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Sift tissue

Deshan Yang, Miao Zhang, Xiao Chang, Yabo Fu, Shi Liu, Harold H Li, Sasa Mutic, Ye Duan
PURPOSES: An image processing procedure was developed in this study to detect large quantity of landmark pairs accurately in pairs of volumetric medical images. The detected landmark pairs can be used to evaluate of deformable image registration (DIR) methods quantitatively. METHODS: Landmark detection and pair matching were implemented in a Gaussian pyramid multi-resolution scheme. A 3D scale-invariant feature transform (SIFT) feature detection method and a 3D Harris-Laplacian corner detection method were employed to detect feature points, i...
August 23, 2017: Medical Physics
Yun Miao, Jun Xiong, Xuelian Zhang, Huajie Huang, Lixin Yu, Jianfan Chen, Wenfeng Deng, Huiling Xu, Rumin Liu, Chenglin Xiang, Xiangmin Xu, Fu Xiong
Polycystic kidney disease (PKD) and Alport syndrome (AS) are serious inherited disorders associated with renal disease, and thalassemia is a hereditary blood disease with a high prevalence in south China. Here, we report an exceptional PKD coincidence of thalassemia minor and AS (diagnosed genetically) in a large Chinese family. Whole genome next-generation sequencing (NGS) was performed on the proband, and all family members underwent clinical evaluation. Sanger sequencing was used to validate the mutations distinguished by NGS...
October 1, 2017: Clinical Science (1979-)
Souvik Ghatak, Payel Chakraborty, Sandeep Roy Sarkar, Biswajit Chowdhury, Arup Bhaumik, Nachimuthu Senthil Kumar
BACKGROUND: The role of adenomatous polyposis coli (APC) gene in mitosis might be critical for regulation of genomic stability and chromosome segregation. APC gene mutations have been associated to have a role in colon cancer and since gastric and colon tumors share some common genetic lesions, it is relevant to investigate the role of APC tumor suppressor gene in gastric cancer. METHODS: We investigated for somatic mutations in the Exons 14 and 15 of APC gene from 40 diffuse type gastric cancersamples...
June 2, 2017: BMC Medical Genetics
Violetta Shestivska, Abigail V Rutter, Josep Sulé-Suso, David Smith, Patrik Spanel
RATIONALE: Peroxidation of lipids in cellular membranes results in the release of volatile organic compounds (VOCs), including saturated aldehydes. The real-time quantification of trace VOCs produced by cancer cells during peroxidative stress presents a new challenge to non-invasive clinical diagnostics, which we have met with some success, as described in this paper. METHODS: A combination of selected ion flow tube mass spectrometry (SIFT-MS), a technique that allows rapid, reliable quantification of VOCs in humid air and liquid headspace, and electrochemistry to generate reactive oxygen species (ROS) in vitro has been used...
May 27, 2017: Rapid Communications in Mass Spectrometry: RCM
Nicholas D Embleton, Janet E Berrington, Jon Dorling, Andrew K Ewer, Edmund Juszczak, John A Kirby, Christopher A Lamb, Clare V Lanyon, William McGuire, Christopher S Probert, Stephen P Rushton, Mark D Shirley, Christopher J Stewart, Stephen P Cummings
Large randomized controlled trials (RCTs) in preterm infants offer unique opportunities for mechanistic evaluation of the risk factors leading to serious diseases, as well as the actions of interventions designed to prevent them. Necrotizing enterocolitis (NEC) a serious inflammatory gut condition and late-onset sepsis (LOS) are common feeding and nutrition-related problems that may cause death or serious long-term morbidity and are key outcomes in two current UK National Institutes for Health Research (NIHR) trials...
2017: Frontiers in Nutrition
Manoj K Bhat, Veerendra P Gadekar, Aditya Jain, Bobby Paul, Padmalatha S Rai, Kapaettu Satyamoorthy
BACKGROUND: The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded...
2017: Public Health Genomics
Lei Wang, Zhuo Shao, Shiyue Chen, Lu Shi, Zhaoshen Li
Pancreatic ductal adenocarcinoma (PDAC) presents as an aggressive malignancy caused by environmental and genetic factors. In order to identify causal genes for PDAC, we performed whole exome sequencing (WES) to detect gene mutations in seven pairs of PDAC tissue and adjacent non-tumor tissue samples. Finally, we found a new nonsynonymous single nucleotide variant (nsSNV) in solute carrier 24 family member 2 (SLC24A2) gene resulting in the substitution of native glutamic acid (E) into aspartic acid (D) at position of 287 amino acid (E287D) in SLC24A2 protein, and confirmed this variant by Sanger gene sequencing...
