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https://www.readbyqxmd.com/read/28549292/globally-supported-radial-basis-function-based-collocation-method-for-evolution-of-level-set-in-mass-segmentation-using-mammograms
#1
Kanchan Lata Kashyap, Manish Kumar Bajpai, Pritee Khanna
Computer-aided detection systems play an important role for the detection of breast abnormalities using mammograms. Global segmentation of mass in mammograms is a complex process due to low contrast mammogram images, irregular shape of mass, speculated margins, and the presence of intensity variations of pixels. This work presents a new approach for mass detection in mammograms, which is based on the variational level set function. Mesh-free based radial basis function (RBF) collocation approach is employed for the evolution of level set function for segmentation of breast as well as suspicious mass region...
May 15, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28549280/protocols-for-the-analytical-characterization-of-therapeutic-monoclonal-antibodies-i-non-denaturing-chromatographic-techniques
#2
Alexandre Goyon, Valentina D'Atri, Balazs Bobaly, Elsa Wagner-Rousset, Alain Beck, Szabolcs Fekete, Davy Guillarme
Size-, charge- and hydrophobicity-related variants of a biopharmaceutical product have to be deeply characterized for batch consistency and for the assessment of immunogenicity and safety effects. Size exclusion chromatography (SEC) and ion exchange chromatography (IEX) are considered as the gold standard for the analysis of high molecular weight species (HMWS) and charge-related variants, respectively. Hydrophobic interaction chromatography (HIC) has drawn renewed attention to monitor the small drug payload distribution in the cysteine-linked antibody-drug conjugates (ADC)...
May 11, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28549249/cd146-mcam-in-human-cs-dlk1-cs-cd34-adipose-stromal-progenitor-cells
#3
Susanne Hörl, Asim Ejaz, Sebastian Ernst, Monika Mattesich, Andreas Kaiser, Brigitte Jenewein, Marit E Zwierzina, Sarina Hammerle, Carina Miggitsch, Maria C Mitterberger-Vogt, Claudia Krautgasser, Gerhard Pierer, Werner Zwerschke
To precisely characterize CD146 in adipose stromal/progenitor cells (ASCs) we sorted the stromal vascular faction (SVF) of human abdominal subcutaneous white adipose tissue (sWAT) according to cell surface (cs) expression of CD146, DLK1 and CD34. This test identified three main SVF cell populations: ~50% cs-DLK1(-)/cs-CD34(+)/cs-CD146(-) ASCs, ~7.5% cs-DLK1(+)/cs-CD34(dim/+)/cs-CD146(+) and ~7.5% cs-DLK1(+)/cs-CD34(dim/+)/cs-CD146(-) cells. All cells contained intracellular CD146. Whole mount fluorescent IHC staining of small vessels detected CD146(+) endothelial cells (CD31(+)/CD34(+)/CD146(+)) and pericytes (CD31(-)/CD34(-)/CD146(+) ASCs)...
May 17, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28549218/exosite-2-directed-ligands-attenuate-protein-c-activation-by-the-thrombin-thrombomodulin-complex
#4
Kai Chen, Alan R Stafford, Chengliang Wu, Calvin Yeh, Paul Y Kim, James C Fredenburgh, Jeffrey I Weitz
Thrombin activity, inhibition, and localization are regulated by two exosites that flank the active site. Substrates, cofactors and inhibitors bind to exosite 1 to promote active site access, whereas exosite 2 interactions retain thrombin on cells, platelets, and proteins. The exosites also serve allosteric roles, whereby ligand binding alters thrombin activity. Previously, we showed that ligands that bind exosite 2 attenuate the exosite 1-mediated interaction of thrombin with fibrin, demonstrating allosteric connection between the exosites...
