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Computable phenotype

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https://www.readbyqxmd.com/read/28544911/arianna-a-research-environment-for-neuroimaging-studies-in-autism-spectrum-disorders
#1
Alessandra Retico, Silvia Arezzini, Paolo Bosco, Sara Calderoni, Alberto Ciampa, Simone Coscetti, Stefano Cuomo, Luca De Santis, Dario Fabiani, Maria Evelina Fantacci, Alessia Giuliano, Enrico Mazzoni, Pietro Mercatali, Giovanni Miscali, Massimiliano Pardini, Margherita Prosperi, Francesco Romano, Elena Tamburini, Michela Tosetti, Filippo Muratori
The complexity and heterogeneity of Autism Spectrum Disorders (ASD) require the implementation of dedicated analysis techniques to obtain the maximum from the interrelationship among many variables that describe affected individuals, spanning from clinical phenotypic characterization and genetic profile to structural and functional brain images. The ARIANNA project has developed a collaborative interdisciplinary research environment that is easily accessible to the community of researchers working on ASD (https://arianna...
May 17, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28544620/phenotyping-cardiac-and-structural-birth-defects-in-fetal-and-newborn-mice
#2
REVIEW
Xiaoqin Liu, Andrew J Kim, William Reynolds, Yijen Wu, Cecilia W Lo
Mouse models are invaluable for investigating the developmental etiology and molecular pathogenesis of structural birth defects. While this has been deployed for studying a wide spectrum of birth defects, mice are particularly valuable for modeling congenital heart disease, given they have the same four-chamber cardiac anatomy as in humans. We have developed the use of noninvasive fetal ultrasound together with micro-computed tomography (micro-CT) imaging for high throughput phenotyping of mice for congenital heart defects (CHD) and other developmental anomalies...
May 22, 2017: Birth Defects Res
https://www.readbyqxmd.com/read/28542217/assessment-of-asthma-severity-in-adults-with-ever-asthma-a-continuous-score
#3
Lucia Calciano, Angelo Guido Corsico, Pietro Pirina, Giulia Trucco, Deborah Jarvis, Christer Janson, Simone Accordini
BACKGROUND: In epidemiological studies, continuous measures of asthma severity should be used to catch the heterogeneity of phenotypes. This study aimed at developing and validating continuous measures of asthma severity in adult patients with ever asthma from the general population, to be used in epidemiological studies. METHODS: Respiratory symptoms, anti-asthmatic treatment and lung function were measured on 520 patients with ever asthma aged 20-64 years from the general Italian population (GEIRD study; 2007/2010)...
2017: PloS One
https://www.readbyqxmd.com/read/28539731/improved-annotations-of-23-differentially-expressed-hypothetical-proteins-in-methicillin-resistant-s-aureus
#4
Jessica Marklevitz, Laura K Harris
Antibiotic resistant Staphylococcus aureus is a major public health concern effecting millions of people annually. Medical science has documented completely untreatable S. aureus infections. These strains are appearing in the community with increasing frequency. New diagnostic and therapeutic options are needed to combat this deadly infection. Interestingly, around 50% of the proteins in S. aureus are annotated as hypothetical. Methods to select hypothetical proteins related to antibiotic resistance have been inadequate...
2017: Bioinformation
https://www.readbyqxmd.com/read/28539123/multilevel-genomics-of-colorectal-cancers-with-microsatellite-instability-clinical-impact-of-jak1-mutations-and-consensus-molecular-subtype-1
#5
Anita Sveen, Bjarne Johannessen, Torstein Tengs, Stine A Danielsen, Ina A Eilertsen, Guro E Lind, Kaja C G Berg, Edward Leithe, Leonardo A Meza-Zepeda, Enric Domingo, Ola Myklebost, David Kerr, Ian Tomlinson, Arild Nesbakken, Rolf I Skotheim, Ragnhild A Lothe
BACKGROUND: Approximately 15% of primary colorectal cancers have DNA mismatch repair deficiency, causing a complex genome with thousands of small mutations-the microsatellite instability (MSI) phenotype. We investigated molecular heterogeneity and tumor immunogenicity in relation to clinical endpoints within this distinct subtype of colorectal cancers. METHODS: A total of 333 primary MSI+ colorectal tumors from multiple cohorts were analyzed by multilevel genomics and computational modeling-including mutation profiling, clonality modeling, and neoantigen prediction in a subset of the tumors, as well as gene expression profiling for consensus molecular subtypes (CMS) and immune cell infiltration...
