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Hidden populations

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https://www.readbyqxmd.com/read/28224497/hidden-markov-models-in-population-genomics
#1
Julien Y Dutheil
With the advent of sequencing techniques population genomics took a major shift. The structure of data sets has evolved from a sample of a few loci in the genome, sequenced in dozens of individuals, to collections of complete genomes, virtually comprising all available loci. Initially sequenced in a few individuals, such genomic data sets are now reaching and even exceeding the size of traditional data sets in the number of haplotypes sequenced. Because all loci in a genome are not independent, this evolution of data sets is mirrored by a methodological change...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28209289/depression-among-current-former-and-never-smokers-from-2005-to-2013-the-hidden-role-of-disparities-in-depression-in-the-ongoing-tobacco-epidemic
#2
Renee D Goodwin, Melanie M Wall, Lorra Garey, Michael J Zvolensky, Lisa Dierker, Sandro Galea, Misato Gbedemah, Andrea H Weinberger, Jill M Williams, Mei-Chen Hu, Deborah S Hasin
BACKGROUND: After declining sharply for many years, the prevalence of smoking has remained fairly stable over the past decade. One possible explanation is that there has been an increase in the prevalence of barriers to cessation, like depression, among remaining smokers. OBJECTIVES: To estimate changes in the prevalence of depression among current, former and never smokers in the United States (U.S.) population from 2005 to 2013 overall and by age, gender, and income...
January 11, 2017: Drug and Alcohol Dependence
https://www.readbyqxmd.com/read/28202089/suicidal-ideation-and-behaviour-among-community-and-health-care-seeking-populations-in-five-low-and-middle-income-countries-a-cross-sectional-study
#3
M Jordans, S Rathod, A Fekadu, G Medhin, F Kigozi, B Kohrt, N Luitel, I Petersen, R Shidhaye, J Ssebunnya, V Patel, C Lund
: Aims Suicidal behaviour is an under-reported and hidden cause of death in most low- and middle-income countries (LMIC) due to lack of national systematic reporting for cause-specific mortality, high levels of stigma and religious or cultural sanctions. The lack of information on non-fatal suicidal behaviour (ideation, plans and attempts) in LMIC is a major barrier to design and implementation of prevention strategies. This study aims to determine the prevalence of non-fatal suicidal behaviour within community- and health facility-based populations in LMIC...
February 16, 2017: Epidemiology and Psychiatric Sciences
https://www.readbyqxmd.com/read/28187874/falling-while-walking-a-hidden-contributor-to-pedestrian-injury
#4
Jennifer Oxley, Steve O'Hern, Duane Burtt, Ben Rossiter
Walking is a sustainable mode of transportation which is beneficial to both individuals and to the broader community, however, there are risks and it is essential that road design and operation provides safe conditions for walking. In Victoria, pedestrians represent one of the most vulnerable road user groups, accounting for approximately 12% of all road fatalities and serious injuries. These figures largely represent injuries where the pedestrian has been struck by a vehicle with the extent of pedestrian-only injuries largely un-reported...
February 7, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28187641/cryptic-within-cryptic-genetics-morphometrics-and-bioacoustics-delimitate%C3%A2-a-new-species-of-i-eleutherodactylus-i-anura-eleutherodactylidae-from-eastern-cuba
#5
Ariel Rodríguez, Álvaro Dugo-Cota, Santiago Montero-Mendieta, Alejandro Gonzalez-Voyer, Roberto Alonso Bosch, Miguel Vences, Carles Vilà
We studied the variation in genetics, bioacustics, and morphology in Eleutherodactylus glamyrus, a regionally endemic frog species restricted to high elevations in the Sierra Maestra Massif, Western Cuba that was originally described as a cryptic species hidden under the name E. auriculatus. Genetic analysis of mtDNA sequences of the 16S and cob genes identify two allopatric and strongly supported mitochondrial clades (phylogroups) which also showed no haplotype sharing in the nuclear Rag-1 gene. Bioacustic, and morphological comparisons concordantly identify these two phylogroups as independent evolutionary lineages...
January 20, 2017: Zootaxa
https://www.readbyqxmd.com/read/28176959/a-systematic-literature-review-on-the-efficacy-effectiveness-gap-comparison-of-randomized-controlled-trials-and-observational-studies-of-glucose-lowering-drugs
#6
REVIEW
Mikkel Z Ankarfeldt, Erpur Adalsteinsson, Rolf Hh Groenwold, M Sanni Ali, Olaf H Klungel
AIM: To identify a potential efficacy-effectiveness gap and possible explanations (drivers of effectiveness) for differences between results of randomized controlled trials (RCTs) and observational studies investigating glucose-lowering drugs. METHODS: A systematic literature review was conducted in English language articles published between 1 January, 2000 and 31 January, 2015 describing either RCTs or observational studies comparing glucagon-like peptide-1 analogs (GLP-1) with insulin or comparing dipeptidyl peptidase-4 inhibitors (DPP-4i) with sulfonylurea, all with change in glycated hemoglobin (HbA1c) as outcome...