May 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28549204/setd5-gene-variant-associated-with-mild-intellectual-disability-a-case-report
#5
E Stur, L A Soares, I D Louro
The recent advent of exome sequencing has allowed for the identification of pathogenic gene variants responsible for a variety of diseases that were previously clinically diagnosed, with no underlying molecular etiology. Among these conditions, intellectual disability is a prevalent heterogeneous condition, presenting itself in a large spectrum of intensity, in some cases associated with congenital malformations, behavioral and various other intellectual development alterations. Here we report on a 36-year-old male patient, with a mild intellectual disability that remained undiagnosed at the molecular level for all his life...
May 25, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28549158/chd2-regulates-chromatin-for-proper-gene-expression-toward-differentiation-in-mouse-embryonic-stem-cells
#6
Yuichiro Semba, Akihito Harada, Kazumitsu Maehara, Shinya Oki, Chikara Meno, Jun Ueda, Kazuo Yamagata, Atsushi Suzuki, Mitsuho Onimaru, Jumpei Nogami, Seiji Okada, Koichi Akashi, Yasuyuki Ohkawa
Chromatin reorganization is necessary for pluripotent stem cells, including embryonic stem cells (ESCs), to acquire lineage potential. However, it remains unclear how ESCs maintain their characteristic chromatin state for appropriate gene expression upon differentiation. Here, we demonstrate that chromodomain helicase DNA-binding domain 2 (Chd2) is required to maintain the differentiation potential of mouse ESCs. Chd2-depleted ESCs showed suppressed expression of developmentally regulated genes upon differentiation and subsequent differentiation defects without affecting gene expression in the undifferentiated state...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28549094/a-novel-dominant-mutation-in-sag-the-arrestin-1-gene-is-a-common-cause-of-retinitis-pigmentosa-in-hispanic-families-in-the-southwestern-united-states
#7
Lori S Sullivan, Sara J Bowne, Daniel C Koboldt, Elizabeth L Cadena, John R Heckenlively, Kari E Branham, Dianna H Wheaton, Kaylie D Jones, Richard S Ruiz, Mark E Pennesi, Paul Yang, David Davis-Boozer, Hope Northrup, Vsevold V Gurevich, Rui Chen, Mingchu Xu, Yumei Li, David G Birch, Stephen P Daiger
Purpose: To identify the causes of autosomal dominant retinitis pigmentosa (adRP) in a cohort of families without mutations in known adRP genes and consequently to characterize a novel dominant-acting missense mutation in SAG. Methods: Patients underwent ophthalmologic testing and were screened for mutations using targeted-capture and whole-exome next-generation sequencing. Confirmation and additional screening were done by Sanger sequencing. Haplotypes segregating with the mutation were determined using short tandem repeat and single nucleotide variant polymorphisms...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28549093/autoantibodies-in-melanoma-associated-retinopathy-recognize-an-epitope-conserved-between-trpm1-and-trpm3
#8
Robert M Duvoisin, Tammie L Haley, Gaoying Ren, Iwona Strycharska-Orczyk, James P Bonaparte, Catherine W Morgans
Purpose: Melanoma-associated retinopathy (MAR) is a paraneoplastic syndrome associated with malignant melanoma and the presence of anti-retinal autoantibodies, including autoantibodies against transient receptor potential melanopsin 1 (TRPM1), a cation channel expressed by both melanocytes and retinal bipolar cells. The goal of this study was to further map the antigenic epitope. Methods: Patient sera were tested by immunofluorescence and Western blotting on HEK293 cells transfected with enhanced green fluorescent protein (EGFP)-TRPM1 fusion constructs and mouse retina sections...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28549031/chd4-as-a-potential-biomarker-in-differentiating-between-cellular-schwannoma-and-malignant-peripheral-nerve-sheath-tumor
#9
Chun-Chieh Wu, Mei-Ren Pan, Yu-Ching Wei, Chih-Hung Lin, Sheau-Fang Yang, Hung-Pei Tsai, Chi-Wen Luo, Chee-Yin Chai
Cellular schwannoma is an uncommon variant of benign peripheral nerve sheath tumors, but is commonly misdiagnosed as malignant peripheral sheath tumor (MPNST). Conventional methods that are used to distinguish cellular schwannoma from MPNST include immunohistochemistry (IHC) staining. However, most markers cannot precisely differentiate these 2 tumor types, and thus identification of a better marker is needed to improve the accuracy of diagnosis. Here, we evaluate the use of chromodomain helicase DNA-binding protein 4 (CHD4) as a specific marker for cellular schwannoma by comparing CHD4 and S-100 IHC staining in 14 cellular schwannoma and 17 MPNST tissue samples...
