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Spatial modeling

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https://www.readbyqxmd.com/read/28817569/long-term-assessment-of-whale-shark-population-demography-and-connectivity-using-photo-identification-in-the-western-atlantic-ocean
#1
Jennifer A McKinney, Eric R Hoffmayer, Jason Holmberg, Rachel T Graham, William B Driggers, Rafael de la Parra-Venegas, Beatriz E Galván-Pastoriza, Steve Fox, Simon J Pierce, Alistair D M Dove
The predictable occurrence of whale sharks, Rhincodon typus, has been well documented in several areas. However, information relating to their migratory patterns, residency times and connectivity across broad spatial scales is limited. In the present study photo-identification data is used to describe whale shark population structure and connectivity among known aggregation sites within the Western Central Atlantic Ocean (WCA). From 1999 to 2015, 1,361 individuals were identified from four distinct areas: the Yucatan Peninsula, Mexico (n = 1,115); Honduras (n = 146); northern Gulf of Mexico, United States (n = 112), and Belize (n = 49)...
2017: PloS One
https://www.readbyqxmd.com/read/28817561/comparing-efficacies-of-moxifloxacin-levofloxacin-and-gatifloxacin-in-tuberculosis-granulomas-using-a-multi-scale-systems-pharmacology-approach
#2
Elsje Pienaar, Jansy Sarathy, Brendan Prideaux, Jillian Dietzold, Véronique Dartois, Denise E Kirschner, Jennifer J Linderman
Granulomas are complex lung lesions that are the hallmark of tuberculosis (TB). Understanding antibiotic dynamics within lung granulomas will be vital to improving and shortening the long course of TB treatment. Three fluoroquinolones (FQs) are commonly prescribed as part of multi-drug resistant TB therapy: moxifloxacin (MXF), levofloxacin (LVX) or gatifloxacin (GFX). To date, insufficient data are available to support selection of one FQ over another, or to show that these drugs are clinically equivalent. To predict the efficacy of MXF, LVX and GFX at a single granuloma level, we integrate computational modeling with experimental datasets into a single mechanistic framework, GranSim...
August 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28817289/how-to-drive-a-flashing-electron-ratchet-to-maximize-current
#3
Ofer Kedem, Bryan Lau, Emily A Weiss
Biological systems utilize a combination of asymmetry, noise, and chemical energy to produce motion in the highly damped environment of the cell with molecular motors, many of which are "ratchets", non-equilibrium devices for producing directed transport using non-directional perturbations, without a net bias. The underlying ratchet principle has been implemented in man-made micro- and nano-devices, to transport charged particles by oscillating an electric potential with repeating asymmetric features. In this experimental study, the ratcheting of electrons in an organic semiconductor is optimized by tuning the temporal modulation of the oscillating potential, applied using nanostructured electrodes...
August 17, 2017: Nano Letters
https://www.readbyqxmd.com/read/28817122/single-cell-mechanogenetics-using-monovalent-magnetoplasmonic-nanoparticles
#4
Ji-Wook Kim, Daeha Seo, Jung-Uk Lee, Kaden M Southard, Yongjun Lim, Daehyun Kim, Zev J Gartner, Young-Wook Jun, Jinwoo Cheon
Spatiotemporal interrogation of signal transduction at the single-cell level is necessary to answer a host of important biological questions. This protocol describes a nanotechnology-based single-cell and single-molecule perturbation tool, termed mechanogenetics, that enables precise spatial and mechanical control over genetically encoded cell-surface receptors in live cells. The key components of this tool are a magnetoplasmonic nanoparticle (MPN) actuator that delivers defined spatial and mechanical cues to receptors through target-specific one-to-one engagement and a micromagnetic tweezers (μMT) that remotely controls the magnitude of force exerted on a single MPN...
