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Computable phenotype

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https://www.readbyqxmd.com/read/27925416/association-of-a-gain-of-function-variant-in-lgr4-with-central-obesity
#1
Yaoyu Zou, Tinglu Ning, Juan Shi, Maopei Chen, Lin Ding, Ya Huang, Sophie Kauderer, Min Xu, Bin Cui, Yufang Bi, Simin Liu, Jie Hong, Ruixin Liu, Guang Ning, Jiqiu Wang
OBJECTIVE: To determine the relationship of the gain-of-function variant A750T in leucine-rich repeat containing G protein-coupled receptor 4 (LGR4) with central obesity and related metabolic phenotypes. METHODS: The LGR4 A750T (c.2248 G > A) variant was detected by Sanger sequencing in a discovery young population and a validation community-based population with obesity from eastern China. Fat indices determined by anthropometry and computed tomography scans and clinical biochemical measurements were collected for association analysis...
December 7, 2016: Obesity
https://www.readbyqxmd.com/read/27924018/disgenet-a-comprehensive-platform-integrating-information-on-human-disease-associated-genes-and-variants
#2
Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I Furlong
The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. To provide the community with a resource free of these hurdles, we have developed DisGeNET (http://www.disgenet.org), one of the largest available collections of genes and variants involved in human diseases...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27922631/dataset-of-eye-disease-related-proteins-analyzed-using-the-unfolding-mutation-screen
#3
Caitlyn L McCafferty, Yuri V Sergeev
A number of genetic diseases are a result of missense mutations in protein structure. These mutations can lead to severe protein destabilization and misfolding. The unfolding mutation screen (UMS) is a computational method that calculates unfolding propensities for every possible missense mutation in a protein structure. The UMS validation demonstrated a good agreement with experimental and phenotypical data. 15 protein structures (a combination of homology models and crystal structures) were analyzed using UMS...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27922113/non-small-cell-lung-cancer-quantitative-phenotypic-analysis-of-ct-images-as-a-potential-marker-of-prognosis
#4
Jiangdian Song, Zaiyi Liu, Wenzhao Zhong, Yanqi Huang, Zelan Ma, Di Dong, Changhong Liang, Jie Tian
This was a retrospective study to investigate the predictive and prognostic ability of quantitative computed tomography phenotypic features in patients with non-small cell lung cancer (NSCLC). 661 patients with pathological confirmed as NSCLC were enrolled between 2007 and 2014. 592 phenotypic descriptors was automatically extracted on the pre-therapy CT images. Firstly, support vector machine (SVM) was used to evaluate the predictive value of each feature for pathology and TNM clinical stage. Secondly, Cox proportional hazards model was used to evaluate the prognostic value of these imaging signatures selected by SVM which subjected to a primary cohort of 138 patients, and an external independent validation of 61 patients...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917600/determination-of-hepatitis-b-phenotype-using-biochemical-and%C3%A2-serological-markers
#5
A M Di Bisceglie, M Lombardero, J Teckman, L Roberts, H L A Janssen, S H Belle, J H Hoofnagle
The aim of this study was to assess the validity of categorization of chronic hepatitis B viral infection into stages or phases based upon measures of disease activity and viral load, assuming these phenotypes will be useful for prognostication and determining the need for antiviral therapy. We assessed the phenotype of hepatitis B of 1,390 adult participants enrolled in the Hepatitis B Research Network Cohort Study, using a computer algorithm. Only 4% were immune tolerant, while 35% had chronic hepatitis B (18% e antigen positive and 17% e antigen negative) while 23% were inactive carriers...
December 5, 2016: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/27917577/inter-and-intra-specific-diversity-in-cistus-l-cistaceae-seeds-analyzed-by-computer-vision-techniques
#6
Marisol Lo Bianco, Oscar Grillo, Eva Cañadas, Gianfranco Venora, Gianluigi Bacchetta
This work aims to discriminate among different species of the genus Cistus, using seeds parameters and following the scientific plant names included as accepted in The Plant List. Also the intra-specific phenotypic differentiation of C. creticus, through the comparison of three subspecies (C. creticus subsp. creticus, C. c. subsp. eriocephalus and C. c. subsp. corsicus) and the inter-population variability among five C. creticus subsp. eriocephalus populations, were evaluated. Seed mean weight and 137 morpho-colorimetric quantitative variables, describing shape, size, color and textural seed traits, were measured using image analysis techniques...
