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https://www.readbyqxmd.com/read/28227424/atrioventricular-junction-avj-motion-tracking-a-software-tool-with-itk-vtk-qt
#1
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
#2
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
#3
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...
February 17, 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
#4
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...
January 30, 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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28026094/phenotypic-characteristics-of-aged-cd4-cd28-null-t-lymphocytes-are-determined-by-changes-in-the-whole-genome-dna-methylation-pattern
#11
Beatriz Suarez-Álvarez, Ramón M Rodríguez, Karin Schlangen, Aroa Baragaño Raneros, Leonardo Márquez-Kisinousky, Agustín F Fernández, Carmen Díaz-Corte, Ana M Aransay, Carlos López-Larrea
Aging is associated with a progressive loss of the CD28 costimulatory molecule in CD4(+) lymphocytes (CD28(null) T cells), which is accompanied by the acquisition of new biological and functional properties that give rise to an impaired immune response. The regulatory mechanisms that govern the appearance and function of this cell subset during aging and in several associated inflammatory disorders remain controversial. Here, we present the whole-genome DNA methylation and gene expression profiles of CD28(null) T cells and its CD28(+) counterpart...
December 27, 2016: Aging Cell
https://www.readbyqxmd.com/read/27936918/post-processing-open-source-software-for-the-cbct-monitoring-of-periapical-lesions-healing-following-endodontic-treatment-technical-report-of-two-cases
#12
Eduardo M Villoria, Antônio R Lenzi, Rodrigo V Soares, Bernardo Q Souki, Asgeir Sigurdsson, Alexandre P Marques, Sandra R Fidel
OBJECTIVES: To describe the use of open-source software for the post-processing of CBCT imaging for the assessment of periapical lesions development after endodontic treatment. METHODS: CBCT scans were retrieved from endodontic records of two patients. Three-dimensional virtual models, voxel counting, volumetric measurement (mm(3)) and mean intensity of the periapical lesion were performed with ITK-SNAP v. 3.0 software. Three-dimensional models of the lesions were aligned and overlapped through the MeshLab software, which performed an automatic recording of the anatomical structures, based on the best fit...
January 2017: Dento Maxillo Facial Radiology
https://www.readbyqxmd.com/read/27896837/cd6-and-linker-of-activated-t-cells-are-potential-interaction-partners-for-t-cell-specific-adaptor-protein
#13
Cecilie Dahl Hem, Marianne Ekornhol, Stine Granum, Vibeke Sundvold-Gjerstad, Anne Spurkland
The T cell specific adaptor protein (TSAd) contains several protein interaction domains, and is merging as a modulator of T cell activation. Several interaction partners for the TSAd proline rich region and phosphotyrosines have been identified, including the Src and Tec family kinases Lymphocyte specific protein tyrosine kinase (Lck) and Interleukin 2-Inducible T-cell kinase (Itk). Via its Src homology 2 (SH2) domain, TSAd may thus function as a link between these enzymes and other signaling molecules. However, few binding partners to the TSAd SH2 domain in T cells are hitherto known...
November 29, 2016: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/27802969/ibrutinib-efficacy-and-tolerability-in-patients-with-relapsed-chronic-lymphocytic-leukemia-following-allogeneic-hct
#14
Christine E Ryan, Bita Sahaf, Aaron C Logan, Susan O'Brien, John C Byrd, Peter Hillmen, Jennifer R Brown, Martin J S Dyer, Anthony R Mato, Michael J Keating, Samantha Jaglowski, Fong Clow, Andrew R Rezvani, Lori Styles, Steven E Coutre, David B Miklos
Ibrutinib, a potent and irreversible small-molecule inhibitor of both Bruton's tyrosine kinase and interleukin-2 inducible kinase (ITK), has been used to treat relapsed/refractory chronic lymphocytic leukemia (CLL) with prolongation of progression-free and overall survival. Here, we present 27 patients with relapsed CLL following allogeneic hematopoietic cell transplant (HCT) who subsequently received ibrutinib salvage therapy. Sixteen of these patients were part of multi-institutional clinical trials and achieved an overall response rate of 87...
December 22, 2016: Blood
https://www.readbyqxmd.com/read/27793034/therapeutic-efficacy-of-the-bromodomain-inhibitor-otx015-mk-8628-in-alk-positive-anaplastic-large-cell-lymphoma-an-alternative-modality-to-overcome-resistant-phenotypes
#15
Michela Boi, Maria Todaro, Valentina Vurchio, Shao Ning Yang, John Moon, Ivo Kwee, Andrea Rinaldi, Heng Pan, Ramona Crescenzo, Mangeng Cheng, Leandro Cerchietti, Olivier Elemento, Maria E Riveiro, Esteban Cvitkovic, Francesco Bertoni, Giorgio Inghirami
Anaplastic large cell lymphomas (ALCL) represent a peripheral T-cell lymphoma subgroup, stratified based on the presence or absence of anaplastic lymphoma kinase (ALK) chimeras. Although ALK-positive ALCLs have a more favorable outcome than ALK-negative ALCL, refractory and/or relapsed forms are common and novel treatments are needed. Here we investigated the therapeutic potential of a novel bromodomain inhibitor, OTX015/MK-8628 in ALK-positive ALCLs.The effects of OTX015 on a panel of ALK+ ALCL cell lines was evaluated in terms of proliferation, cell cycle and downstream signaling, including gene expression profiling analyses...
