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https://www.readbyqxmd.com/read/27933738/exploratory-analysis-of-textual-data-from-the-mother-and-child-handbook-using-a-text-mining-method-ii-monthly-changes-in-the-words-recorded-by-mothers
#1
Miki Tagawa, Yoshio Matsuda, Tomoko Manaka, Makiko Kobayashi, Michitaka Ohwada, Shigeki Matsubara
AIM: The aim of the study was to examine the possibility of converting subjective textual data written in the free column space of the Mother and Child Handbook (MCH) into objective information using text mining and to compare any monthly changes in the words written by the mothers. METHODS: Pregnant women without complications (n = 60) were divided into two groups according to State-Trait Anxiety Inventory grade: low trait anxiety (group I, n = 39) and high trait anxiety (group II, n = 21)...
December 9, 2016: Journal of Obstetrics and Gynaecology Research
https://www.readbyqxmd.com/read/27933671/causal-inference-in-obesity-research
#2
REVIEW
P W Franks, N Atabaki-Pasdar
Obesity is a risk factor for a plethora of severe morbidities and premature death. Most supporting evidence comes from observational studies that are prone to chance, bias and confounding. Even data on the protective effects of weight loss from randomized controlled trials will be susceptible to confounding and bias if treatment assignment cannot be masked, which is usually the case with lifestyle and surgical interventions. Thus, whilst obesity is widely considered the major modifiable risk factor for many chronic diseases, its causes and consequences are often difficult to determine...
December 8, 2016: Journal of Internal Medicine
https://www.readbyqxmd.com/read/27933649/using-chiral-peptide-substitutions-to-probe-the-structure-function-relationship-of-a-key-residue-of-a%C3%AE-42
#3
Christopher J A Warner, Subrata Dutta, Alejandro R Foley, Eefei Chen, David S Kliger, Jevgenij A Raskatov
Amyloid beta-protein 42 plays an important role in the onset and progression of Alzheimer's disease. Familial mutations have identified the glutamate residue 22 as a hotspot with regard to peptide neurotoxicity. We introduce an approach to study the influence of systematic sidechain modification at this residue, employing chirality as a structural probe. Circular dichroism experiments reveal that charge-preserving alterations of the amino acid sidechain attenuate the characteristic random coil to β-sheet transition associated with the wildtype peptide...
December 8, 2016: Chirality
https://www.readbyqxmd.com/read/27933557/atypical-presentation-and-treatment-response-in-a-child-with-familial-hypercholesterolemia-having-a-novel-ldlr-mutation
#4
S Varma, A D McIntyre, R A Hegele
Familial hypercholesterolemia (FH) is an autosomal codominantly inherited disease. The severity of clinical presentation depends on the zygosity of the mutations in the LDLR, APOB, or PCSK9 genes. The homozygous form (HoFH) is associated with high mortality rate by third decade of life, while individuals with HeFH begin to suffer from premature cardiovascular disease in fourth or fifth decade of life. Statin drugs have helped to improve the biochemical profile and life expectancy in HeFH, while they are only minimally effective in HoFH...
December 9, 2016: JIMD Reports
https://www.readbyqxmd.com/read/27933544/dissection-of-host-susceptibility-to-bacterial-infections-and-its-toxins
#5
Aysar Nashef, Mahmoud Agbaria, Ariel Shusterman, Nicola Ivan Lorè, Alessandra Bragonzi, Ervin Wiess, Yael Houri-Haddad, Fuad A Iraqi
Infection is one of the leading causes of human mortality and morbidity. Exposure to microbial agents is obviously required. However, also non-microbial environmental and host factors play a key role in the onset, development and outcome of infectious disease, resulting in large of clinical variability between individuals in a population infected with the same microbe. Controlled and standardized investigations of the genetics of susceptibility to infectious disease are almost impossible to perform in humans whereas mouse models allow application of powerful genomic techniques to identify and validate causative genes underlying human diseases with complex etiologies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933543/integrative-analysis-of-genetic-genomic-and-phenotypic-data-for-ethanol-behaviors-a-network-based-pipeline-for-identifying-mechanisms-and-potential-drug-targets
#6
James W Bogenpohl, Kristin M Mignogna, Maren L Smith, Michael F Miles
Complex behavioral traits, such as alcohol abuse, are caused by an interplay of genetic and environmental factors, producing deleterious functional adaptations in the central nervous system. The long-term behavioral consequences of such changes are of substantial cost to both the individual and society. Substantial progress has been made in the last two decades in understanding elements of brain mechanisms underlying responses to ethanol in animal models and risk factors for alcohol use disorder (AUD) in humans...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933542/complex-genetics-of-behavior-bxds-in-the-automated-home-cage
#7
Maarten Loos, Matthijs Verhage, Sabine Spijker, August B Smit