September 2017: Nature Protocols
https://www.readbyqxmd.com/read/28816702/as-above-so-below-towards-understanding-inverse-models-in-bci
#5
Jussi T Lindgren
In Brain-Computer Interfaces (BCI), measurements of the users brain activity are classified into commands for the computer. With EEG-based BCIs, the origins of the classified phenomena are often considered to be spatially localized in the cortical volume and mixed in the EEG. Does the reconstruction of the source activities in the volume help in building more accurate BCIs? The answer remains inconclusive despite previous work. In this paper, we study the question by contrasting the physiology-driven source reconstruction with data-driven representations obtained by statistical machine learning...
August 17, 2017: Journal of Neural Engineering
https://www.readbyqxmd.com/read/28816679/adaptive-unknown-input-estimation-by-sliding-modes-and-differential-neural-network-observer
#6
Ivan Salgado, Isaac Chairez
In this paper, a differential neural network (DNN) implemented as a robust observer estimates the dynamics of perturbed uncertain nonlinear systems affected by exogenous unknown inputs. In the first stage, the identification error converges into a neighborhood around the origin. Then, the second-order sliding mode supertwisting algorithm implemented as a robust exact differentiator reconstructed the unknown inputs. The approach proposed in this paper can be applied in the case of full access to the state vector (identification problem) and in the case of partial access to the state vector (estimation problem)...
August 15, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28816664/gradient-based-tone-mapping-for-rate-distortion-optimized-backward-compatible-high-dynamic-range-compression
#7
David Gommelet, Aline Roumy, Christine Guillemot, Michael Ropert, Julien Le Le Tanou
This paper addresses the problem of designing a global tone mapping operator for rate distortion optimized backward compatible compression of HDR images. We address the problem of tone mapping design for two different use cases leading to two different minimization problems. The first problem considered is the minimization of the distortion on the reconstructed HDR signal under a rate constraint on the SDR layer. The second problem remains the same minimization with an additional constraint to preserve a good quality for the SDR signal...
August 14, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28816521/plume-activity-and-tidal-deformation-on-enceladus-influenced-by-faults-and-variable-ice-shell-thickness
#8
Marie Běhounková, Ondřej Souček, Jaroslav Hron, Ondřej Čadek
We investigated the effect of variations in ice shell thickness and of the tiger stripe fractures crossing Enceladus' south polar terrain on the moon's tidal deformation by performing finite element calculations in three-dimensional geometry. The combination of thinning in the polar region and the presence of faults has a synergistic effect that leads to an increase of both the displacement and stress in the south polar terrain by an order of magnitude compared to that of the traditional model with a uniform shell thickness and without faults...
August 17, 2017: Astrobiology
https://www.readbyqxmd.com/read/28816478/towards-a-unified-model-of-vision-and-attention-effects-of-visual-landmarks-and-identity-cues-on-covert-and-overt-attention-movements
#9
Anthony J Lambert, Jaimie Wilkie, Andrea Greenwood, Nathan Ryckman, Evatte Sciberras-Lim, Laura-Jane Booker, Lenore Tahara-Eckl
To what extent are shifts of attention driven by encoding of visual-spatial landmarks, associated with useful locations, or by encoding of environmental cues that act as symbolic representations, providing information about where to look next? In Experiment 1 we found that when cues were presented with a long exposure time (300 ms) attention shifts were driven by the symbolic identity of cue stimuli, independently of their visual-spatial (landmark) features; but when cues were exposed very briefly, (66 ms), attention shifts were independent of symbolic information, and were driven instead by visual landmark features...
August 17, 2017: Journal of Experimental Psychology. Human Perception and Performance
https://www.readbyqxmd.com/read/28815874/white-matter-alterations-associate-with-onset-symptom-dimension-in-obsessive-compulsive-disorder
#10
Irene Bollettini, Mario Gennaro Mazza, Laura Muzzarelli, Sara Dallaspezia, Sara Poletti, Benedetta Vai, Enrico Smeraldi, Francesco Benedetti
AIM: The high heterogeneity of obsessive-compulsive disorder is best described by a multidimensional model involving symptom dimensions. Our study aimed at investigating white matter alterations associated with obsessive-compulsive disorder focusing on the impact of long lasting effect of symptom dimensions assessed at onset of the illness. Furthermore, we investigate white matter alterations associated with this disorder controlling for the impact of medications and for the prevailing current symptom dimension...
