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https://www.readbyqxmd.com/read/28448599/simulation-of-the-dynamics-of-primary-immunodeficiencies-in-cd4-t-cells
#1
Gabriel N Teku, Mauno Vihinen
Primary immunodeficiencies (PIDs) form a large and heterogeneous group of mainly rare disorders that affect the immune system. T-cell deficiencies account for about one-tenth of PIDs, most of them being monogenic. Apart from genetic and clinical information, lots of other data are available for PID proteins and genes, including functions and interactions. Thus, it is possible to perform systems biology studies on the effects of PIDs on T-cell physiology and response. To achieve this, we reconstructed a T-cell network model based on literature mining and TPPIN, a previously published core T-cell network, and performed semi-quantitative dynamic network simulations on both normal and T-cell PID failure modes...
2017: PloS One
https://www.readbyqxmd.com/read/28423830/bridging-the-semantic-gap-between-diagnostic-histopathology-and-image-analysis
#2
Lamine Traore, Yannick Kergosien, Daniel Racoceanu
With the wider acceptance of Whole Slide Images (WSI) in histopathology domain, automatic image analysis algorithms represent a very promising solution to support pathologist's laborious tasks during the diagnosis process, to create a quantification-based second opinion and to enhance inter-observer agreement. In this context, reference vocabularies and formalization of the associated knowledge are especially needed to annotate histopathology images with labels complying with semantic standards. In this work, we elaborate a sustainable triptych able to bridge the gap between pathologists and image analysis scientists...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28414508/dissociating-affective-and-semantic-valence
#3
Oksana Itkes, Ruth Kimchi, Hadeel Haj-Ali, Avia Shapiro, Assaf Kron
We examined the possible dissociation between two modes of valence: affective valence (valence of e emotional response) and semantic valence (stored knowledge about valence of an object or event). In Experiment 1, 50 participants viewed affective pictures that were repeatedly presented while their facial electromyography (EMG) activation and heart rate response were continuously recorded. Half of the participants provided self-report ratings about the valence of their feelings and half about the valence of the stimulus...
April 17, 2017: Journal of Experimental Psychology. General
https://www.readbyqxmd.com/read/28406139/t-bet-independent-development-of-ifn%C3%AE-secreting-natural-t-helper-1-cell-population-in-the-absence-of-itk
#4
Arun K Kannan, Sonia Mohinta, Weishan Huang, Lu Huang, Nicholas Koylass, Judith A Appleton, Avery August
Th1, Th2, Th9 and Th17 cells are conventional CD4(+) effector T cells identified as secretors of prototypical cytokines IFNγ, IL4, IL9, and IL-17A respectively. Recently, populations of natural Th17 and Th1 cells (nTh17 and nTh1) with innate-like phenotype have been identified in the thymus that are distinct from conventional Th17 and Th1 cells. The absence of the Tec family kinase Interleukin-2 inducible T cell kinase (Itk) results in T cell immunodeficiency in mice and humans. Here we show that Itk negatively regulates the development of nTh1 cells that express IFNγ in a Tbet independent manner, and whose expansion can be enhanced by IL4...
April 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28353193/exome-sequencing-for-simultaneous-mutation-screening-in-children-with-hemophagocytic-lymphohistiocytosis
#5
Ekchol Mukda, Objoon Trachoo, Ekawat Pasomsub, Rawiphorn Tiyasirichokchai, Nareenart Iemwimangsa, Darintr Sosothikul, Wasun Chantratita, Samart Pakakasama
In the present study, we used exome sequencing to analyze PRF1, UNC13D, STX11, and STXBP2, as well as genes associated with primary immunodeficiency disease (RAB27A, LYST, AP3B1, SH2D1A, ITK, CD27, XIAP, and MAGT1) in Thai children with hemophagocytic lymphohistiocytosis (HLH). We performed mutation analysis of HLH-associated genes in 25 Thai children using an exome sequencing method. Genetic variations found within these target genes were compared to exome sequencing data from 133 healthy individuals. Variants identified with minor allele frequencies <5% and novel mutations were confirmed using Sanger sequencing...
