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Ákos Kovács, Dániel Dudola, László Nyitray, Gábor Tóth, Zoltán Nagy, Zoltán Gáspári
Single alpha-helices (SAHs) are increasingly recognized as important structural and functional elements of proteins. Comprehensive identification of SAH segments in large protein datasets was largely hindered by the slow speed of the most restrictive prediction tool for their identification, FT_CHARGE on common hardware. We have previously implemented an FPGA-based version of this tool allowing fast analysis of a large number of sequences. Using this implementation, we have set up of a semi-automated pipeline capable of analyzing full UniProt releases in reasonable time and compiling monthly updates of a comprehensive database of SAH segments...
June 13, 2018: Journal of Structural Biology
Aditya P Apte, Aditi Iyer, Mireia Crispin-Ortuzar, Rutu Pandya, Lisanne V van Dijk, Emiliano Spezi, Maria Thor, Hyemin Um, Harini Veeraraghavan, Jung Hun Oh, Amita Shukla-Dave, Joseph O Deasy
PURPOSE: Radiomics is a growing field of image quantification, but it lacks stable and high-quality software systems. We extended the capabilities of the Computational Environment for Radiological Research (CERR) to create a comprehensive, open-source, MATLAB-based software platform with an emphasis on reproducibility, speed, and clinical integration of radiomics research. METHOD: The radiomics tools in CERR were designed specifically to quantify medical images in combination with CERR's core functionalities of radiological data import, transformation, management, image segmentation, and visualization...
June 13, 2018: Medical Physics
Sujal Ghosh, Ingo Drexler, Sanil Bhatia, Andrew R Gennery, Arndt Borkhardt
Patients with primary immunodeficiency can be prone to severe Epstein-Barr virus (EBV) associated immune dysregulation. Individuals with mutations in the interleukin-2-inducible T-cell kinase ( ITK ) gene experience Hodgkin and non-Hodgkin lymphoma, EBV lymphoproliferative disease, hemophagocytic lymphohistiocytosis, and dysgammaglobulinemia. In this review, we give an update on further reported patients. We believe that current clinical data advocate early definitive treatment by hematopoietic stem cell transplantation, as transplant outcome in primary immunodeficiency disorders in general has gradually improved in recent years...
2018: Frontiers in Immunology
Gül Sönmez, Cemre Koç, Kıvanç Kamburoğlu
OBJECTIVE: To compare the accuracy of linear and volumetric measurements of artificial external root resorption (ERR) cavities by cone beam computerized tomography (CBCT) images obtained at 4 voxel sizes and by using 4 different softwares ex vivo. METHODS: ERR cavities were created on 40 extracted single rooted anterior teeth. Images were obtained by using Planmeca CBCT unit at endo mode (0.075mm); high resolution mode (0.1 mm); high definition mode (0.15 mm) and normal resolution mode (0...
May 31, 2018: Dento Maxillo Facial Radiology
Marilia Sayako Yatabe-Ioshida, Letícia Dominguez Campos, Renato Yassukata Yaedu, Ivy Kiemle Trindade-Suedam
OBJECTIVES: The purpose of this study was to 3-dimensionally assess the airway characteristics of patients with unilateral cleft lip and palate (UCLP) and bilateral cleft lip and palate (BCLP) who underwent orthognathic surgery. DESIGN: This was a retrospective study. SETTING: The study took place at a national referral center for cleft lip and palate rehabilitation. PATIENTS AND PARTICIPANTS: The sample comprised cone-beam computed tomography (CBCT) scans obtained before and after orthognathic surgery of 15 individuals (30 CBCT scans), divided into 2 groups: UCLP group (n = 9 patients/18 CBCT scans) and BCLP group (n = 6/12 CBCT scans)...
January 1, 2018: Cleft Palate-craniofacial Journal
Jean-Baptiste Vimort, Antonio Ruellas, Jack Prothero, J S Marron, Matthew McCormick, Lucia Cevidanes, Erika Benavides, Beatriz Paniagua
To date, there is no single sign, symptom, or test that can clearly diagnose early stages of Temporomandibular Joint Osteoarthritis (TMJ OA). However, it has been observed that changes in the bone occur in early stages of this disease, involving structural changes both in the texture and morphometry of the bone marrow and the subchondral cortical plate. In this paper we present a tool to detect and highlight subtle variations in subchondral bone structure obtained from high resolution Cone Beam Computed Tomography (hr-CBCT) in order to help with detecting early TMJ OA...
February 2018: Proceedings of SPIE
Mohammed Almuzian, Hind Mohammed Al Ghatam, Lubna Al-Muzian
INTRODUCTION: The purpose of this study is to evaluate the validity of a free-access software package (ITK-SNAP) in segmenting and measuring the volume of upper airway spaces secondary to rapid maxillary expansion (RME). MATERIALS AND METHODS: Sixteen participants who required RME were recruited for this study. Preoperative (T1) and 6-month postoperative (T2) cone-beam computed tomographic scans of all participants were analyzed. OnDemand3D software packages was used for superimposition and orientation of the images, while ITK-SNAP software was used to measure the volume of airway spaces...