May 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28536534/a-bio-realistic-finite-element-model-to-evaluate-the-effect-of-masticatory-loadings-on-mouse-mandible-related-tissues
#6
Alexander Tsouknidas, Lucia Jimenez-Rojo, Evangelos Karatsis, Nikolaos Michailidis, Thimios A Mitsiadis
Mice are arguably the dominant model organisms for studies investigating the effect of genetic traits on the pathways to mammalian skull and teeth development, thus being integral in exploring craniofacial and dental evolution. The aim of this study is to analyse the functional significance of masticatory loads on the mouse mandible and identify critical stress accumulations that could trigger phenotypic and/or growth alterations in mandible-related structures. To achieve this, a 3D model of mouse skulls was reconstructed based on Micro Computed Tomography measurements...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28535296/metasra-normalized-human-sample-specific-metadata-for-the-sequence-read-archive
#7
Matthew N Bernstein, AnHai Doan, Colin N Dewey
Motivation: The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants, and references to outside sources of information...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28535199/genotype-phenotype-correlation-in-patients-with-isovaleric-acidemia-comparative-structural-modelling-and-computational-analysis-of-novel-variants
#8
Osama K Zaki, George Priya Doss C, Salsabil A Ali, Ghadeer G Murad, Shaima A Elashi, Maryam Sa Ebnou, D Thirumal Kumar, Ola Khalifa, Radwa Gamal, Heba S A El Abd, Bilal N Nasr, Hatem Zayed
Isovaleric acidemia (IVA) is an autosomal recessive inborn error of leucine metabolism. It is caused by a deficiency in the mitochondrial isovaleryl-CoA dehydrogenase (IVD) enzyme. In this study, we investigated eight patients with IVA. The patients diagnoses were confirmed by urinary organic acid analysis and the blood C5-Carnitine value. A molecular genetic analysis of the IVD gene revealed nine different variants: five were missense variants (c.1193G>A; p. R398Q, c.1207T>A; p. Y403N, c.872C>T; p...
May 23, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28533456/colour-vision-and-coevolution-in-avian-brood-parasitism
#9
REVIEW
Mary Caswell Stoddard, Mark E Hauber
The coevolutionary interactions between avian brood parasites and their hosts provide a powerful system for investigating the diversity of animal coloration. Specifically, reciprocal selection pressure applied by hosts and brood parasites can give rise to novel forms and functions of animal coloration, which largely differ from those that arise when selection is imposed by predators or mates. In the study of animal colours, avian brood parasite-host dynamics therefore invite special consideration. Rapid advances across disciplines have paved the way for an integrative study of colour and vision in brood parasite-host systems...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28533317/cardiovascular-toxicity-of-illicit-anabolic-androgenic-steroid-use
#10
Aaron L Baggish, Rory B Weiner, Gen Kanayama, James I Hudson, Michael T Lu, Udo Hoffmann, Harrison G Pope
BACKGROUND: Millions of individuals have used illicit anabolic-androgenic steroids (AAS), but the long-term cardiovascular associations of these drugs remain incompletely understood. METHODS: Using a cross-sectional cohort design, we recruited 140 experienced male weightlifters 34 to 54 years of age, comprising 86 men reporting ≥2 years of cumulative lifetime AAS use and 54 nonusing men. Using transthoracic echocardiography and coronary computed tomography angiography, we assessed 3 primary outcome measures: left ventricular (LV) systolic function (left ventricular ejection fraction), LV diastolic function (early relaxation velocity), and coronary atherosclerosis (coronary artery plaque volume)...
May 23, 2017: Circulation
https://www.readbyqxmd.com/read/28532442/an-integrated-enhancement-and-reconstruction-strategy-for-the-quantitative-extraction-of-actin-stress-fibers-from-fluorescence-micrographs
#11
Zhen Zhang, Shumin Xia, Pakorn Kanchanawong
BACKGROUND: The stress fibers are prominent organization of actin filaments that perform important functions in cellular processes such as migration, polarization, and traction force generation, and whose collective organization reflects the physiological and mechanical activities of the cells. Easily visualized by fluorescence microscopy, the stress fibers are widely used as qualitative descriptors of cell phenotypes. However, due to the complexity of the stress fibers and the presence of other actin-containing cellular features, images of stress fibers are relatively challenging to quantitatively analyze using previously developed approaches, requiring significant user intervention...
May 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28531258/the-reproducibility-of-racial-differences-in-ambulatory-blood-pressure-phenotypes-and-measurements
#12
Aamir Husain, Feng-Chang Lin, Laura A Tuttle, Emily Olsson, Anthony J Viera
BACKGROUND: We examined the reproducibility of differences in ambulatory blood pressure (BP) monitoring (ABPM) phenotypes and other parameters (sustained hypertension, masked hypertension, nocturnal hypertension, and nondipping) between African Americans and Whites. METHODS: A total of 420 participants untreated for hypertension attended 2 research visits 1 week apart during which traditional office BP averages and ABPM session averages were determined. We computed percent agreement in ABPM phenotypes across the 2 visits stratified by race and associated kappa statistics with 95% confidence intervals...
May 22, 2017: American Journal of Hypertension
https://www.readbyqxmd.com/read/28525263/yellow-and-orange-fluorescent-proteins-with-tryptophan-based-chromophores
#13
Nina G Bozhanova, Mikhail S Baranov, Karen S Sarkisyan, Roman Gritсenko, Konstantin V Mineev, Svetlana V Golodukhina, Nadezhda S Baleeva, Konstantin A Lukyanov, Alexander S Mishin
Rapid development of new microscopy techniques exposed the need for genetically encoded fluorescent tags with special properties. Recent works demonstrated the potential of fluorescent proteins with tryptophan-based chromophores. We applied rational design and random mutagenesis to the monomeric red fluorescent protein FusionRed and found two groups of mutants carrying tryptophan-based chromophore: with yellow (535 nm) or orange (565 nm) emission. On the basis of the properties of proteins, a model synthetic chromophore, and a computational modelling we concluded that the presence of a ketone-containing chromophore in different isomeric forms can explain the observed yellow and orange phenotypes...