March 28, 2017: International Journal of Hematology
https://www.readbyqxmd.com/read/28323840/htc-vive-mevislab-integration-via-openvr-for-medical-applications
#6
Jan Egger, Markus Gall, Jürgen Wallner, Pedro Boechat, Alexander Hann, Xing Li, Xiaojun Chen, Dieter Schmalstieg
Virtual Reality, an immersive technology that replicates an environment via computer-simulated reality, gets a lot of attention in the entertainment industry. However, VR has also great potential in other areas, like the medical domain, Examples are intervention planning, training and simulation. This is especially of use in medical operations, where an aesthetic outcome is important, like for facial surgeries. Alas, importing medical data into Virtual Reality devices is not necessarily trivial, in particular, when a direct connection to a proprietary application is desired...
2017: PloS One
https://www.readbyqxmd.com/read/28321524/what-are-the-true-volumes-of-sega-tumors-reliability-of-planimetric-and-popular-semi-automated-image-segmentation-methods
#7
Konrad Stawiski, Joanna Trelińska, Dobromiła Baranska, Iwona Dachowska, Katarzyna Kotulska, Sergiusz Jóźwiak, Wojciech Fendler, Wojciech Młynarski
OBJECTIVE: To evaluate the reliability of the standard planimetric methodology of volumetric analysis and three different open-source semi-automated approaches of brain tumor segmentation. MATERIALS AND METHODS: The volumes of subependymal giant cell astrocytomas (SEGA) examined by 30 MRI studies of 10 patients from a previous everolimus-related trial (EMINENTS study) were estimated using four methods: planimetric method (modified MacDonald ellipsoid method), ITK-Snap (pixel clustering, geodesic active contours, region competition methods), 3D Slicer (level-set thresholding), and NIRFast (k-means clustering, Markov random fields)...
March 20, 2017: Magma
https://www.readbyqxmd.com/read/28321386/computerized-assessment-of-superior-semicircular-canal-dehiscence-size-using-advanced-morphological-imaging-operators
#8
Joel S Beckett, Carlito Lagman, Lawrance K Chung, Timothy T Bui, Seung J Lee, Brittany L Voth, Bilwaj Gaonkar, Quinton Gopen, Isaac Yang
Superior semicircular canal dehiscence (SSCD) describes a pathological aperture at the level of the arcuate eminence. Techniques for quantifying defect size are described with most studies using two-dimensional lengths that underestimate the pathology. The objective of this study is to describe a novel method of measurement that combines manual segmentation of high-resolution computed tomography (HRCT) images of the temporal bone and a morphological skeletonization transform to calculate dehiscence volume. Images were imported into a freely available image segmentation tool: ITK-SNAP (version 3...
April 2017: Journal of Neurological Surgery. Part B, Skull Base
https://www.readbyqxmd.com/read/28269194/atrioventricular-junction-avj-motion-tracking-a-software-tool-with-itk-vtk-qt
#9
Pengdong Xiao, Shuang Leng, Xiaodan Zhao, Hua Zou, Ru San Tan, Philip Wong, Liang Zhong
The quantitative measurement of the Atrioventricular Junction (AVJ) motion is an important index for ventricular functions of one cardiac cycle including systole and diastole. In this paper, a software tool that can conduct AVJ motion tracking from cardiovascular magnetic resonance (CMR) images is presented by using Insight Segmentation and Registration Toolkit (ITK), The Visualization Toolkit (VTK) and Qt. The software tool is written in C++ by using Visual Studio Community 2013 integrated development environment (IDE) containing both an editor and a Microsoft complier...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28269019/itk-snap-an-interactive-tool-for-semi-automatic-segmentation-of-multi-modality-biomedical-images
#10
Paul A Yushkevich, Yang Gao, Guido Gerig
