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Computer and Visual

Stephanie Koller, Lars C Ebert, Rosa Maria Martinez, Till Sieberth
The ability to accurately determine injury dimensions is an essential property of forensic documentation. The current standard for injury documentation is photography using a scale to approximate the injury dimensions in the image. The technical qualities of the photograph, such as orthogonality, depth of the field and sharpness of the desired area, are vital to obtaining a correct measurement. Adequate training of the forensic staff can reduce technical errors; nonetheless, there will always be some loss of information when visualizing an injury as a three-dimensional (3D) object on a two-dimensional (2D) photograph...
November 16, 2018: Forensic Science International
Riccardo Calandrelli, Qiuyang Wu, Jihong Guan, Sheng Zhong
Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool...
December 13, 2018: Genomics, Proteomics & Bioinformatics
Tushar H Jaware, K B Khanchandani, Anita Zurani
BACKGROUND:  Segmentation of brain MR images of neonates is a primary step for assessment of brain evolvement. Advanced segmentation techniques used for adult brain MRI are not companionable for neonates, due to extensive dissimilarities in tissue properties and head structure. Existing segmentation methods for neonates utilizes brain atlases or requires manual elucidation, which results into improper and atlas dependent segmentation. OBJECTIVE:  The primary objective of this work is to develop fully automatic, atlas free, and robust system to segment and classify brain tissues of newborn infants from magnetic resonance images...
December 15, 2018: American Journal of Perinatology
Leonid Emerel, James Thunes, Trevor Kickliter, Marie Billaud, Julie A Phillippi, David A Vorp, Spandan Maiti, Thomas G Gleason
OBJECTIVE: To assess ascending aortic distensibility and build geometry and distensibility-based patient-specific stress distribution maps in patients sustaining type A aortic dissection (TAAD) using predissection noninvasive imaging. METHODS: Review of charts from patients undergoing surgical repair of TAAD (n = 351) led to the selection of a subset population (n = 7) with 2 or more predissection computed tomography angiography scans and echocardiograms at least 1 year before dissection...
November 3, 2018: Journal of Thoracic and Cardiovascular Surgery
Greg Finak, Wenxin Jiang, Raphael Gottardo
CytoML is an R/Bioconductor package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R. Once data are available in R, the data can be further manipulated. For example it can be combined with other computational and analytic approaches, and the results can be exported to FlowJo or Cytobank to be explored by researchers using those platforms. We demonstrate how CytoML and related R packages can be used as a tool to import, modify and export several samples stained with the T cell panel from the FlowCAP IV Lyoplate data set...
December 2018: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Zejia Zheng, Xiang Wu, Juyang Weng
Traditional Turing Machines (TMs) are symbolic whose hand-crafted representations are static and limited. Developmental Network 1 (DN-1) uses emergent representation to perform Turing Computation. But DN-1 lacks hierarchy in its internal representations, and is hard to handle the complex visual navigation tasks. In this paper, we improve DN-1 with several new mechanisms and presenta new emergent neural Turing Machine - Developmental Network 2 (DN-2). By neural, we mean that the control of the TM has neurons as basic computing elements...
November 27, 2018: Neural Networks: the Official Journal of the International Neural Network Society
Zhe-Xin Xu, Yan Chen, Shu-Guang Kuai
Angle perception is an important middle-level visual process, combining line features to generate an integrated shape percept. Previous studies have proposed two theories of angle perception-a combination of lines and a holistic feature following Weber's law. However, both theories failed to explain the dual-peak fluctuations of the just-noticeable difference (JND) across angle sizes. In this study, we found that the human visual system processes the angle feature in two stages: first, by encoding the orientation of the bounding lines and combining them into an angle feature; and second, by estimating the angle in an orthogonal internal reference frame (IRF)...