April 2017: Tohoku Journal of Experimental Medicine
Allie Simpson, Armin Avdic, Ben R Roos, Adam DeLuca, Kathy Miller, Michael J Schnieders, Todd E Scheetz, Wallace L M Alward, John H Fingert
PURPOSE: Lacrimo-auriculo-dento-digital (LADD) syndrome is an autosomal dominant disorder displaying variable expression of multiple congenital anomalies including hypoplasia or aplasia of the lacrimal and salivary systems causing abnormal tearing and dry mouth. Mutations in the FGF10, FGFR2, and FGFR3 genes were found to cause some cases of LADD syndrome in prior genetic studies. The goal of this study is to identify the genetic basis of a case of LADD syndrome with glaucoma and thin central corneal thickness (CCT)...
2017: Molecular Vision
Matthew D Martin, Vladimir P Badovinac
In this issue of Immunity, Gerlach et al. (2016) describe three distinct memory CD8(+) T cell subsets based upon expression of the fractalkine receptor CX3CR1. Their findings revise the paradigm of effector and central memory T cells by revealing a subset of CD8(+) memory T cells defined by intermediate levels of expression of CX3CR1 that conducts tissue surveillance.
December 20, 2016: Immunity
Lei Wang, Peder C Pedersen, Emmanuel Agu, Diane M Strong, Bengisu Tulu
The standard chronic wound assessment method based on visual examination is potentially inaccurate and also represents a significant clinical workload. Hence, computer-based systems providing quantitative wound assessment may be valuable for accurately monitoring wound healing status, with the wound area the best suited for automated analysis. Here, we present a novel approach, using support vector machines (SVM) to determine the wound boundaries on foot ulcer images captured with an image capture box, which provides controlled lighting and range...
September 2017: IEEE Transactions on Bio-medical Engineering
Zeynep Kosaloglu, Julia Bitzer, Niels Halama, Zhiqin Huang, Marc Zapatka, Andreas Schneeweiss, Dirk Jäger, Inka Zörnig
BACKGROUND: Breast cancer is one of the most common malignancies with increasing incidences every year and a leading cause of death among women. Although early stage breast cancer can be effectively treated, there are limited numbers of treatment options available for patients with advanced and metastatic disease. The novel breast cancer associated antigen NY-BR-1 was identified by SEREX analysis and is expressed in the majority (>70%) of breast tumors as well as metastases, in normal breast tissue, in testis and occasionally in prostate tissue...
November 18, 2016: BMC Cancer
Shahab Ensafi, Shijian Lu, Ashraf A Kassim, Chew Lim Tan
Autoimmune diseases (AD) are the abnormal response of the immune system of the body to healthy tissues. ADs have generally been on the increase. Efficient computer aided diagnosis of ADs through classification of the human epithelial type 2 (HEp-2) cells become beneficial. These methods make lower diagnosis costs, faster response and better diagnosis repeatability. In this paper, we present an automated HEp-2 cell image classification technique that exploits the sparse coding of the visual features together with the Bag of Words model (SBoW)...
April 2017: Computerized Medical Imaging and Graphics: the Official Journal of the Computerized Medical Imaging Society
Yan Xu, Chenchao Xu, Xiao Kuang, Hongkai Wang, Eric I-Chao Chang, Weimin Huang, Yubo Fan
PURPOSE: In this paper, the authors proposed a new 3D registration algorithm, 3D-scale invariant feature transform (SIFT)-Flow, for multiatlas-based liver segmentation in computed tomography (CT) images. METHODS: In the registration work, the authors developed a new registration method that takes advantage of dense correspondence using the informative and robust SIFT feature. The authors computed the dense SIFT features for the source image and the target image and designed an objective function to obtain the correspondence between these two images...
May 2016: Medical Physics
Yuli Christine Chang, Ya-Sian Chang, Chun-Chi Chang, Ta-Chih Liu, Ying-Chin Ko, Chien-Chin Lee, Shun-Jen Chang, Jan-Gowth Chang
Tumor necrosis factor, α-induced protein 3 (TNFAIP3) which encodes a ubiquitin-modifying enzyme (A20), acts as a negative regulator of the NF-κB pathway, and in lymphoma and autoimmune diseases it is frequently inactivated by mutations and/or deletions. We investigated the prevalence of the inactivation of TNFAIP3 in oral squamous cell carcinoma (OSCC). DNA was extracted from 81 cases of OSCC and 50 peripheral blood samples from normal controls. A high-resolution melting (HRM) analysis was used to characterize TNFAIP3 mutations, and the results were confirmed by direct DNA sequencing...