Obtaining quantitative measures from biomedical images often requires segmentation, i.e., finding and outlining the structures of interest. Multi-modality imaging datasets, in which multiple imaging measures are available at each spatial location, are increasingly common, particularly in MRI. In applications where fully automatic segmentation algorithms are unavailable or fail to perform at desired levels of accuracy, semi-automatic segmentation can be a time-saving alternative to manual segmentation, allowing the human expert to guide segmentation, while minimizing the effort expended by the expert on repetitive tasks that can be automated...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227424/atrioventricular-junction-avj-motion-tracking-a-software-tool-with-itk-vtk-qt
#11
Pengdong Xiao, Shuang Leng, Xiaodan Zhao, Hua Zou, Ru San Tan, Philip Wong, Liang Zhong, Pengdong Xiao, Shuang Leng, Xiaodan Zhao, Hua Zou, Ru San Tan, Philip Wong, Liang Zhong, Ru San Tan, Pengdong Xiao, Philip Wong, Hua Zou, Shuang Leng, Liang Zhong, Xiaodan Zhao
The quantitative measurement of the Atrioventricular Junction (AVJ) motion is an important index for ventricular functions of one cardiac cycle including systole and diastole. In this paper, a software tool that can conduct AVJ motion tracking from cardiovascular magnetic resonance (CMR) images is presented by using Insight Segmentation and Registration Toolkit (ITK), The Visualization Toolkit (VTK) and Qt. The software tool is written in C++ by using Visual Studio Community 2013 integrated development environment (IDE) containing both an editor and a Microsoft complier...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227232/itk-snap-an-interactive-tool-for-semi-automatic-segmentation-of-multi-modality-biomedical-images
#12
Paul A Yushkevich, Yang Gao, Guido Gerig, Paul A Yushkevich, Yang Gao, Guido Gerig, Yang Gao, Paul A Yushkevich, Guido Gerig
Obtaining quantitative measures from biomedical images often requires segmentation, i.e., finding and outlining the structures of interest. Multi-modality imaging datasets, in which multiple imaging measures are available at each spatial location, are increasingly common, particularly in MRI. In applications where fully automatic segmentation algorithms are unavailable or fail to perform at desired levels of accuracy, semi-automatic segmentation can be a time-saving alternative to manual segmentation, allowing the human expert to guide segmentation, while minimizing the effort expended by the expert on repetitive tasks that can be automated...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28213500/inducible-t-cell-kinase-regulates-the-acquisition-of-cytolytic-capacity-and-degranulation-in-cd8-ctls
#13
Senta M Kapnick, Jane C Stinchcombe, Gillian M Griffiths, Pamela L Schwartzberg
Patients with mutations in inducible T cell kinase (ITK) are susceptible to viral infections, particularly EBV, suggesting that these patients have defective function of CD8(+) CTLs. In this study, we evaluated the effects of ITK deficiency on cytolysis in murine CTLs deficient in ITK, and both human and murine cells treated with an ITK inhibitor. We find that ITK deficiency leads to a global defect in the cytolysis of multiple targets. The absence of ITK both affected CTL expansion and delayed the expression of cytolytic effectors during activation...
April 1, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28152433/the-epa-guidance-on-suicide-treatment-and-prevention-needs-to-be-adjusted-to-fight-the-epidemics-of-suicide-at-the-north-pole-area-and-other-autochthonous-communities
#14
P Charlier, J Malaurie, D Wasserman, V Carli, M Sarchiapone, C Dagenais-Everell, C Herve
More and more, youth suicide in the Inuit community is gaining importance, with a frequency in Greenland rising from 14.4 (1960-64) to 110.4 per 100,000 person-years (2010-11). The huge cultural/educational changes during the last 20 years and the role of globalization, especially of the occidental influence on this community may be at the origin of such an "epidemics" of suicide in this cultural region. Recently, a political organization representing the Inuit community in Canada (ITK for Inuit Tapiriit Kanatami) launched a National Inuit Suicide Prevention Strategy (NISP) based on the specificities of this community in comparison to the occidental civilization...