October 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27787834/cx-dpx-and-pcw-web-servers-for-the-visualization-of-interior-and-protruding-regions-of-protein-structures-in-3d-and-1d
#16
Balázs Ligeti, Roberto Vera, János Juhász, Sándor Pongor
The CX and DPX web-based servers at http://pongor.itk.ppke.hu/bioinfoservices are dedicated to the analysis of protein 3D structures submitted by the users as Protein Data Bank (PDB) files. CX computes an atomic protrusion index, cx that makes it possible to highlight the protruding atoms within a protein 3D structure. DPX calculates a depth index, dpx for buried atoms, and allows one to visualize the distribution of buried residues. CX and DPX visualize 3D structures colored according to the calculated indices and return PDB files that can be visualized using standard programs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27787817/consensus-prediction-of-charged-single-alpha-helices-with-csahserver
#17
Dániel Dudola, Gábor Tóth, László Nyitray, Zoltán Gáspári
Charged single alpha-helices (CSAHs) constitute a rare structural motif. CSAH is characterized by a high density of regularly alternating residues with positively and negatively charged side chains. Such segments exhibit unique structural properties; however, there are only a handful of proteins where its existence is experimentally verified. Therefore, establishing a pipeline that is capable of predicting the presence of CSAH segments with a low false positive rate is of considerable importance. Here we describe a consensus-based approach that relies on two conceptually different CSAH detection methods and a final filter based on the estimated helix-forming capabilities of the segments...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27780854/t-cell-receptor-signaling-activates-an-itk-nf-%C3%AE%C2%BAb-gata-3-axis-in-t-cell-lymphomas-facilitating-resistance-to-chemotherapy
#18
Tianjiao Wang, Ye Lu, Avery Polk, Pinki Chowdhury, Carlos Murga-Zamalloa, Hiroshi Fujiwara, Koichiro Suemori, Niklas Beyersdorf, Alexandra C Hristov, Megan S Lim, Nathanael G Bailey, Ryan A Wilcox
PURPOSE: T-cell lymphomas are a molecularly heterogeneous group of non-Hodgkin lymphomas (NHL) that account for a disproportionate number of NHL disease-related deaths due to their inherent and acquired resistance to standard multiagent chemotherapy regimens. Despite their molecular heterogeneity and frequent loss of various T-cell specific receptors, the T-cell antigen receptor is retained in the majority of these lymphomas. As T-cell receptor (TCR) engagement activates a number of signaling pathways and transcription factors that regulate T-cell growth and survival, we examined the TCR's role in mediating resistance to chemotherapy...
October 25, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27780224/glioblastoma-segmentation-comparison-of-three-different-software-packages
#19
Even Hovig Fyllingen, Anne Line Stensjøen, Erik Magnus Berntsen, Ole Solheim, Ingerid Reinertsen
To facilitate a more widespread use of volumetric tumor segmentation in clinical studies, there is an urgent need for reliable, user-friendly segmentation software. The aim of this study was therefore to compare three different software packages for semi-automatic brain tumor segmentation of glioblastoma; namely BrainVoyagerTM QX, ITK-Snap and 3D Slicer, and to make data available for future reference. Pre-operative, contrast enhanced T1-weighted 1.5 or 3 Tesla Magnetic Resonance Imaging (MRI) scans were obtained in 20 consecutive patients who underwent surgery for glioblastoma...
2016: PloS One
https://www.readbyqxmd.com/read/27756551/influence-of-the-volume-of-soft-tissue-herniation-on-clinical-symptoms-of-patients-with-orbital-floor-fractures
#20
Ali-Farid Safi, Marie-Theres Richter, Daniel Rothamel, Hans-Joachim Nickenig, Martin Scheer, Joachim Zöller, Matthias Kreppel
INTRODUCTION: One of the most important complications of orbital floor fractures is diplopia and restricted ocular movement. The role of the volume of soft tissue herniation on these clinical symptoms after orbital floor fractures is unclear and potentially may predict development of persistent clinical symptoms. Therefore the aim of this study was to assess pre- and postoperative complications associated to the volume of soft tissue herniation, with special interest to diplopia and bulbus motility impairment...
December 2016: Journal of Cranio-maxillo-facial Surgery
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