December 5, 2016: Plant Biology
https://www.readbyqxmd.com/read/27915291/the-landscape-of-microbial-phenotypic-traits-and-associated-genes
#7
Maria Brbić, Matija Piškorec, Vedrana Vidulin, Anita Kriško, Tomislav Šmuc, Fran Supek
Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27914708/generation-and-phenotypic-analysis-of-mice-lacking-all-urea-transporters
#8
Tao Jiang, Yingjie Li, Anita T Layton, Weiling Wang, Yi Sun, Min Li, Hong Zhou, Baoxue Yang
Urea transporters (UT) are a family of transmembrane urea-selective channel proteins expressed in multiple tissues and play an important role in the urine concentrating mechanism of the mammalian kidney. UT inhibitors have diuretic activity and could be developed as novel diuretics. To determine if functional deficiency of all UTs in all tissues causes physiological abnormality, we established a novel mouse model in which all UTs were knocked out by deleting an 87 kb of DNA fragment containing most parts of Slc14a1 and Slc14a2 genes...
November 30, 2016: Kidney International
https://www.readbyqxmd.com/read/27914078/computer-vision-based-image-analysis-of-bacteria
#9
Jonas Danielsen, Pontus Nordenfelt
Microscopy is an essential tool for studying bacteria, but is today mostly used in a qualitative or possibly semi-quantitative manner often involving time-consuming manual analysis. It also makes it difficult to assess the importance of individual bacterial phenotypes, especially when there are only subtle differences in features such as shape, size, or signal intensity, which is typically very difficult for the human eye to discern. With computer vision-based image analysis - where computer algorithms interpret image data - it is possible to achieve an objective and reproducible quantification of images in an automated fashion...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913356/a-framework-for-integrating-multiple-biological-networks-to-predict-microrna-disease-associations
#10
Wei Peng, Wei Lan, Zeng Yu, Jianxin Wang, Yi Pan
MicroRNAs have close relationship with human diseases. Therefore, identifying disease related MicroRNAs plays an important role in disease diagnosis, prognosis and therapy. However, designing an effective computational method which can make good use of various biological resources and correctly predict the associations between MicroRNA and disease is still a big challenge. Previous researchers have pointed out that there are complex relationships among microRNAs, diseases and environment factors. There are inter-relationships between microRNAs, diseases or environment factors based on their functional similarity or phenotype similarity or chemical structure similarity and so on...
November 29, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27907011/uncover-mirna-disease-association-by-exploiting-global-network-similarity
#11
Min Chen, Xingguo Lu, Bo Liao, Zejun Li, Lijun Cai, Changlong Gu
Identification of miRNA-disease association is a fundamental challenge in human health clinic. However, the known miRNA-disease associations are rare and experimental verification methods are expensive and time-consuming. Therefore, there is a strong incentive to develop computational methods. In this paper, we calculate the similarity score for each miRNAs pair by integrating miRNA functional similarity and miRNA family information. We use the disease phenotype similarity data to construct the disease similarity network...
2016: PloS One
https://www.readbyqxmd.com/read/27905547/in-silico-mapping-of-protein-unfolding-mutations-for-inherited-disease
#12
Caitlyn L McCafferty, Yuri V Sergeev
The effect of disease-causing missense mutations on protein folding is difficult to evaluate. To understand this relationship, we developed the unfolding mutation screen (UMS) for in silico evaluation of the severity of genetic perturbations at the atomic level of protein structure. The program takes into account the protein-unfolding curve and generates propensities using calculated free energy changes for every possible missense mutation at once. These results are presented in a series of unfolding heat maps and a colored protein 3D structure to show the residues critical to the protein folding and are available for quick reference...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27903462/radiomic-based-pathological-response-prediction-from-primary-tumors-and-lymph-nodes-in-nsclc
#13
Thibaud P Coroller, Vishesh Agrawal, Elizabeth Huynh, Vivek Narayan, Stephanie W Lee, Raymond H Mak, Hugo J W L Aerts
INTRODUCTION: Non-invasive biomarkers that capture the total tumor burden could provide important complementary information for precision medicine to aid clinical decision-making. We investigated the value of radiomic data, extracted from pre-treatment computed tomography (CT) images of the primary tumor and lymph nodes, in predicting pathological response following neoadjuvant chemoradiation prior to surgery. METHODS: Eighty-five patients with resectable locally-advanced (stage II-III) non-small cell lung cancer (NSCLC) (median age: 60...