March 2017: European Psychiatry: the Journal of the Association of European Psychiatrists
https://www.readbyqxmd.com/read/28128774/smart-cloud-system-with-image-processing-server-in-diagnosing-brain-diseases-dedicated-for-hospitals-with-limited-resources
#15
Fahmi Fahmi, Tigor H Nasution
The use of medical imaging in diagnosing brain disease is growing. The challenges are related to the big size of data and complexity of the image processing. High standard of hardware and software are demanded, which can only be provided in big hospitals. Our purpose was to provide a smart cloud system to help diagnosing brain diseases for hospital with limited infrastructure. The expertise of neurologists was first implanted in cloud server to conduct an automatic diagnosis in real time using image processing technique developed based on ITK library and web service...
January 19, 2017: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
https://www.readbyqxmd.com/read/28110733/simulation-of-mr-angiography-imaging-for-validation-of-cerebral-arteries-segmentation-algorithms
#16
Artur Klepaczko, Piotr Szczypiński, Andreas Deistung, Jürgen R Reichenbach, Andrzej Materka
BACKGROUND AND OBJECTIVE: Accurate vessel segmentation of magnetic resonance angiography (MRA) images is essential for computer-aided diagnosis of cerebrovascular diseases such as stenosis or aneurysm. The ability of a segmentation algorithm to correctly reproduce the geometry of the arterial system should be expressed quantitatively and observer-independently to ensure objectivism of the evaluation. METHODS: This paper introduces a methodology for validating vessel segmentation algorithms using a custom-designed MRA simulation framework...
December 2016: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28048842/su-f-r-18-updates-to-the-computational-environment-for-radiological-research-for-image-analysis
#17
Aditya P Apte, Joseph O Deasy
PURPOSE: To present new tools in CERR for Texture Analysis and Visualization. METHOD: (1) Quantitative Image Analysis: We added the ability to compute Haralick texture features based on local neighbourhood. The Texture features depend on many parameters used in their derivation. For example: (a) directionality, (b) quantization of image, (c) patch-size for the neighborhood, (d) handling of the edge voxels within the region of interest, (e) Averaging co-occurance matrix vs texture features for different directions etc...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048724/su-f-j-84-comparison-of-quantitative-deformable-image-registration-evaluation-tools-application-to-prostate-igart
#18
N Dogan, E Weiss, W Sleeman, G Christensen, J Williamson, J Ford
PURPOSE: Errors in displacement vector fields (DVFs) generated by Deformable Image Registration (DIR) algorithms can give rise to significant uncertainties in contour propagation and dose accumulation in Image-Guided Adaptive Radiotherapy (IGART). The purpose of this work is to assess the accuracy of two DIR algorithms using a variety of quality metrics for prostate IGART. METHODS: Pelvic CT images were selected from an anonymized database of nineteen prostate patients who underwent 8-12 serial scans during radiotherapy...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048429/we-h-207a-07-image-based-versus-atlas-based-internal-dosimetry
#19
M Fallahpoor, M Abbasi, A Parach, F Kalantari
PURPOSE: Monte Carlo (MC) simulation is known as the gold standard method for internal dosimetry. It requires radionuclide distribution from PET or SPECT and body structure from CT for accurate dose calculation. The manual or semi-automatic segmentation of organs from CT images is a major obstacle. The aim of this study is to compare the dosimetry results based on patient's own CT and a digital humanoid phantom as an atlas with pre-specified organs. METHODS: SPECT-CT images of a 50 year old woman who underwent bone pain palliation with Samarium-153 EDTMP for osseous metastases from breast cancer were used...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047061/su-f-r-07-radiomics-of-ct-features-and-associations-and-correlation-with-outcomes-following-lung-sbrt
#20
E Schreibmann, A Iwinski Sutter, D Whitaker, J Switchenko, E Elder, K Higgins, P Patel
OBJECTIVE: To investigate the prognostic significance of image gradients and in predicting clinical outcomes in a patients with non-small cell lung cancer treated with stereotactic body radiotherapy (SBRT) on 71 patients with 83 treated lesions. METHODS: The records of patients treated with lung SBRT were retrospectively reviewed. When applicable, SBRT target volumes were modified to exclude any overlap with pleura, chestwall, or mediastinum. The ITK software package was utilized to generate quantitative measures of image intensity, inhomogeneity, shape morphology and first and second-order CT textures...
June 2016: Medical Physics
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