This chapter describes a use case for the genetic dissection and automated analysis of complex behavioral traits using the genetically diverse panel of BXD mouse recombinant inbred strains. Strains of the BXD resource differ widely in terms of gene and protein expression in the brain, as well as in their behavioral repertoire. A large mouse resource opens the possibility for gene finding studies underlying distinct behavioral phenotypes, however, such a resource poses a challenge in behavioral phenotyping. To address the specifics of large-scale screening we describe how to investigate: (1) how to assess mouse behavior systematically in addressing a large genetic cohort, (2) how to dissect automation-derived longitudinal mouse behavior into quantitative parameters, and (3) how to map these quantitative traits to the genome, deriving loci underlying aspects of behavior...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933541/social-interactions-and-indirect-genetic-effects-on-complex-juvenile-and-adult-traits
#8
David G Ashbrook, Reinmar Hager
Most animal species are social in one form or another, yet many studies in rodent model systems use either individually housed animals or ignore potential confounds caused by group housing. While such social interaction effects on developmental and behavioral traits are well established, the genetic basis of social interactions has not been researched in as much detail. Specifically, the effects of genetic variation in social partners on the phenotype of a focal individual have mostly been studied at the phenotypic level...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933540/systems-genetics-of-obesity
#9
Gudrun A Brockmann, Danny Arends, Sebastian Heise, Ayca Dogan
Obesity is a complex trait, determined by many genes and influenced by environmental factors. Mapping genomic loci contributing to obesity helps to identify gene variants responsible for differences in the phenotype. However, measuring fat content alone is often not sufficient to identify the underlying gene or genes. Besides in-depth phenotyping, well-designed genetic populations and the combined analysis of data of different origins are necessary to detect one of several genetic determinants. Structured mouse populations and linking information from different experiments help to simplify the complexity in the search for direct genetic effects or factors that are hidden in the genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933538/systems-genetics-of-liver-fibrosis
#10
Rabea A Hall, Frank Lammert
This systems genetics analysis comprises quantitative measurements of hepatic fibrogenesis in mouse models and mapping of quantitative traits in mouse genetic reference populations. It is part of a large mapping project of fibrogenic genes including the analyses of experimental crosses from different inbred mouse strains. Extensive quantitative trait loci (QTL) mapping of fibrosis phenotypes and liver expression profiling in combination with in silico mapping facilitated the identification of QTL regions and underlying candidate genes that confer fibrosis susceptibility also in humans...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933537/complex-genetics-of-cardiovascular-traits-in-mice-f2-mapping-of-qtls-and-their-underlying-genes
#11
Svitlana Podliesna, Connie R Bezzina, Elisabeth M Lodder
In this chapter, we will use the example of the identification of Tnni3k as a modulator of cardiac conduction to introduce you to the use of a murine F2-generation intercross as a powerful method for the identification of novel genes relevant for cardiovascular traits. Murine F2-progeny is a genetically diverse panel of mice with differences in phenotype manifestations, e.g. cardiovascular traits such as cardiomyopathy and ECG parameters. This chapter discusses the best strategies for using F2-mice for genetic mapping...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933536/genetic-dissection-of-variation-in-hippocampal-intra-and-infrapyramidal-mossy-fibers-in-the-mouse
#12
Anna Delprato, Wim E Crusio
This chapter describes the genetic analysis of a morphometric neuroanatomic trait. We used the extended BXD family of recombinant inbred mouse strains with the intent to analyze the genetic bases of heritable differences in hippocampal neurocircuitry and to identify Quantitative Trait Loci that underlie these variations. A detailed description of a GeneNetwork analysis is provided using data for the intra- and infrapyramidal mossy fiber (IIPMF) terminal fields which are strongly correlated with spatial navigation/radial maze learning...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933534/genomic-control-of-retinal-cell-number-challenges-protocol-and-results
#13
Patrick W Keeley, Irene E Whitney, Benjamin E Reese
This chapter considers some of the challenges in obtaining accurate and consistent estimates of neuronal population size in the mouse retina, in order to identify the genetic control of cell number through QTL mapping and candidate gene analysis. We first discuss a variety of best practices for analyzing large numbers of recombinant inbred strains of mice over the course of a year in order to amass a satisfactory dataset for QTL mapping. We then consider the relative merits of using average cell density versus estimated total cell number as the target trait to be assessed, and why estimates of heritability may differ for these two traits when studying the retina in whole-mount preparations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933533/systems-genetics-as-a-tool-to-identify-master-genetic-regulators-in-complex-disease