May 25, 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/28548852/unification-of-the-w1x-and-g4-mp2-6x-composite-protocols
#10
Bun Chan
We have devised the composite procedures WG and WGh to unify the W1X and the (computationally more economical) G4(MP2)-6X protocols. The WG procedure employs a combination of MP2, MP2-F12, CCSD-F12b, and CCSD(T) to approximate the all-electron scalar-relativistic CCSD(T)/CBS energy. In addition, it incorporates features such as the scaling of the energy components and an empirical "higher-level-correction" term. The WGh protocol represents a somewhat more economical variant of WG with partial removal of diffuse functions...
May 26, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28548707/phenotypes-and-genotypes-in-individuals-with-smc1a-variants
#11
Sylvia Huisman, Paul A Mulder, Egbert Redeker, Ingrid Bader, Anne-Marie Bisgaard, Alice Brooks, Anna Cereda, Constanza Cinca, Dinah Clark, Valerie Cormier-Daire, Matthew A Deardorff, Karin Diderich, Mariet Elting, Anthonie van Essen, David Fitz Patrick, Cristina Gervasini, Gabriele Gillessen-Kaesbach, Katta M Girisha, Yvonne Hilhorst-Hofstee, Saskia Hopman, Denise Horn, Mala Isrie, Sandra Jansen, Cathrine Jespersgaard, Frank J Kaiser, Maninder Kaur, Tjitske Kleefstra, Ian D Krantz, Phillis Lakeman, Annemiek Landlust, Davor Lessel, Caroline Michot, Jo Moss, Sarah E Noon, Chris Oliver, Ilaria Parenti, Juan Pie, Feliciano J Ramos, Claudine Rieubland, Silvia Russo, Angelo Selicorni, Zeynep Tümer, Rieneke Vorstenbosch, Tara L Wenger, Ingrid van Balkom, Sigrid Piening, Jolanta Wierzba, Raoul C Hennekam
SMC1A encodes one of the proteins of the cohesin complex. SMC1A variants are known to cause a phenotype resembling Cornelia de Lange syndrome (CdLS). Exome sequencing has allowed recognizing SMC1A variants in individuals with encephalopathy with epilepsy who do not resemble CdLS. We performed an international, interdisciplinary study on 51 individuals with SMC1A variants for physical and behavioral characteristics, and compare results to those in 67 individuals with NIPBL variants. For the Netherlands all known individuals with SMC1A variants were studied, both with and without CdLS phenotype...
May 26, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28548500/the-photochemical-hexadehydro-diels-alder-hv-hdda-reaction
#12
Feng Xu, Xiao Xiao, Thomas R Hoye
We demonstrate that the hexadehydro-Diels-Alder cycloisomerization reaction to produce reactive benzyne derivatives can be initiated photochemically. As with the thermal variant of the HDDA process, the reactive intermediates are formed in the absence of reagents or the resulting byproducts required for the generation of benzynes by traditional methods. This photo-HDDA (or hv-HDDA) reaction occurs at much lower temperatures (including even at -70 °C) than the thermal HDDA, but the benzynes produced behave in the same fashion with respect to their trapping reactions, suggesting that they are of the same electronic state...