August 16, 2017: Psychiatry and Clinical Neurosciences
https://www.readbyqxmd.com/read/28815472/comparison-of-pet-ct-and-whole-mount-histopathology-sections-of-the-human-prostate-a-new-strategy-for-voxel-wise-evaluation
#11
F Schiller, T Fechter, C Zamboglou, A Chirindel, N Salman, C A Jilg, V Drendel, M Werner, P T Meyer, A-L Grosu, M Mix
BACKGROUND: Implementation of PET/CT in diagnosis of primary prostate cancer (PCa) requires a profound knowledge about the tracer, preferably from a quantitative evaluation. Direct visual comparison of PET/CT slices to whole prostate sections is hampered by considerable uncertainties from imperfect coregistration and fundamentally different image modalities. In the current study, we present a novel method for advanced voxel-wise comparison of histopathology from excised prostates to pre-surgical PET...
August 17, 2017: EJNMMI Physics
https://www.readbyqxmd.com/read/28815452/-18-f-fdg-pet-radiomics-approaches-comparing-and-clustering-features-in-cervical-cancer
#12
Tetsuya Tsujikawa, Tasmiah Rahman, Makoto Yamamoto, Shizuka Yamada, Hideaki Tsuyoshi, Yasushi Kiyono, Hirohiko Kimura, Yoshio Yoshida, Hidehiko Okazawa
OBJECTIVES: The aims of our study were to find the textural features on (18)F-FDG PET/CT which reflect the different histological architectures between cervical cancer subtypes and to make a visual assessment of the association between (18)F-FDG PET textural features in cervical cancer. METHODS: Eighty-three cervical cancer patients [62 squamous cell carcinomas (SCCs) and 21 non-SCCs (NSCCs)] who had undergone pretreatment (18)F-FDG PET/CT were enrolled. A texture analysis was performed on PET/CT images, from which 18 PET radiomics features were extracted including first-order features such as standardized uptake value (SUV), metabolic tumor volume (MTV) and total lesion glycolysis (TLG), second- and high-order textural features using SUV histogram, normalized gray-level co-occurrence matrix (NGLCM), and neighborhood gray-tone difference matrix, respectively...
August 16, 2017: Annals of Nuclear Medicine
https://www.readbyqxmd.com/read/28814763/spatial-genomic-heterogeneity-in-multiple-myeloma-revealed-by-multi-region-sequencing
#13
L Rasche, S S Chavan, O W Stephens, P H Patel, R Tytarenko, C Ashby, M Bauer, C Stein, S Deshpande, C Wardell, T Buzder, G Molnar, M Zangari, F van Rhee, S Thanendrarajan, C Schinke, J Epstein, F E Davies, B A Walker, T Meissner, B Barlogie, G J Morgan, N Weinhold
In multiple myeloma malignant plasma cells expand within the bone marrow. Since this site is well-perfused, a rapid dissemination of "fitter" clones may be anticipated. However, an imbalanced distribution of multiple myeloma is frequently observed in medical imaging. Here, we perform multi-region sequencing, including iliac crest and radiology-guided focal lesion specimens from 51 patients to gain insight into the spatial clonal architecture. We demonstrate spatial genomic heterogeneity in more than 75% of patients, including inactivation of CDKN2C and TP53, and mutations affecting mitogen-activated protein kinase genes...