#14
Aida Moreno-Moral, Francesco Pesce, Jacques Behmoaras, Enrico Petretto
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933531/using-baseline-transcriptional-connectomes-in-rat-to-identify-genetic-pathways-associated-with-predisposition-to-complex-traits
#15
Laura Saba, Paula Hoffman, Boris Tabakoff
Although rat is a critical model organism in preclinical medications development, its use in systems genetics studies remains sparse. The PhenoGen database and website contain detailed information on the qualitative and quantitative aspects of the rat brain, liver, heart, and brown adipose transcriptome. This database has been generated using the HXB/BXH recombinant inbred panel and is being expanded to a hybrid rat diversity panel that includes many common inbred strains as well. By using such a panel, the PhenoGen project has created a renewable and cumulative resource for the rat genomics community...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933529/qtl-mapping-and-identification-of-candidate-genes-in-do-mice-a-use-case-model-derived-from-a-benzene-toxicity-experiment
#16
Dan Gatti, John E French, Klaus Schughart
Diversity Outbred (DO) mice are a multiparental advanced generation intercross population derived from eight inbred strains which are genetically very diverse. They are maintained as an outbred population using a randomized mating design. Thus DO mice represent an ideal population to map phenotypic traits. Here, we provide a case study in which male DO mice were exposed to benzene and phenotyped for the number of micronucleated reticulocytes. We provide step-by-step R scripts for the analysis of phenotypes, genotypes, mapping of resistance gene loci and identification of candidate genes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933527/integrating-multidimensional-data-sources-to-identify-genes-regulating-complex-phenotypes
#17
Rupert W Overall
Phenotypes collected with a view to quantitative trait locus mapping can be augmented with compatible whole-transcriptome expression data and information from several other sources. These different data sources can be assembled into multidimensional network models which allow the identification of key genes potentially driving the phenotype of interest. The following chapter describes this approach using an example workflow. Several alternatives and potential limitations are discussed to aid the researcher when applying these techniques to their own work...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933526/epigenetics-and-control-of-rnas
#18
Henrike Maatz, Sebastiaan van Heesch, Franziska Kreuchwig, Allison Faber, Eleonora Adami, Norbert Hubner, Matthias Heinig
Histone modifications are epigenetic marks that fundamentally impact the regulation of gene expression. Integrating histone modification information in the analysis of gene expression traits (eQTL mapping) has been shown to significantly enhance the prediction of eQTLs. In this chapter, we describe (1) how to perform quantitative trait locus (QTL) analysis using histone modification levels as traits and (2) how to integrate these data with information on RNA expression for the elucidation of the epigenetic control of transcript levels...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933525/expression-qtls-mapping-and-analysis-a-bayesian-perspective
#19
Martha Imprialou, Enrico Petretto, Leonardo Bottolo
The aim of expression Quantitative Trait Locus (eQTL) mapping is the identification of DNA sequence variants that explain variation in gene expression. Given the recent yield of trait-associated genetic variants identified by large-scale genome-wide association analyses (GWAS), eQTL mapping has become a useful tool to understand the functional context where these variants operate and eventually narrow down functional gene targets for disease. Despite its extensive application to complex (polygenic) traits and disease, the majority of eQTL studies still rely on univariate data modeling strategies, i...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933523/integrative-functional-genomics-for-systems-genetics-in-geneweaver-org
#20
Jason A Bubier, Michael A Langston, Erich J Baker, Elissa J Chesler
The abundance of existing functional genomics studies permits an integrative approach to interpreting and resolving the results of diverse systems genetics studies. However, a major challenge lies in assembling and harmonizing heterogeneous data sets across species for facile comparison to the positional candidate genes and coexpression networks that come from systems genetic studies. GeneWeaver is an online database and suite of tools at www.geneweaver.org that allows for fast aggregation and analysis of gene set-centric data...
2017: Methods in Molecular Biology
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