May 26, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28548478/influencing-of-antioxidants-gene-variants-on-risk-of-diabetes-mellitus-and-its-complications-a-systematic-review
#13
Fatemeh Bitarafan, Mehrnoosh Khodaeian, Ozra Tabatabaei-Malazy, Mahsa M Amoli
INTRODUCTION: Oxidative stress has a key role in pathophysiology of type 2 diabetes mellitus (T2DM) and its complications as a most common health problem. Due to controversial evidence regarding the association between antioxidants' gene varients and T2DM, our aim was a systematic review of the current meta-analyses. EVIDENCE ACQUISTION: All meta-analysis' studies which assessed the association of single nucleotide polymorphisms of superoxide dismutase (SOD), catalase, glutathione peroxidase (GPX), glutathione S transferase (GST), nitric oxide synthase (NOS) and nicotinamide adenine dinucleotide phosphate oxidase (NOX) with T2DM and its complications were systematically extracted from PubMed, Scopus and Web of Science databases up to January 2016...
May 26, 2017: Minerva Endocrinologica
https://www.readbyqxmd.com/read/28548470/whole-exome-sequencing-of-etv6-runx1-in-four-childhood-acute-lymphoblastic-leukaemia-cases
#14
Zubaidah Zakaria, Norodiyah Othman, Azli Ismail, Nor Rizan Kamaluddin, Ezalia Esa, Eni Juraida Abdul Rahman, Yuslina Mat Yusoff, Fazlin Mohd Fauzi, Ten Sew Keoh
Background: ETV6/RUNX1 gene fusion is the most frequently seen chromosomal abnormality in childhood acute lymphobastic leukamia (ALL). However, additional genetic changes are known to be required for the development of this type of leukaemia. Therefore, we here aimed to assess the somatic mutational profile of four ALL cases carrying the ETV6/RUNX1 fusion gene using whole-exome sequencing. Methods: DNA was isolated from bone marrow samples using a QIAmp DNA Blood Mini kit and subsequently sequenced using the Illumina MiSeq system...
April 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28548292/hypertriglyceridemic-acute-pancreatitis-in-an-emergency-department-the-typical-clinical-features-and-genetic-variants
#15
Wan Jun Chen, Xiao Fan Sun, Rui Xue Zhang, Min Jie Xu, Tong Hai Dou, Xiao Bin Zhang, Min Zhong, Wei Qiang Yang, Li Liu, Xiao Ye Lu, Chang Qing Zhu
OBJECTIVE: To investigate the clinical characteristics of hypertriglyceridemic acute pancreatitis (HTGAP), and the molecular foundation contributing to the hypertriglyceridemia in this group of patients. METHODS: Clinical data from 329 patients with AP were collected and analyzed. All the patients were divided into 1) HTGAP group (n = 40), with fasting serum triglyceride ≥ 500 mg/dL; and 2) NHTGAP group (n = 289). Next, the targeted next-generation sequencing was applied in 11 HTGAP patients to detect the genetic mutation associated with hypertriglyceridemia that included apolipoprotein A-5 (APOA5), apolipoprotein C-3 (APOC3), apolipoprotein E (APOE), BLK proto-oncogene, lipoprotein lipase (LPL), apolipoprotein C-2 (APOC2), glycosylphosphatidylinositol anchored high density lipoprotein binding protein-1(GPIHBP1), and lipase maturation factor-1(LMF1)...
May 26, 2017: Journal of Digestive Diseases
https://www.readbyqxmd.com/read/28548211/a-haplotype-block-downstream-of-plasminogen-is-associated-with-chronic-and-aggressive-periodontitis
#16
Matthias Munz, Hong Chen, Yvonne Jockel-Schneider, Knut Adam, Per Hoffman, Klaus Berger, Thomas Kocher, Jörg Meyle, Peter Eickholz, Christof Doerfer, Matthias Laudes, André Uitterlinden, Wolfgang Lieb, Andre Franke, Stefan Schreiber, Steven Offenbacher, Kimon Divaris, Corinna Bruckmann, Bruno G Loos, Soeren Jepsen, Henrik Dommisch, Arne S Schaefer
AIM: The intronic variant rs4252120 in the plasminogen gene (PLG) is known to be associated with aggressive periodontitis (AgP) and atherosclerosis. Here, we examined the chromosomal region spanning PLG for associations with both chronic periodontitis (CP) and AgP. MATERIAL AND METHODS: The association of PLG candidate rs4252120 was tested in a German case-control sample of 1,419 CP cases using the genotyping assay hCV11225947 and 4,562 controls, genotyped with HumanOmni BeadChips...