May 19, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28523350/comparison-of-a-radiomic-biomarker-with-volumetric-analysis-for-decoding-tumour-phenotypes-of-lung-adenocarcinoma-with-different-disease-specific-survival
#14
Mei Yuan, Yu-Dong Zhang, Xue-Hui Pu, Yan Zhong, Hai Li, Jiang-Fen Wu, Tong-Fu Yu
OBJECTIVES: To compare a multi-feature-based radiomic biomarker with volumetric analysis in discriminating lung adenocarcinomas with different disease-specific survival on computed tomography (CT) scans. METHODS: This retrospective study obtained institutional review board approval and was Health Insurance Portability and Accountability Act (HIPAA) compliant. Pathologically confirmed lung adenocarcinoma (n = 431) manifested as subsolid nodules on CT were identified...
May 18, 2017: European Radiology
https://www.readbyqxmd.com/read/28521083/inflammatory-infiltrate-and-mucosal-remodeling-in-chronic-rhinosinusitis-with-and-without-polyps-structured-histopathologic-analysis
#15
Hannah N Kuhar, Bobby A Tajudeen, Mahboobeh Mahdavinia, Paolo Gattuso, Ritu Ghai, Pete S Batra
BACKGROUND: Chronic rhinosinusitis (CRS) is commonly classified into CRS with nasal polyps (CRSwNP) and CRS without nasal polyps (CRSsNP). Structured histopathologic reporting has the potential to identify salient histologic markers to differentiate subtypes and provide insights into pathophysiologic mechanisms in CRS. METHODS: A structured histopathology report of 13 variables was prospectively employed to analyze ethmoid sinus tissue removed during endoscopic sinus surgery for 99 patients, including 43 CRSsNP and 56 CRSwNP...
May 18, 2017: International Forum of Allergy & Rhinology
https://www.readbyqxmd.com/read/28520848/pattern-fusion-analysis-by-adaptive-alignment-of-multiple-heterogeneous-omics-data
#16
Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng, Juan Liu, Luonan Chen
Motivation: Integrating different omics profiles is a challenging task, which provides a comprehensive way to understand complex diseases in a multi-view manner. One key for such an integration is to extract intrinsic patterns in concordance with data structures, so as to discover consistent information across various data types even with noise pollution. Thus, we proposed a novel framework called "pattern fusion analysis" (PFA), which performs automated information alignment and bias correction, to fuse local sample-patterns (e...
May 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28513203/automating-the-incremental-evolution-of-controllers-for-physical-robots
#17
Andrés Faíña, Lars Toft Jacobsen, Sebastian Risi
Evolutionary robotics is challenged with some key problems that must be solved, or at least mitigated extensively, before it can fulfill some of its promises to deliver highly autonomous and adaptive robots. The reality gap and the ability to transfer phenotypes from simulation to reality constitute one such problem. Another lies in the embodiment of the evolutionary processes, which links to the first, but focuses on how evolution can act on real agents and occur independently from simulation, that is, going from being, as Eiben, Kernbach, & Haasdijk [2012, p...
May 17, 2017: Artificial Life
https://www.readbyqxmd.com/read/28511181/1-cmdb-a-curated-database-of-genomic-variations-of-the-one-carbon-metabolism-pathway
#18
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...
May 17, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28508489/prediction-of-whole-genome-risk-for-selection-and-management-of-hyperketonemia-in-holstein-dairy-cattle
#19
K A Weigel, R S Pralle, H Adams, K Cho, C Do, H M White
Hyperketonemia (HYK), a common early postpartum health disorder characterized by elevated blood concentrations of β-hydroxybutyrate (BHB), affects millions of dairy cows worldwide and leads to significant economic losses and animal welfare concerns. In this study, blood concentrations of BHB were assessed for 1,453 Holstein cows using electronic handheld meters at four time points between 5 and 18 days postpartum. Incidence rates of subclinical (1.2 ≤ maximum BHB ≤ 2.9 mmol/L) and clinical ketosis (maximum BHB ≥ 3...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508486/pedigree-based-estimation-of-covariance-between-dominance-deviations-and-additive-genetic-effects-in-closed-rabbit-lines-considering-inbreeding-and-using-a-computationally-simpler-equivalent-model
#20
E N Fernández, A Legarra, R Martínez, J P Sánchez, M Baselga
Inbreeding generates covariances between additive and dominance effects (breeding values and dominance deviations). In this work, we developed and applied models for estimation of dominance and additive genetic variances and their covariance, a model that we call "full dominance," from pedigree and phenotypic data. Estimates with this model such as presented here are very scarce both in livestock and in wild genetics. First, we estimated pedigree-based condensed probabilities of identity using recursion. Second, we developed an equivalent linear model in which variance components can be estimated using closed-form algorithms such as REML or Gibbs sampling and existing software...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
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