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https://www.readbyqxmd.com/read/28635957/itk-signalling-via-the-ras-irf4-pathway-regulates-the-development-and-function-of-tr1-cells
#1
Weishan Huang, Sabrina Solouki, Nicholas Koylass, Song-Guo Zheng, Avery August
Type 1 regulatory T (Tr1) cells differentiate in response to signals engaging the T cell receptor (TCR), express high levels of the immunosuppressive cytokine IL-10, but not Foxp3, and can suppress inflammation and promote immune tolerance. Here we show that ITK, an important modulator of TCR signalling, is required for the TCR-induced development of Tr1 cells in various organs, and in the mucosal system during parasitic and viral infections. ITK kinase activity is required for mouse and human Tr1 cell differentiation...
June 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28634120/highly-reproducible-improved-label-free-quantitative-analysis-of-cellular-phosphoproteome-by-optimization-of-lc-ms-ms-gradient-and-analytical-column-construction
#2
Nagib Ahsan, Judson Belmont, Zhuo Chen, James G Clifton, Arthur R Salomon
Expanding the sequencing depth of the peptides with a statistically significant quantitative change derived from a biological stimulation is critical. Here we demonstrate that optimization of LC gradient and analytical column construction can reveal over 30,000 unique peptides and 23,000 phosphopeptides at high confidence. The quantitative reproducibility of different analytical workflows was evaluated by comparing the phosphoproteome of CD3/4 stimulated and unstimulated T-cells as a model system. A fritless, 50cm-long column packed with 1...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28610931/can-cyst-volume-be-used-to-stratify-risk-of-complications-following-cyst-defect-reconstruction-with-iliac-crest-graft
#3
Ali-Farid Safi, Andrea Grandoch, Timo Dreiseidler, Hans-Joachim Nickenig, Joachim Zöller, Matthias Kreppel
INTRODUCTION: The role of the volume of radicular and dentigerous cysts on clinical symptoms is unclear and potentially may predict development of pre- and postoperative complications, especially after cystectomies with large bony defects. Therefore the aim of this study was to assess pre- and postoperative symptoms associated to the volume of jaw cysts. MATERIAL AND METHODS: Retrospective chart review of 111 patients with follicular or dentigerous cysts from 2008-2012...
May 17, 2017: Journal of Cranio-maxillo-facial Surgery
https://www.readbyqxmd.com/read/28581816/serial-changes-in-3-dimensional-supraspinatus-muscle-volume-after-rotator-cuff-repair
#4
Seok Won Chung, Kyung-Soo Oh, Sung Gyu Moon, Na Ra Kim, Ji Whan Lee, Eungjune Shim, Sehyung Park, Youngjun Kim
BACKGROUND: There is considerable debate on the recovery of rotator cuff muscle atrophy after rotator cuff repair. PURPOSE: To evaluate the serial changes in supraspinatus muscle volume after rotator cuff repair by using semiautomatic segmentation software and to determine the relationship with functional outcomes. STUDY DESIGN: Case series; Level of evidence, 4. METHODS: Seventy-four patients (mean age, 62.8 ± 8.8 years) who underwent arthroscopic rotator cuff repair and obtained 3 consecutive (preoperatively, immediately postoperatively, and later postoperatively [≥1 year postoperatively]) magnetic resonance imaging (MRI) scans having complete Y-views were included...
June 1, 2017: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/28570811/allosteric-fine-tuning-of-the-binding-pocket-dynamics-in-the-itk-sh2-domain-by-a-distal-molecular-switch-an-atomistic-perspective
#5
Mohamed Momin, Yao Xin, Donald Hamelberg
Although the regulation of function of proteins by allosteric interactions has been identified in many subcellular processes, molecular switches are also known to induce long-range conformational changes in proteins. A less well understood molecular switch involving cis-trans isomerization of a peptidyl-prolyl bond could induce a conformational change directly to the backbone that is propagated to other parts of the protein. However, these switches are elusive and hard to identify because they are intrinsic to biomolecules that are inherently dynamic...
June 15, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28527841/a-comparison-of-2-and-3-dimensional-healing-assessment-after-endodontic-surgery-using-cone-beam-computed-tomographic-volumes-or-periapical-radiographs
#6
Tom Schloss, David Sonntag, Meetu R Kohli, Frank C Setzer
INTRODUCTION: The aim of this study was to compare the assessment of healing after endodontic microsurgery using 2-dimensional (2D) periapical films versus 3-dimensional (3D) cone-beam computed tomographic (CBCT) imaging. METHODS: The healing of 51 teeth from 44 patients was evaluated using Molven's criteria (2D) and modified PENN 3D criteria. The absolute area (2D) and volume (3D) changes of apical lesions preoperatively and at follow-up were calculated by segmentation using OsiriX software (Pixmeo, Bernex, Switzerland) and ITK-Snap (free software)...