December 3, 2018: Journal of Vision
Hans-Ulrich Kauczor, Mark O Wielpütz, Bertram J Jobst, Oliver Weinheimer, Daniela Gompelmann, Felix J F Herth, Claus P Heussel
Novel therapeutic options in chronic obstructive pulmonary disease (COPD) require delicate patient selection and thus demand for expert radiologists visually and quantitatively evaluating high-resolution computed tomography (CT) with additional functional acquisitions such as paired inspiratory-expiratory scans or dynamic airway CT. The differentiation between emphysema-dominant and airway-dominant COPD phenotypes by imaging has immediate clinical value for patient management. Assessment of emphysema severity, distribution patterns, and fissure integrity are essential for stratifying patients for different surgical and endoscopic lung volume reduction procedures...
December 13, 2018: Journal of Thoracic Imaging
Saeed Jerban, Yajun Ma, Lidi Wan, Adam C Searleman, Hyungseok Jang, Robert L Sah, Eric Y Chang, Jiang Du
Intracortical bone porosity is a key microstructural parameter that determines bone mechanical properties. While clinical MRI visualizes the cortical bone with a signal void, ultrashort echo time (UTE) MRI can acquire high signal from cortical bone, thus enabling quantitative assessments. Magnetization transfer (MT) imaging combined with UTE-MRI can indirectly assess protons in the bone collagenous matrix, which are inversely related to porosity. This study aimed to examine UTE-MT MRI techniques to evaluate intracortical bone porosity...
December 14, 2018: NMR in Biomedicine
Tsuneo Saga, Yuji Nakamoto, Takayoshi Ishimori, Takahiro Inoue, Yoichi Shimizu, Hiroyuki Kimura, Shusuke Akamatsu, Takayuki Goto, Hiroyuki Watanabe, Kosuke Kitaguchi, Masao Watanabe, Masahiro Ono, Hideo Saji, Osamu Ogawa, Kaori Togashi
This first-in-man study was performed to evaluate the safety, whole-body distribution, dose estimation and lesion accumulation of 18 F-FSU-880, a newly-developed probe targeting prostate-specific membrane antigen (PSMA). Six prostate cancer patients with known metastatic lesions underwent serial whole-body positron emission tomography/computed tomography (PET/CT) with 18 F-FSU-880. Blood and urine were analyzed before and after PET/CT. Accumulation of 18 F-FSU-880 in organs and metastatic lesions in serial PET images were evaluated by measuring the standardized uptake values...
December 13, 2018: Cancer Science
Mihai Udrescu, Lucreţia Udrescu
Complex network representations of reported drug-drug interactions foster computational strategies that can infer pharmacological functions which, in turn, create incentives for drug repositioning. Here, we use Gephi (a platform for complex network visualization and analysis) to represent a drug-drug interaction network with drug interaction information from DrugBank 4.1. Both modularity class- and force-directed layout ForceAtlas2 are employed to generate drug clusters which correspond to nine specific drug properties...
2019: Methods in Molecular Biology
Kingsley O Asiedu, Munira Ferdousi, Phuongnga T Ton, Stephen S Adler, Peter L Choyke, Noriko Sato
BACKGROUND: Bone fracture healing is dependent upon the rapid migration and engraftment of bone marrow (BM) progenitor and stem cells to the site of injury. Stromal cell-derived factor-1 plays a crucial role in recruiting BM cells expressing its receptor CXCR4. Recently, a CXCR4 antagonist, plerixafor, has been used to mobilize BM cells into the blood in efforts to enhance cell migration to sites of injury presumably improving healing. In this study, we employed zirconium-89 (89 Zr)-oxine-labeled BM cells imaged with positron emission tomography (PET)/computed tomography (CT) to visualize and quantitate BM cell trafficking following acute bone injury and to investigate the effect of plerixafor on BM cell homing...
December 13, 2018: EJNMMI Research
Zhehuan Chen, Songmin He, Jenny Zilberberg, Woo Lee
We report here a novel pumpless, 96-well plate-based platform for high-throughput dynamic multicellular culture and chemosensitivity evaluation. A gravity-driven flow strategy was developed to generate and sustain the flow rate of culture medium within 10% in the platform's 20 culture chambers. The ability of the platform to generate and sustain the medium flow was demonstrated by computational simulation, flow visualization, and ascertaining the previously known effect of flow-induced shear stress on the stimulated osteogenic differentiation of osteoblasts...
