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https://www.readbyqxmd.com/read/28938023/exploration-of-genetic-architecture-through-sib-ship-reconstruction-in-advanced-breeding-population-of-eucalyptus-nitens
#1
Jaroslav Klápště, Mari Suontama, Emily Telfer, Natalie Graham, Charlie Low, Toby Stovold, Russel McKinley, Heidi Dungey
Accurate inference of relatedness between individuals in breeding population contributes to the precision of genetic parameter estimates, effectiveness of inbreeding management and the amount of genetic progress delivered from breeding programs. Pedigree reconstruction has been proven to be an efficient tool to correct pedigree errors and recover hidden relatedness in open pollinated progeny tests but the method can be limited by the lack of parental genotypes and the high proportion of alien pollen from outside the breeding population...
2017: PloS One
https://www.readbyqxmd.com/read/28934591/combining-traditional-mutagenesis-with-new-high-throughput-sequencing-and-genome-editing-to-reveal-hidden-variation-in-polyploid-wheat
#2
Cristobal Uauy, Brande B H Wulff, Jorge Dubcovsky
Induced mutations have been used to generate novel variation for breeding purposes since the early 1900s. However, the combination of this old technology with the new capabilities of high-throughput sequencing has resulted in powerful reverse genetic approaches in polyploid crops. Sequencing genomes or exomes of large mutant populations can generate extensive databases of mutations for most genes. These mutant collections, together with genome editing, are being used in polyploid species to combine mutations in all copies of a gene (homoeologs), and to expose phenotypic variation that was previously hidden by functional redundancy among homoeologs...
September 20, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28928297/malnutrition-free-india-dream-or-reality
#3
C P Mishra
In spite of great efforts done by the Government of India to tackle the problem of malnutrition, proportion of population normal on nutrition scale has been stationary; nearly half of them have been a victim of under- and over-nutrition. Over a period, undernutrition has declined but this has been compensated by overnutrition. Hidden hunger is a still an unfinished agendum. The achievement of food grain security at the national level did not percolate down, and households' food insecurity and level of chronic food insecurity are still high...
July 2017: Indian Journal of Public Health
https://www.readbyqxmd.com/read/28926617/hidden-biodiversity-in-entomological-collections-the-overlooked-co-occurrence-of-dipteran-and-hymenopteran-ant-parasitoids-in-stored-biological-material
#4
Gabriela Pérez-Lachaud, Jean-Paul Lachaud
Biological collections around the world are the repository of biodiversity on Earth; they also hold a large quantity of unsorted, unidentified, or misidentified material and can house behavioral information on species that are difficult to access or no longer available to science. Among the unsorted, alcohol-preserved material stored in the Formicidae Collection of the 'El Colegio de la Frontera Sur' Research Center (Chetumal, Mexico), we found nine colonies of the ponerine ant Neoponera villosa, that had been collected in bromeliads at Calakmul (Campeche, Mexico) in 1999...
2017: PloS One
https://www.readbyqxmd.com/read/28924351/moving-on-from-representativeness-testing-the-utility-of-the-global-drug-survey
#5
Monica J Barratt, Jason A Ferris, Renee Zahnow, Joseph J Palamar, Larissa J Maier, Adam R Winstock
A decline in response rates in traditional household surveys, combined with increased internet coverage and decreased research budgets, has resulted in increased attractiveness of web survey research designs based on purposive and voluntary opt-in sampling strategies. In the study of hidden or stigmatised behaviours, such as cannabis use, web survey methods are increasingly common. However, opt-in web surveys are often heavily criticised due to their lack of sampling frame and unknown representativeness. In this article, we outline the current state of the debate about the relevance of pursuing representativeness, the state of probability sampling methods, and the utility of non-probability, web survey methods especially for accessing hidden or minority populations...
2017: Substance Abuse: Research and Treatment
https://www.readbyqxmd.com/read/28923058/a-model-of-plasmodium-vivax-concealment-based-on-plasmodium-cynomolgi-infections-in-macaca-mulatta
#6
Luis L Fonseca, Chester J Joyner, Mary R Galinski, Eberhard O Voit
BACKGROUND: Plasmodium vivax can cause severe malaria. The total parasite biomass during infections is correlated with the severity of disease but not necessarily quantified accurately by microscopy. This finding has raised the question whether there could be sub-populations of parasites that are not observed in peripheral blood smears but continue to contribute to the increase in parasite numbers that drive pathogenesis. Non-human primate infection models utilizing the closely related simian malaria parasite Plasmodium cynomolgi hold the potential for quantifying the magnitude of possibly unobserved infected red blood cell (iRBC) populations and determining how the presence of this hidden reservoir correlates with disease severity...