2018: Journal of Orthodontic Science
Rafaela de Oliveira Torres, Andréa Vaz Braga Pintor, Fábio Ribeiro Guedes, Lucia Helena Soares Cevidanes, Liana Bastos Freitas-Fernandes, Antônio Carlos de Oliveira Ruellas, Ivete Pomarico Ribeiro de Souza
The objective of this study was to report the clinical evaluation results and 3-dimensional (3-D) dental and craniofacial characteristics observed in 2 male patients with mucopolysaccharidosis type II. The patients were evaluated clinically (soft tissue evaluation, evaluation of occlusion, periodontal and dental examinations) and by using craniofacial computed tomography, with evaluation of 3-D images in ITK-Snap v. 2.2 (Penn Image Computing and Science Laboratory, Philadelphia, PA; and 3-D Slicer (http://www...
April 16, 2018: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
Marek Dostál, Miloš Keřkovský, Eva Korit Áková, Eva Němcová, Jakub Stulík, Monika Staňková, Vladan Bernard
BACKGROUND: Segmentation of the gray and white matter (GM, WM) of the human spinal cord in MRI images as well as the analysis of spinal cord diffusivity are challenging. When appropriately segmented, diffusion tensor imaging (DTI) of the spinal cord might be beneficial in the diagnosis and prognosis of several diseases. PURPOSE: To evaluate the applicability of a semiautomatic algorithm provided by ITK-SNAP in classification mode (CLASS) for segmenting cervical spinal cord GM, WM in MRI images and analyzing DTI parameters...
April 29, 2018: Journal of Magnetic Resonance Imaging: JMRI
Amy H Andreotti, Raji E Joseph, James M Conley, Janet Iwasa, Leslie J Berg
Signaling through the T cell antigen receptor (TCR) activates a series of tyrosine kinases. Directly associated with the TCR, the SRC family kinase LCK and the SYK family kinase ZAP-70 are essential for all downstream responses to TCR stimulation. In contrast, the TEC family kinase ITK is not an obligate component of the TCR cascade. Instead, ITK functions as a tuning dial, to translate variations in TCR signal strength into differential programs of gene expression. Recent insights into TEC kinase structure have provided a view into the molecular mechanisms that generate different states of kinase activation...
April 26, 2018: Annual Review of Immunology
Anita Kumar, Santosha Vardhana, Alison J Moskowitz, Pierluigi Porcu, Ahmet Dogan, Jason A Dubovsky, Matthew J Matasar, Zhigang Zhang, Anas Younes, Steven M Horwitz
Ibrutinib has previously been shown to inhibit Bruton's tyrosine kinase (BTK) and interleukin-2-inducible T-cell kinase (ITK), which mediate B-cell and T-cell receptor signaling, respectively. BTK inhibition with ibrutinib has demonstrated impressive clinical responses in a variety of B-cell malignancies. Whether ibrutinib inhibition of ITK can lead to clinical response in T-cell malignancies is unknown. We hypothesized that ibrutinib-mediated ITK inhibition in T-cell lymphoma would result in decreased signaling through the T-cell receptor pathway and promote antitumor immune response by driving selective cytotoxic Th1 CD4 effector T-cell differentiation...
April 24, 2018: Blood Advances
Florent L Besson, Théophraste Henry, Céline Meyer, Virgile Chevance, Victoire Roblot, Elise Blanchet, Victor Arnould, Gilles Grimon, Malika Chekroun, Laurence Mabille, Florence Parent, Andrei Seferian, Sophie Bulifon, David Montani, Marc Humbert, Philippe Chaumet-Riffaud, Vincent Lebon, Emmanuel Durand
Purpose To assess the performance of the ITK-SNAP software for fluorodeoxyglucose (FDG) positron emission tomography (PET) segmentation of complex-shaped lung tumors compared with an optimized, expert-based manual reference standard. Materials and Methods Seventy-six FDG PET images of thoracic lesions were retrospectively segmented by using ITK-SNAP software. Each tumor was manually segmented by six raters to generate an optimized reference standard by using the simultaneous truth and performance level estimate algorithm...
April 3, 2018: Radiology
Shoeb Yakub Shaikh, Safia Shoeb Shaikh
Aim: The purpose of the present study was direct linear measurement of dentin thickness and dentin volume changes for post space preparation with cone-beam computed tomography (CBCT). Materials and Methods: Ten maxillary central incisors were scanned, before and after root canal and post space preparation, with Orthophos XG three-dimensional hybrid unit. Thirteen axial section scans of each tooth from orifice to apex and dentin thickness for buccal, lingual, mesial, and distal were measured using proprietary measuring tool and thereafter subjected to statistical analysis...
January 2018: Contemporary Clinical Dentistry
Bo Jin, Wenhan Hu, Linmei Ye, Balu Krishnan, Thandar Aung, Stephen E Jones, Imad M Najm, Andreas V Alexopoulos, Kai Zhang, Junming Zhu, Jianguo Zhang, Meiping Ding, Zhong Chen, Shuang Wang, Zhong Irene Wang
Objective: To investigate the neuroimaging and clinical features associated with sleep-related epilepsy (SRE) in patients with focal cortical dysplasia (FCD) type II. Methods: Patients with histopathologically proven FCD type II were included from three epilepsy centers. SRE was defined according to the video EEG findings and seizure history. Cortical surface reconstruction and volume calculation were performed using FreeSurfer. The lesions were manually delineated on T1 volumetric MRI using the ITK-SNAP software...