November 26, 2016: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/27902803/alphasim-software-for-breeding-program-simulation
#14
Anne-Michelle Faux, Gregor Gorjanc, R Chris Gaynor, Mara Battagin, Stefan M Edwards, David L Wilson, Sarah J Hearne, Serap Gonen, John M Hickey
This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree; (ii) drop haplotypes into the base generation of the pedigree and select single-nucleotide polymorphism (SNP) and quantitative trait nucleotide (QTN); (iii) assign QTN effects, calculate genetic values, and simulate phenotypes; (iv) drop haplotypes into the burn-in generations; and (v) perform selection and simulate new generations...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27900088/favorable-control-of-advanced-colon-adenocarcinoma-with-severe-bone-marrow-metastasis-a-case-report
#15
Fumiyasu Hanamura, Yoshihiro Shibata, Tsuyoshi Shirakawa, Miyuki Kuwayama, Hisanobu Oda, Hiroshi Ariyama, Kenichi Taguchi, Taito Esaki, Eishi Baba
Colorectal cancer (CRC) has a propensity to metastasize to the liver, lungs and regional abdominal lymph nodes, but rarely to the bone marrow. A 60-year-old man presented to the National Hospital Organization Kyushu Cancer Center with a 4-week history of persistent lower back pain, anorexia and difficulty defecating. Complete blood count revealed severe thrombocytopenia and erythroblastosis, suggesting a hematological malignancy. However, the bone marrow examination demonstrated involvement by a moderately to poorly differentiated adenocarcinoma, but no hematopoietic abnormalities...
November 2016: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/27900005/fluoro-edenite-induces-fibulin-3-overexpression-in-non-malignant-human-mesothelial-cells
#16
Venerando Rapisarda, Rossella Salemi, Andrea Marconi, Carla Loreto, Adriana C Graziano, Venera Cardile, Maria S Basile, Saverio Candido, Luca Falzone, Demetrios A Spandidos, Concettina Fenga, Massimo Libra
Exposure to asbestos is associated with the development of mesothelioma. In addition to asbestos, other fibers have been identified as risk factors for malignant and non-malignant diseases of the lungs. Among these, fluoro-edenite (FE) was found in patients from Biancavilla (Sicily, Italy) with pleural and lung disease, suggesting its role for tumor expansion. In this context, the identification of early biomarkers useful for the diagnosis of cancer is mandatory. Fibulin-3 represents an important marker for the diagnosis of mesothelioma...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899624/microscope-in-2017-an-expanding-and-evolving-integrated-resource-for-community-expertise-of-microbial-genomes
#17
David Vallenet, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Aurélie Lajus, Adrien Josso, Jonathan Mercier, Alexandre Renaux, Johan Rollin, Zoe Rouy, David Roche, Claude Scarpelli, Claudine Médigue
The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899621/cooperative-genomic-alteration-network-reveals-molecular-classification-across-12-major-cancer-types
#18
Hongyi Zhang, Yulan Deng, Yong Zhang, Yanyan Ping, Hongying Zhao, Lin Pang, Xinxin Zhang, Li Wang, Chaohan Xu, Yun Xiao, Xia Li
The accumulation of somatic genomic alterations that enables cells to gradually acquire growth advantage contributes to tumor development. This has the important implication of the widespread existence of cooperative genomic alterations in the accumulation process. Here, we proposed a computational method HCOC that simultaneously consider genetic context and downstream functional effects on cancer hallmarks to uncover somatic cooperative events in human cancers. Applying our method to 12 TCGA cancer types, we totally identified 1199 cooperative events with high heterogeneity across human cancers, and then constructed a pan-cancer cooperative alteration network...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899602/the-human-phenotype-ontology-in-2017
#19
Sebastian Köhler, Nicole A Vasilevsky, Mark Engelstad, Erin Foster, Julie McMurry, Ségolène Aymé, Gareth Baynam, Susan M Bello, Cornelius F Boerkoel, Kym M Boycott, Michael Brudno, Orion J Buske, Patrick F Chinnery, Valentina Cipriani, Laureen E Connell, Hugh J S Dawkins, Laura E DeMare, Andrew D Devereau, Bert B A de Vries, Helen V Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna A Jähn, Roger James, Roland Krause, Stanley J F Laulederkind, Hanns Lochmüller, Gholson J Lyon, Soichi Ogishima, Annie Olry, Willem H Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H Scott, Michael Segal, Panagiotis I Sergouniotis, Richard Sever, Cynthia L Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W M Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O B Jacobsen, Tudor Groza, Damian Smedley, Christopher J Mungall, Melissa Haendel, Peter N Robinson
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898905/opportunities-for-genomic-prediction-for-fertility-using-endocrine-and-classical-fertility-traits-in-dairy-cattle
#20
A M M Tenghe, B Berglund, E Wall, R F Veerkamp, D J de Koning
Endocrine fertility traits, defined from progesterone concentration levels in milk, have been suggested as alternative indicators for fertility in dairy cows because they are less biased by farm management decisions and more directly reflect a cow's reproductive physiology than classical traits derived from insemination and calving data. To determine the potential use of endocrine fertility traits in genomic evaluations, the improvement in accuracy from using endocrine fertility traits concurrent with classical traits in the genomic prediction of fertility was quantified...
September 2016: Journal of Animal Science
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