Martin, Stephen A Matthews, Barrett A Lee
Although increasing racial and ethnic diversity is a demographic trend with society-wide implications, it has advanced farther in some parts of the United States than others. Our research seeks to understand this unevenness at the local level. Drawing on 1980-2010 census data, we use an innovative spatial analytic approach to examine the spread or diffusion of diversity across counties in the 48 contiguous states. Three perspectives-locational persistence, spatial assimilation, and institutional hub-offer different expectations about the nature of the diffusion process...
October 2017: Spatial Demography
Yan Yang, Zhongyin Zhou, Rong Liu, Lu Chen, Hongyu Xiang, Na Chen
Endoscopic retrograde cholangiopancreatography (ERCP) is an important treatment for inoperable hilar cholangiocarcinoma (HCC). The aim of the present study as to evaluate the clinical value of three-dimensional visualization (3DV) and 3D printing (3DP) technologies for ERCP in patients with HCC. The clinical data of 15 patients with HCC admitted for ERCP were analyzed retrospectively, including 9 males and 6 females. Thin-sliced data of computed tomography and magnetic resonance cholangiopancreatography (MRCP) were acquired and imported into Mimics Innovation Suite v17...
April 2018: Experimental and Therapeutic Medicine
Sue Kimbrough, R Chris Owen, Michelle Snyder, Jennifer Richmond-Bryant
The nitrogen dioxide/oxides of nitrogen (NO2 /NOX ) ratio is an important surrogate for NO to NO2 chemistry in dispersion models when estimating NOX impacts in a near-road environment. Existing dispersion models use different techniques and assumptions to represent NO to NO2 conversion and do not fully characterize all of the important atmospheric chemical and mechanical processes. Thus, "real-world" ambient measurements must be analyzed to assess the behavior of NO2 /NOX ratios near roadways. An examination of NO2 /NOX ratio data from a field study conducted in Las Vegas, Nevada (NV), from mid-December, 2008 through mid-December, 2009 provides insights into the appropriateness of assumptions about the NO2 /NOX ratio included in dispersion models...
September 7, 2017: Atmospheric Environment
Nathan H Schumaker, Allen Brookes
Context: Simulation models are increasingly used in both theoretical and applied studies to explore system responses to natural and anthropogenic forcing functions, develop defensible predictions of future conditions, challenge simplifying assumptions that facilitated past research, and to train students in scientific concepts and technology. Researcher's increased use of simulation models has created a demand for new platforms that balance performance, utility, and flexibility. Objectives: We describe HexSim, a powerful new spatially-explicit, individual-based modeling framework that will have applications spanning diverse landscape settings, species, stressors, and disciplines (e...
February 1, 2018: Landscape Ecology
Long Chen, Wen Tang, Nigel W John, Tao Ruan Wan, Jian Jun Zhang
BACKGROUND AND OBJECTIVE: While Minimally Invasive Surgery (MIS) offers considerable benefits to patients, it also imposes big challenges on a surgeon's performance due to well-known issues and restrictions associated with the field of view (FOV), hand-eye misalignment and disorientation, as well as the lack of stereoscopic depth perception in monocular endoscopy. Augmented Reality (AR) technology can help to overcome these limitations by augmenting the real scene with annotations, labels, tumour measurements or even a 3D reconstruction of anatomy structures at the target surgical locations...
May 2018: Computer Methods and Programs in Biomedicine
Yining Han, Jaehyeok Jin, Jacob W Wagner, Gregory A Voth
Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals...
March 14, 2018: Journal of Chemical Physics
Louise Wogelred, Fredrik Höök, Björn Agnarsson, Peter Sjövall
Accurate detection and quantification of individual molecules is important for the development of improved diagnostic methods as well as biochemical characterization of disease progression and treatments. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a surface analysis technique capable of imaging the distribution of specific molecules on surfaces with a high spatial resolution (<1 μm) and high sensitivity. ToF-SIMS is particularly suitable for detection of molecules up to ∼2 kDa, including lipids, whereas larger molecules, such as peptides and proteins, are fragmented during analysis, which makes them difficult to identify...
March 15, 2018: Biointerphases
Prakash Chandra, Alain M Jonas, Antony E Fernandes
Confinement and cooperativity are important design principles used by Nature to optimize catalytic activity in enzymes. In these biological systems, the precise sequence of the protein encodes for specific chain folding to preorganize critical amino acid side chains within defined binding pockets, allowing to express and trigger synergistic catalytic activation pathways. Here we show that short synthetic precision oligomers with the optimal sequence of catalytic units, spatially arranged by dense surface grafting to form confined cooperative "pockets", display an up to 5-fold activity improvement compared to a "mismatched" sequence or free oligomers using the (pyta)Cu/TEMPO/NMI-catalyzed aerobic selective oxidation of alcohols as a model reaction...
March 15, 2018: Journal of the American Chemical Society
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