2018: Frontiers in Neurology
Yangyang Gu, Bo Huang, Yanfei Yang, Mengdie Qi, Guohua Lu, Dajing Xia, Hequan Li
Idiopathic pulmonary fibrosis (IPF) is a progressive and irreversible lung disease with high mortality rate. The etiology is unknown and treatment choices are limited. Thus, there is great interest to investigate novel agents for IPF therapy. Ibrutinib, BTK, and ITK irreversible inhibitor is a FDA-approved small molecule for the clinical therapy of B cell lymphoma. Its role in pulmonary fibrosis remains unknown. In this study, we investigated the anti-fibrotic activity of ibrutinib. Strikingly, ibrutinib did not inhibit but exacerbated bleomycin-induced pulmonary fibrosis by increased epithelial cell apoptosis, and inflammation in the lung...
March 13, 2018: Inflammation
Anika Hain, Melanie Krämer, René M Linka, Saeideh Nakhaei-Rad, Mohammad Reza Ahmadian, Dieter Häussinger, Arndt Borkhardt, Carsten Münk
Successful replication of Human immunodeficiency virus (HIV)-1 depends on the expression of various cellular host factors, such as the interleukin-2 inducible T-cell kinase (ITK), a member of the protein family of TEC-tyrosine kinases. ITK is selectively expressed in T-cells and coordinates signaling pathways downstream of the T-cell receptor and chemokine receptors, including PLC-1 activation, Ca2+ -release, transcription factor mobilization, and actin rearrangements. The exact role of ITK during HIV-1 infection is still unknown...
February 16, 2018: Scientific Reports
Theophilus N Akudjedu, Leila Nabulsi, Migle Makelyte, Cathy Scanlon, Sarah Hehir, Helen Casey, Srinath Ambati, Joanne Kenney, Stefani O'Donoghue, Emma McDermott, Liam Kilmartin, Peter Dockery, Colm McDonald, Brian Hallahan, Dara M Cannon
Manual tracing of magnetic resonance imaging (MRI) represents the gold standard for segmentation in clinical neuropsychiatric research studies, however automated approaches are increasingly used due to its time limitations. The accuracy of segmentation techniques for subcortical structures has not been systematically investigated in large samples. We compared the accuracy of fully automated [(i) model-based: FSL-FIRST; (ii) patch-based: volBrain], semi-automated (FreeSurfer) and stereological (Measure®) segmentation techniques with manual tracing (ITK-SNAP) for delineating volumes of the caudate (easy-to-segment) and the hippocampus (difficult-to-segment)...
February 13, 2018: Brain Imaging and Behavior
Yankai Meng, Yuchen Zhang, Di Dong, Chunming Li, Xiao Liang, Chongda Zhang, Lijuan Wan, Xinming Zhao, Kai Xu, Chunwu Zhou, Jie Tian, Hongmei Zhang
BACKGROUND: Locally advanced rectal cancer (LARC) patient stratification by clinicoradiologic factors may yield variable results. Therefore, more efficient prognostic biomarkers are needed for improved risk stratification of LARC patients, personalized treatment, and prognostication. PURPOSE/HYPOTHESIS: To compare the ability of a radiomic signature to predict disease-free survival (DFS) with that of a clinicoradiologic risk model in individual patients with LARC...
February 13, 2018: Journal of Magnetic Resonance Imaging: JMRI
J Todeschi, Y Pin, F Lersy, F Séverac, I Ollivier, S Kremer, F Proust, H Cebula
BACKGROUND: If the complete microsurgical resection of a brain tumor is a logical oncologic goal, the surgical strategy for the cystic component remains controversial secondary to the risk of morbidity. The objective of this study was to analyze the interest of using fibrin glue in the resection of malignant cystic brain tumors (MCBT). METHODS: Seven patients (median: 60-years-old (range [52-72]/sex ratio M/F: 2.5) were analyzed prospectively in the Neurosurgery Department at Strasbourg University Hospital, from October 2014 to November 2016...
March 2018: Neuro-Chirurgie
Benjamin F Tillman, James M Pauff, Gowri Satyanarayana, Mahsa Talbott, Jeremy L Warner
OBJECTIVE: Ibrutinib is an irreversible inhibitor of Bruton tyrosine kinase (BTK) in B lymphocytes as well as other kinases including interleukin-2-inducible T-cell kinase (ITK) in CD4+ Th2 regulatory T cells. Increased infections have been observed in patients taking ibrutinib. The overall incidence has not been systematically evaluated. METHODS: The published literature and conference abstracts of prospective clinical trials using ibrutinib in hematologic malignancies were identified and reviewed using PubMed, Google Scholar, and HemOnc...
April 2018: European Journal of Haematology
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