September 18, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28920931/single-molecule-fret-reveals-the-energy-landscape-of-the-full-length-sam-i-riboswitch
#7
Christoph Manz, Andrei Yu Kobitski, Ayan Samanta, Bettina G Keller, Andres Jäschke, G Ulrich Nienhaus
S-adenosyl-L-methionine (SAM) ligand binding induces major structural changes in SAM-I riboswitches, through which gene expression is regulated via transcription termination. Little is known about the conformations and motions governing the function of the full-length Bacillus subtilis yitJ SAM-I riboswitch. Therefore, we have explored its conformational energy landscape as a function of Mg(2+) and SAM ligand concentrations using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling analysis...
September 18, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28915487/genetic-backgrounds-and-hidden-trait-complexity-in-natural-populations
#8
REVIEW
Téo Fournier, Joseph Schacherer
Dissecting the genetic basis of natural phenotypic variation is a major goal in biology. We know that most traits are strongly heritable. However, their genetic architecture is a long-standing question, which is unfortunately confounded by the lack of complete knowledge of the genetic components as well as their phenotypic effect in a specific genetic background. Many genetic variants are known to affect phenotypes but the same functional variant can have a different effect on the phenotype in different individuals of the same species...
September 12, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28899390/-if-it-s-a-medical-issue-i-would-have-covered-it-by-now-learning-about-fibromyalgia-through-the-hidden-curriculum-a-qualitative-study
#9
V Silverwood, C A Chew-Graham, I Raybould, B Thomas, S Peters
BACKGROUND: Fibromyalgia syndrome (FMS) is a long-term condition that affects between 1 and 5% of the general population and lies within the spectrum of medically unexplained symptoms (MUS). FMS can be difficult to diagnose and is usually done so as a diagnosis of exclusion. There is continuing debate regarding its legitimacy excluding other causes of symptoms. It is known that the diagnosis and management of MUS, including FMS, receives little attention in medical curricula and attitudes towards patients with FMS amongst medical professionals and trainees can be negative...
September 12, 2017: BMC Medical Education
https://www.readbyqxmd.com/read/28893720/the-case-for-universal-screening-of-private-well-water-quality-in-the-u-s-and-testing-requirements-to-achieve-it-evidence-from-arsenic
#10
Yan Zheng, Sara V Flanagan
BACKGROUND: The 1974 Safe Drinking Water Act (SDWA) regulates >170,000 public water systems to protect health, but not >13 million private wells. State and local government requirements for private well water testing are rare and inconsistent; the responsibility to ensure water safety remains with individual households. Over the last two decades, geogenic arsenic has emerged as a significant public health concern due to high prevalence in many rural American communities. OBJECTIVES: We build the case for universal screening of private well water quality around arsenic, the most toxic and widespread of common private water contaminants...
August 3, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28885182/cataloging-plant-genome-structural-variations
#11
Xingtan Zhang, Xuequn Chen, Pingping Liang, Haibao Tang
Structural variation (SV) is a type of genetic variation identified through the comparison of genome structures which often have direct and significant associations with phenotypic variations. Building on the next generation sequencing (NGS) technologies, research on plant structural variations are gaining momentum and have revolutionized our view on the functional impact of the 'hidden' diversity that were largely understudied before. Herein, we first describe the current state of plant genomic SV research based on NGS and in particular focus on the biological insights gained from the large-scale identification of various types of plant SVs...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28878807/distribution-and-functionality-of-copy-number-variation-across-european-cattle-populations
#12
Maulik Upadhyay, Vinicus H da Silva, Hendrik-Jan Megens, Marleen H P W Visker, Paolo Ajmone-Marsan, Valentin A Bâlteanu, Susana Dunner, Jose F Garcia, Catarina Ginja, Juha Kantanen, Martien A M Groenen, Richard P M A Crooijmans
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28877655/developing-a-strategy-for-interventional-molecular-imaging-of-oxidized-low-density-lipoprotein-in-atherosclerosis
#13
Samata S Pandey, Dorian O Haskard, Ramzi Y Khamis
The identification of vulnerable coronary artery atherosclerotic plaques offers the prospect of either localized or systematic therapeutic targeting in order to prevent myocardial infarction. Molecular imaging of atherosclerosis adds to morphological imaging by focusing on the immunobiology hidden in and behind the endothelium and therefore may be able to improve the identification of prospective culprit lesions. Our focus has been on identifying arterial accumulation of oxidized low-density lipoprotein (oxLDL) by exploiting advances in knowledge of vascular pathobiology...