May 17, 2017: Journal of Endodontics
https://www.readbyqxmd.com/read/28520562/reliability-and-repeatability-of-pulp-volume-reconstruction-through-three-different-volume-calculations
#7
T Y Marroquin Penaloza, S Karkhanis, S I Kvaal, S Vasudavan, E Castelblanco, E Kruger, M Tennant
OBJECTIVE: To test the variability of the volume measurements when different segmentation methods are applied in pulp volume reconstruction. MATERIALS AND METHODS: Osirix® and ITK-SNAP software were used. Different segmentation methods (Part A) and volume approaches (Part B) were tested in a sample of 21 dental CBCT's from upper canines. Different combinations of the data set were also tested on one lower molar and one upper canine (Part C) to determine the variability of the results when automatic segmentation is performed...
December 1, 2016: Journal of Forensic Odonto-stomatology
https://www.readbyqxmd.com/read/28516764/an-autoinhibitory-role-for-the-pleckstrin-homology-domain-of-interleukin-2-inducible-tyrosine-kinase-and-its-interplay-with-canonical-phospholipid-recognition
#8
Sujan Devkota, Raji E Joseph, Scott E Boyken, D Bruce Fulton, Amy H Andreotti
Pleckstrin homology (PH) domains are well-known as phospholipid binding modules, yet evidence that PH domain function extends beyond lipid recognition is mounting. In this work, we characterize a protein binding function for the PH domain of interleukin-2-inducible tyrosine kinase (ITK), an immune cell specific signaling protein that belongs to the TEC family of nonreceptor tyrosine kinases. Its N-terminal PH domain is a well-characterized lipid binding module that localizes ITK to the membrane via phosphatidylinositol 3,4,5-trisphosphate (PIP3) binding...
May 25, 2017: Biochemistry
https://www.readbyqxmd.com/read/28499271/atom-and-receptor-based-3d-qsar-models-for-generating-new-conformations-from-pyrazolopyrimidine-as-il-2-inducible-tyrosine-kinase-inhibitors
#9
Zaheer Ul-Haq, Juweria Shahrukh Effendi, Sajda Ashraf, Majdi M Bkhaitan
In the current study, quantitative three-dimensional structure-activity-relationship (3D-QSAR) method was performed to design a model for new chemical entities by utilizing pyrazolopyrimidines. Their inhibiting activity on receptor IL-2 Itk correlates descriptors based on topology and hydrophobicity. The best model developed by ligand-based (atom-based) approach has correlation-coefficient of r(2): 0.987 and cross-validated squared correlation-coefficient of q(2): 0.541 with an external prediction capability of r(2): 0...
March 27, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28473706/molecular-mechanisms-underlying-the-evolution-of-the-slp76-signalosome
#10
Xuemei Qu, Xin Lan, Chong Deng, Jiatao Zhou, Jingjing Du, Shengfeng Huang, Yingqiu Li
The well-defined mammalian slp76-signalosome is crucial for T-cell immune response, yet whether slp76-signalosome exists in invertebrates and how it evolved remain unknown. Here we investigated slp76-signalosome from an evolutionary perspective in amphioxus Branchiostoma belcheri (bb). We proved slp76-signalosome components bbslp76, bbGADS and bbItk are present in amphioxus and bbslp76 interacts with bbGADS and bbItk, but differences exist between the interaction manners within slp76-signalosome components of amphioxus and human (h)...
May 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28459680/highly-accurate-facial-nerve-segmentation-refinement-from-cbct-ct-imaging-using-a-super-resolution-classification-approach
#11
Ping Lu, Livia Barazzetti, Vimal Chandran, Kate Gavaghan, Stefan Weber, Nicolas Gerber, Mauricio Reyes
Facial nerve segmentation is of considerable importance for pre-operative planning of cochlear implantation. However, it is strongly influenced by the relatively low resolution of the cone-beam computed tomography (CBCT) images used in clinical practice. In this paper, we propose a super-resolution classification method, which refines a given initial segmentation of the facial nerve to a sub-voxel classification level from CBCT/CT images. The super-resolution classification method learns the mapping from low-resolution CBCT/CT images to high-resolution facial nerve label images, obtained from manual segmentation on micro-CT images...
April 25, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28448599/simulation-of-the-dynamics-of-primary-immunodeficiencies-in-cd4-t-cells
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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