May 26, 2017: Journal of Clinical Periodontology
https://www.readbyqxmd.com/read/28548104/genomic-analysis-of-oesophageal-squamous-cell-carcinoma-identifies-alcohol-drinking-related-mutation-signature-and-genomic-alterations
#17
Jiang Chang, Wenle Tan, Zhiqiang Ling, Ruibin Xi, Mingming Shao, Mengjie Chen, Yingying Luo, Yanjie Zhao, Yun Liu, Xiancong Huang, Yuchao Xia, Jinlin Hu, Joel S Parker, David Marron, Qionghua Cui, Linna Peng, Jiahui Chu, Hongmin Li, Zhongli Du, Yaling Han, Wen Tan, Zhihua Liu, Qimin Zhan, Yun Li, Weimin Mao, Chen Wu, Dongxin Lin
Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1-E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28548082/whole-genome-sequencing-and-imputation-in-isolated-populations-identify-genetic-associations-with-medically-relevant-complex-traits
#18
Lorraine Southam, Arthur Gilly, Dániel Süveges, Aliki-Eleni Farmaki, Jeremy Schwartzentruber, Ioanna Tachmazidou, Angela Matchan, Nigel W Rayner, Emmanouil Tsafantakis, Maria Karaleftheri, Yali Xue, George Dedoussis, Eleftheria Zeggini
Next-generation association studies can be empowered by sequence-based imputation and by studying founder populations. Here we report ∼9.5 million variants from whole-genome sequencing (WGS) of a Cretan-isolated population, and show enrichment of rare and low-frequency variants with predicted functional consequences. We use a WGS-based imputation approach utilizing 10,422 reference haplotypes to perform genome-wide association analyses and observe 17 genome-wide significant, independent signals, including replicating evidence for association at eight novel low-frequency variant signals...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28547974/diagnostic-value-of-trop-2-expression-in-papillary-thyroid-carcinoma-and-comparison-with-hbme-1-galectin-3-and-cytokeratin-19
#19
Afsin Rahman Murtezaoglu, Hasan Gucer
In this study, we compared the diagnostic value of TROP-2 expression in distinguishing between benign and malignant thyroid lesions to those of HBME-1, CK19 and galectin-3. We selected 102 cases from our archive including 20 normal thyroid tissues, 23 follicular nodular diseases, 17 follicular adenomas, 20 follicular variant papillary carcinomas and 22 classical variant papillary carcinomas. Tissue microarrays constructed from these cases were immunohistochemically analyzed with HBME-1, CK19, galectin-3 and TROP-2...
2017: Polish Journal of Pathology: Official Journal of the Polish Society of Pathologists
https://www.readbyqxmd.com/read/28547909/identification-and-expression-of-conserved-and-novel-rna-variants-of-medaka-pax6b-gene
#20
Tiansheng Chen, Benzion Cavari, Manfred Schartl, Yunhan Hong
Gene duplication is a major driving force of evolution. How gene duplicates have evolved remains a mystery. A highly conserved gene such as Pax6 is an ideal model to study functional conservation and divergence via comparisons among diverse organisms. One pax6 gene has been characterized in the Japanese medaka (Oryzias latipes), which is annotated as pax6b on chromosome 3. Here, we report that Medaka pax6b is homolog to Pax6 of mammals in sequence, chromosomal synteny, and genomic organization. Cloning and sequencing led to the identification of up to 43 pax6b RNA variants predicting six protein isoforms, 22 of which are similar to those reported in other organisms and 21 represent novel RNA variants...
May 26, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
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