keyword
MENU ▼
Read by QxMD icon Read
search

Itk

keyword
https://www.readbyqxmd.com/read/28048842/su-f-r-18-updates-to-the-computational-environment-for-radiological-research-for-image-analysis
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/27730414/survey-of-non-rigid-registration-tools-in-medicine
#15
András P Keszei, Benjamin Berkels, Thomas M Deserno
We catalogue available software solutions for non-rigid image registration to support scientists in selecting suitable tools for specific medical registration purposes. Registration tools were identified using non-systematic search in Pubmed, Web of Science, IEEE Xplore® Digital Library, Google Scholar, and through references in identified sources (n = 22). Exclusions are due to unavailability or inappropriateness. The remaining (n = 18) tools were classified by (i) access and technology, (ii) interfaces and application, (iii) living community, (iv) supported file formats, and (v) types of registration methodologies emphasizing the similarity measures implemented...
October 11, 2016: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/27729219/interleukin-2-inducible-t-cell-kinase-expression-and-relation-to-disease-severity-in-systemic-lupus-erythematosus
#16
Wang-Dong Xu, Lin-Chong Su, Qi-Bing Xie, Yi Zhao, Yi Liu
BACKGROUND: Interleukin-2 inducible T-cell kinase (ITK) is expressed in T cells, and plays an important role in autoimmune inflammatory diseases through regulating the balance of Th17/Treg. However, its role in human systemic lupus erythematosus (SLE) remains unclear. The present study aims to measure the activation status of ITK in T cells from SLE patients and healthy controls, and identify its possible correlation to disease severity. We also discuss the serum levels of Th17, Treg related cytokines including IL-17, IL-21, IL-22, IL-10, analyzing correlation between ITK and Th17/Treg related cytokines...
December 1, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/27678331/ibrutinib-inhibits-erbb-receptor-tyrosine-kinases-and-her2-amplified-breast-cancer-cell-growth
#17
Jun Chen, Taisei Kinoshita, Juthamas Sukbuntherng, Betty Y Chang, Laurence Elias
Ibrutinib is a potent, small-molecule Bruton tyrosine kinase (BTK) inhibitor developed for the treatment of B-cell malignancies. Ibrutinib covalently binds to Cys481 in the ATP-binding domain of BTK. This cysteine residue is conserved among 9 other tyrosine kinases, including HER2 and EGFR, which can be targeted. Screening large panels of cell lines demonstrated that ibrutinib was growth inhibitory against some solid tumor cells, including those inhibited by other HER2/EGFR inhibitors. Among sensitive cell lines, breast cancer lines with HER2 overexpression were most potently inhibited by ibrutinib (<100 nmol/L); in addition, the IC50s were lower than that of lapatinib and dacomitinib...
December 2016: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/27628052/volumetric-study-of-sphenoid-sinuses-anatomical-analysis-in-helical-computed-tomography
#18
Juliana Mayara Magalhães Oliveira, Maria Beatriz Carrazzone Cal Alonso, Maria José Albuquerque Pereira de Sousa E Tucunduva, Acácio Fuziy, Ana Carla Raphaelli Nahás Scocate, André Luiz Ferreira Costa
PURPOSE: The sphenoid sinus is the most inaccessible part of the face, being inside the sphenoid bone and closely related to numerous vital neural and vascular structures. The objective of this study was to analyze and evaluate the variation of anatomy and the volume of the sphenoid sinus using helical computed tomography and medical imaging software. MATERIALS AND METHODS: A total of 47 helical CT scans of sinuses of male and female individuals aged 18-86 years were selected...
September 15, 2016: Surgical and Radiologic Anatomy: SRA
https://www.readbyqxmd.com/read/27590878/second-generation-inhibitors-of-bruton-tyrosine-kinase
#19
REVIEW
Jingjing Wu, Christina Liu, Stella T Tsui, Delong Liu
Bruton tyrosine kinase (BTK) is a critical effector molecule for B cell development and plays a major role in lymphoma genesis. Ibrutinib is the first-generation BTK inhibitor. Ibrutinib has off-target effects on EGFR, ITK, and Tec family kinases, which explains the untoward effects of ibrutinib. Resistance to ibrutinib was also reported. The C481S mutation in the BTK kinase domain was reported to be a major mechanism of resistance to ibrutinib. This review summarizes the clinical development of novel BTK inhibitors, ACP-196 (acalabrutinib), ONO/GS-4059, and BGB-3111...
September 2, 2016: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/27577778/a-robust-method-for-high-precision-quantification-of-the-complex-three-dimensional-vasculatures-acquired-by-x-ray-microtomography
#20
Hai Tan, Dadong Wang, Rongxin Li, Changming Sun, Ryan Lagerstrom, You He, Yanling Xue, Tiqiao Xiao
The quantification of micro-vasculatures is important for the analysis of angiogenesis on which the detection of tumor growth or hepatic fibrosis depends. Synchrotron-based X-ray computed micro-tomography (SR-µCT) allows rapid acquisition of micro-vasculature images at micrometer-scale spatial resolution. Through skeletonization, the statistical features of the micro-vasculature can be extracted from the skeleton of the micro-vasculatures. Thinning is a widely used algorithm to produce the vascular skeleton in medical research...
September 1, 2016: Journal of Synchrotron Radiation
keyword
keyword
36935
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"