December 14, 2018: Lab on a Chip
Xiangdong Huang, Jingwen Xu, Zheng Wang
This paper proposes a novel phase estimator based on fully-traversed Discrete Fourier Transform (DFT) which takes all possible truncated DFT spectra into account such that it possesses two merits of `direct phase extraction' (namely accurate instantaneous phase information can be extracted without any correction) and suppressing spectral leakage. This paper also proves that the proposed phase estimator complies with the 2-parameter joint estimation model rather than the conventional 3-parameter joint model...
December 7, 2018: Sensors
Bin Liu, Zhenyu Wang, Guozhong Lin, Jia Zhang
RATIONALE: Currently, interventional injection of albumin glue and nerve sleeve plasty by cyst excision is the main treatment for sacral cysts. However, albumin glue can only be used in patients with partial cystic neck stenosis, and surgical treatment may result in postoperative complications such as numbness and cyst recurrence. Here, a modified radiculoplasty is presented, in which the lamina is restored with the nerve root wrapped with 3-dimensional (3D)-printed artificial dura mater...
December 2018: Medicine (Baltimore)
Tomohiko Shiina, Ryotaro Takashima, Roberto D Pascual-Marqui, Keisuke Suzuki, Yuka Watanabe, Koichi Hirata
BACKGROUND: Photophobia is a common feature of migraine, which may involve abnormal cortical information processing. In electroencephalograms (EEG), photic driving is known as a reaction to visual stimulation. Both photophobia and photic driving response are present during light stimulation. We hypothesized that cortical response to photic stimulation would differ between migraine patients with and without aura. METHODS: We recruited 50 migraine patients (migraine with aura [MWA] = 21; migraine without aura [MWOA] = 29)...
December 13, 2018: Neuropsychobiology
Anton du Plessis, Chris Broeckhoven
Albert Einstein once said "look deep into nature, and then you will understand everything better". Looking deep into nature has in the last few years become much more achievable through the use of high-resolution X-ray micro-computed tomography (microCT). The non-destructive nature of microCT, combined with three-dimensional visualization and analysis, allows for the most complete internal and external "view" of natural materials and structures at both macro- and micro-scale. This capability brings with it the possibility to learn from nature at an unprecedented level of detail in full three dimensions, allowing us to improve our current understanding of structures, learn from them and apply them to solve engineering problems...
December 10, 2018: Acta Biomaterialia
Dor Oppenheim, Guy Shani, Orly Erlich, Leah Tsror
Many plant diseases have distinct visual symptoms which can be used to identify and classify them correctly. This paper presents a potato disease classification algorithm which leverages these distinct appearances and the recent advances in computer vision made possible by deep learning. The algorithm uses a deep convolutional neural network training it to classify the tubers into five classes, namely, four disease classes and a healthy potato class. The database of images used in this study, containing potato tubers of different cultivars, sizes and diseases, was acquired, classified, and labeled manually by experts...
December 13, 2018: Phytopathology
Juliana B Araújo, Mark L Brusseau
Pore-scale fluid processes in geological media are critical for numerous applications in several fields. Continued improvement of high-resolution image acquisition and processing methods has provided a means to directly characterize pore-scale fluid processes for natural geomedia, and to test the representativeness of theoretical and computational models developed to simulate them. High-resolution synchrotron X-ray microtomography (XMT) combined with advanced 3-D image visualization was used to investigate the impact of larger-scale solid-surface heterogeneity on nonwetting-wetting (air-water) interfacial area for two natural geomedia (a sand and a soil)...
December 13, 2018: Environmental Science. Processes & Impacts
Parviz Ghaderi, Hamid Reza Marateb, Mir-Shahram Safari
A lot of efforts have been made to understand the structure and function of neocortical circuits. In fact, a promising way to understand the functions of cortical circuits is the classification of the neural types, based on their different properties. Recent studies focused on applying modern computational methods to classify neurons based on molecular, morphological, physiological, or mixed of these criteria. Although there are studies in the literature on in vitro /vivo extracellular or in vitro intracellular recordings, a study on the classification of neuronal types using in vivo whole-cell patch-clamp recordings is still lacking...
2018: Frontiers in Neuroscience
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