January 2017: Molecular Imaging
https://www.readbyqxmd.com/read/28873409/fine-scale-mapping-of-genomic-introgressions-within-the-drosophila-yakuba-clade
#14
David A Turissini, Daniel R Matute
The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28862132/the-complex-relationship-of-exposure-to-new-plasmodium-infections-and-incidence-of-clinical-malaria-in-papua-new-guinea
#15
Natalie E Hofmann, Stephan Karl, Rahel Wampfler, Benson Kiniboro, Albina Teliki, Jonah Iga, Andreea Waltmann, Inoni Betuela, Ingrid Felger, Leanne J Robinson, Ivo Mueller
The molecular force of blood-stage infection (molFOB) is a quantitative surrogate metric for malaria transmission at population level and for exposure at individual level. Relationships between molFOB, parasite prevalence and clinical incidence were assessed in a treatment-to-reinfection cohort, where P.vivax (Pv) hypnozoites were eliminated in half the children by primaquine (PQ). Discounting relapses, children acquired equal numbers of new P. falciparum (Pf) and Pv blood-stage infections/year (Pf-molFOB = 0-18, Pv-molFOB = 0-23) resulting in comparable spatial and temporal patterns in incidence and prevalence of infections...
September 1, 2017: ELife
https://www.readbyqxmd.com/read/28861695/pharmacometrics-models-with-hidden-markovian-dynamics
#16
Marc Lavielle
The aim of this paper is to provide an overview of pharmacometric models that involve some latent process with Markovian dynamics. Such models include hidden Markov models which may be useful for describing the dynamics of a disease state that jumps from one state to another at discrete times. On the contrary, diffusion models are continuous-time and continuous-state Markov models that are relevant for modelling non observed phenomena that fluctuate continuously and randomly over time. We show that an extension of these models to mixed effects models is straightforward in a population context...
August 31, 2017: Journal of Pharmacokinetics and Pharmacodynamics
https://www.readbyqxmd.com/read/28857678/somali-american-female-refugees-discuss-their-attitudes-toward-homosexuality-and-the-gay-and-lesbian-community
#17
Shanda L Hunt, Jennifer J Connor, Amanda Ciesinski, Cawo Abdi, Beatrice 'Bean' E Robinson
Minnesota is home to the largest population of Somalis in the USA - most arriving as refugees from the civil war in Somalia. As Somali Americans adjust to life in the USA, they are likely to undergo shifts in their belief systems - including changes in their attitudes toward gays and lesbians. We examined the attitudes of 29 Somali American women in the Minneapolis-St. Paul metropolitan area toward homosexuality via face-to-face, semi-structured interviews. Transcripts were translated, transcribed and analysed using an approach informed by grounded theory...
August 31, 2017: Culture, Health & Sexuality
https://www.readbyqxmd.com/read/28845485/emphysema-quantification-on-cardiac-ct-scans-using-hidden-markov-measure-field-model-the-mesa-lung-study
#18
Jie Yang, Elsa D Angelini, Pallavi P Balte, Eric A Hoffman, Colin O Wu, Bharath A Venkatesh, R Graham Barr, Andrew F Laine
Cardiac computed tomography (CT) scans include approximately 2/3 of the lung and can be obtained with low radiation exposure. Large cohorts of population-based research studies reported high correlations of emphysema quantification between full-lung (FL) and cardiac CT scans, using thresholding-based measurements. This work extends a hidden Markov measure field (HMMF) model-based segmentation method for automated emphysema quantification on cardiac CT scans. We show that the HMMF-based method, when compared with several types of thresholding, provides more reproducible emphysema segmentation on repeated cardiac scans, and more consistent measurements between longitudinal cardiac and FL scans from a diverse pool of scanner types and thousands of subjects with ten thousands of scans...
October 2016: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/28832587/social-venue-range-and-referral-chain-impact-implications-for-the-sampling-of-hidden-communities
#19
Benjamin Cornwell, John A Schneider
BACKGROUND: It has been argued that the success of respondent-driven sampling (RDS) in generating unbiased estimates for epidemiologic outcomes depends on participants' abilities to generate long referral chains. While this is thought to depend on the number of people participants know in the target population, this idea is rarely tested. Furthermore, little attention has been paid to the role of other aspects of social connectedness in recruitment, such as participants' involvement in local clubs and venues...
2017: PloS One
https://www.readbyqxmd.com/read/28829634/estimation-of-individual-growth-trajectories-when-repeated-measures-are-missing
#20
Mollie E Brooks, Christopher Clements, Josephine Pemberton, Arpat Ozgul
Individuals in a population vary in their growth due to hidden and observed factors such as age, genetics, environment, disease, and carryover effects from past environments. Because size affects fitness, growth trajectories scale up to affect population dynamics. However, it can be difficult to estimate growth in data from wild populations with missing observations and observation error. Previous work has shown that linear mixed models (LMMs) underestimate hidden individual heterogeneity when more than 25% of repeated measures are missing...
September 2017: American Naturalist
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