May 2016: Oncology Reports
Thomas R Mazur, Benjamin W Fischer-Valuck, Yuhe Wang, Deshan Yang, Sasa Mutic, H Harold Li
PURPOSE: To first demonstrate the viability of applying an image processing technique for tracking regions on low-contrast cine-MR images acquired during image-guided radiation therapy, and then outline a scheme that uses tracking data for optimizing gating results in a patient-specific manner. METHODS: A first-generation MR-IGRT system-treating patients since January 2014-integrates a 0.35 T MR scanner into an annular gantry consisting of three independent Co-60 sources...
January 2016: Medical Physics
Fakhri Kallabi, Emna Ellouz, Mouna Tabebi, Ghada Ben Salah, Naziha Kaabechi, Leila Keskes, Chahnez Triki, Hassen Kamoun
INTRODUCTION: X-linked adrenoleukodystrophy is a neurodegenerative recessive disorder that affects the brain white matter and associated with adrenal insufficiency. It is characterized by an abnormal function of the peroxisomes, which leads to an accumulation of the Very Long Chain Fatty Acids (VLCFA) in plasma and tissues, especially in the cortex of the adrenal glands and the white matter of the central nervous system. Mutations in the ABCD1 gene affect the function of the encoded protein ALDP, an ATP-binding cassette transporter located in the peroxisomal membrane protein...
January 30, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
A Narayana Swamy, Harika Valasala, Sreenivasulu Kamma
BACKGROUND: The human ADIPOQ gene encodes adiponectin protein hormone, which is involved in regulating glucose levels as well as fatty acid breakdown. It is exclusively produced by adipose tissue and abundantly present in the circulation, with concentration of around 0.01% of total serum proteins, with important effect on metabolism. METHODS: Most deleterious nonsynonymous single nucleotide polymorphisms in the coding region of the ADIPOQ gene were investigated using SNP databases, and detected nonsynonymous variants were analyzed in silico from the standpoint of relevant protein function and stability by using SIFT, PolyPhen-2, PROVEAN and MUpro, I-Mutant2...
July 2015: Avicenna Journal of Medical Biotechnology
Mingchang Zhang, Aimin Xue, Yiwen Shen, Joao Bosco Oliveira, Ling Li, Ziqin Zhao, Allen Burke
Desmoglein-2 (DSG2), a member of the desmosomal cadherin superfamily, has been linked to arrhythmogenic right ventricular cardiomyopathy (ARVC)which may cause life-threatening ventricular arrhythmias and sudden death. Fatal arrhythmias resulting in sudden death also occur in the absence of morphologic cardiac abnormalities at autopsy. We sequenced all 15 exons of DSG2 in DNA extracted from post-mortem heart tissues of 25 patients dying with ARVC and 25 from sudden unexplained death (SUD). The primers were designed using the Primer Express 3...
October 2015: Forensic Science International
Achintya Mohan Goswami
Single-nucleotide polymorphisms (SNPs), a most common type of genetic mutations, result from single base pair alterations. Non-synonymous SNPs (nsSNP) occur in the coding regions of a gene and result in single amino acid substitution which might have the potential to affect the function as well as structure of the corresponding protein. In human the 3β-hydroxysteroid dehydrogenases/Δ(4,5)-isomerase type 2 (HSD3B2) is an important membrane-bound enzyme involved in the dehydrogenation and Δ(4,5)-isomerization of the Δ(5)-steroid precursors into their respective Δ(4)-ketosteroids in the biosynthesis of steroid hormones such as glucocorticoids, mineralocorticoids, progesterone, androgens, and estrogens in tissues such as adrenal gland, ovary, and testis...
September 2015: Meta Gene
Rohit Shetty, Rudy M M A Nuijts, Soumya Ganesh Nanaiah, Venkata Ramana Anandula, Arkasubhra Ghosh, Chaitra Jayadev, Natasha Pahuja, Govindasamy Kumaramanickavel, Jeyabalan Nallathambi
BACKGROUND: Visual system homeobox gene (VSX1) plays a major role in the early development of craniofacial and ocular tissues including cone opsin gene in the human retina. To date, few disease-causing mutations of VSX1 have been linked to familial and sporadic keratoconus (KC) in humans. In this study, we describe the clinical features and screening for VSX1 gene in families with KC from India. METHODS: Clinical data and genomic DNA were collected from patients with clinically diagnosed KC and their family members...
2015: BMC Medical Genetics
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