August 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28814744/monocyte-infiltration-and-proliferation-reestablish-myeloid-cell-homeostasis-in-the-mouse-retina-following-retinal-pigment-epithelial-cell-injury
#14
Wenxin Ma, Yikui Zhang, Chun Gao, Robert N Fariss, Johnny Tam, Wai T Wong
Age-related macular degeneration (AMD), a leading contributor of vision loss, currently lacks comprehensive treatment. While AMD histopathology involves retinal pigment epithelium (RPE) injury associated with immune cell infiltration, the nature of immune cell responses to RPE injury remains undefined. We induced RPE injury pharmacologically and genetically in transgenic mouse models in which microglia and systemic monocytes were separately tagged, enabling a spatial and temporal dissection of the relative contributions of microglia vs...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814731/spatial-regression-and-prediction-of-water-quality-in-a-watershed-with-complex-pollution-sources
#15
Xiaoying Yang, Qun Liu, Xingzhang Luo, Zheng Zheng
Fast economic development, burgeoning population growth, and rapid urbanization have led to complex pollution sources contributing to water quality deterioration simultaneously in many developing countries including China. This paper explored the use of spatial regression to evaluate the impacts of watershed characteristics on ambient total nitrogen (TN) concentration in a heavily polluted watershed and make predictions across the region. Regression results have confirmed the substantial impact on TN concentration by a variety of point and non-point pollution sources...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814718/adaptive-and-non-adaptive-divergence-in-a-common-landscape
#16
Joost A M Raeymaekers, Anurag Chaturvedi, Pascal I Hablützel, Io Verdonck, Bart Hellemans, Gregory E Maes, Luc De Meester, Filip A M Volckaert
Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes-three-spined and nine-spined stickleback-differ in the strength and nature of neutral and adaptive divergence along a salinity gradient...
August 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28814635/perception-of-the-dynamic-visual-vertical-during-sinusoidal-linear-motion
#17
Antonella Pomante, Luc P J Selen, W Pieter Medendorp
The vestibular system provides information for spatial orientation. However, this information is ambiguous: because the otoliths sense the gravito-inertial force, they cannot distinguish gravitational and inertial components. As a consequence, prolonged linear acceleration of the head can be interpreted as tilt, referred to as the somatogravic effect. Previous modeling work suggests that the brain disambiguates the otolith signal according to the rules of Bayesian inference, combining noisy canal cues with the a priori assumption that prolonged linear accelerations are unlikely...
August 16, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28813944/robotic-set-up-to-quantify-hand-eye-behavior-in-motor-execution-and-learning-of-children-with-autism-spectrum-disorder
#18
Claudia Casellato, Marta Gandolla, Alessandro Crippa, Alessandra Pedrocchi
Autism spectrum disorder (ASD) is a multifaceted neurodevelopmental disorder characterized by a persistence of social and communication impairment, and restricted and repetitive behaviors. However, motor disorders have also been described, but not objectively assessed. Most studies showed inefficient eye-hand coordination and motor learning in children with ASD; in other experiments, mechanisms of acquisition of internal models in self-generated movements appeared to be normal in autism. In this framework, we have developed a robotic protocol, recording gaze and hand data during upper limb tasks, in which a haptic pen-like handle is moved along specific trajectories displayed on the screen...
July 2017: IEEE ... International Conference on Rehabilitation Robotics: [proceedings]
https://www.readbyqxmd.com/read/28813816/computational-rehabilitation-of-neglect-using-state-space-models-to-understand-the-recovery-mechanisms
#19
Giulia Sedda, Marcella Ottonello, Elena Fiabane, Caterina Pistarini, Anna Sedda, Vittorio Sanguineti
Unilateral spatial neglect is a neuropsychological syndrome often observed in right hemisphere stroke patients. The symptoms differ from subject to subject. A few rehabilitation approaches, e.g. prism adaptation, have demonstrated some effect in reducing the symptoms, but the underlying mechanisms are still largely unclear. Recently, neural models have been proposed to qualitatively describe cortical lesions, the resulting neglect symptoms and the effects of treatment. However, these predictions are qualitative and cannot be used to compare different hypotheses or to interpret symptoms at individual subjects level...
July 2017: IEEE ... International Conference on Rehabilitation Robotics: [proceedings]
https://www.readbyqxmd.com/read/28813680/antibiotics-disrupt-coordination-between-transcriptional-and-phenotypic-stress-responses-in-pathogenic-bacteria
#20
Paul A Jensen, Zeyu Zhu, Tim van Opijnen
Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude...
August 15, 2017: Cell Reports
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