2017: Clinical Epidemiology
https://www.readbyqxmd.com/read/28176929/onset-of-mortality-increase-with-age-and-age-trajectories-of-mortality-from-all-diseases-in-the-four-nordic-countries
#7
Josef Dolejs, Petra Marešová
BACKGROUND: The answer to the question "At what age does aging begin?" is tightly related to the question "Where is the onset of mortality increase with age?" Age affects mortality rates from all diseases differently than it affects mortality rates from nonbiological causes. Mortality increase with age in adult populations has been modeled by many authors, and little attention has been given to mortality decrease with age after birth. MATERIALS AND METHODS: Nonbiological causes are excluded, and the category "all diseases" is studied...
2017: Clinical Interventions in Aging
https://www.readbyqxmd.com/read/28166813/hidden-reservoir-of-resistant-parasites-the-missing-link-in-the-elimination-of-falciparum-malaria
#8
Rashad Abdul-Ghani, Mohammed A K Mahdy, John C Beier, Leonardo K Basco
BACKGROUND: To successfully eliminate malaria, an integrated system that includes a number of approaches and interventions-aimed at overcoming the threat of antimalarial drug resistance-is required. Significant progress has been made in reducing malaria incidence through large-scale use of artemisinin-based combination therapies and insecticide-treated nets. To consolidate these gains, attention should be paid to the missing links in the elimination of malaria. One of these gaps is the residual reservoir of submicroscopic resistant parasites, which remains after case management or other control measures have been carried out...
February 6, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/28162786/base-excess-a-useful-marker-in-the-prognosis-of-chest-trauma-in-the-geriatric-population
#9
Y Peñasco, A González-Castro, J C Rodríguez-Borregán, J Llorca
OBJECTIVE: To determine the usefulness of the determination of base excess in a cohort of elderly patients admitted to an intensive care unit (ICU) with a diagnosis of chest trauma. MATERIAL AND METHOD: Two hundred and forty-nine patients were included aged 65 years and over with a diagnosis of thoracic trauma who required admission to the ICU. We made a statistical analysis in order to determine the association of the first base excess levels with mortality during the unit stay...
February 2, 2017: Revista Española de Anestesiología y Reanimación
https://www.readbyqxmd.com/read/28161495/should-the-presence-of-metastatic-para-aortic-lymph-nodes-in-locally-advanced-cervical-cancer-lead-to-more-aggressive-treatment-strategies
#10
Virginia Benito, Sonia Carballo, Patricia Silva, Miriam Esparza, Octavio Arencibia, Mario Federico, Miguel Andújar, Marta Mori, Norberto Medina, Amina Lubrano
OBJECTIVE: To evaluate risk factors in patients with locally advanced cervical cancer (LACC) undergoing pretherapeutic laparoscopic paraaortic lymphadenectomy (LPL), as well as the progression-free and overall survival rates specifically in the subgroup of patients with metastatic paraaortic lymph nodes (PLN). DESIGN: Retrospective study conducted on demographic data, pathological and surgical findings, complications and disease-status, recorded for LACC patients undergoing LPL during the period 2009-2015...
February 1, 2017: Journal of Minimally Invasive Gynecology
https://www.readbyqxmd.com/read/28157496/revealing-the-hidden-powers-that-fuel-adult-neurogenesis
#11
Weijun Feng, Hai-Kun Liu
A defining characteristic of diverse stem cell populations is their distinct metabolic state, although how these states change during adult hippocampal neurogenesis is unclear. Recently in Neuron, Beckervordersandforth et al. (2017) report that adult neurogenesis requires mitochondrial electron transport and oxidative phosphorylation and that disrupting these pathways induces premature aging phenotypes.
February 2, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28155657/a-machine-learning-approach-for-the-identification-of-key-markers-involved-in-brain-development-from-single-cell-transcriptomic-data
#12
Yongli Hu, Takeshi Hase, Hui Peng Li, Shyam Prabhakar, Hiroaki Kitano, See Kiong Ng, Samik Ghosh, Lawrence Jin Kiat Wee
BACKGROUND: The ability to sequence the transcriptomes of single cells using single-cell RNA-seq sequencing technologies presents a shift in the scientific paradigm where scientists, now, are able to concurrently investigate the complex biology of a heterogeneous population of cells, one at a time. However, till date, there has not been a suitable computational methodology for the analysis of such intricate deluge of data, in particular techniques which will aid the identification of the unique transcriptomic profiles difference between the different cellular subtypes...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28139544/a-single-weighting-approach-to-analyze-respondent-driven-sampling-data
#13
Vadivoo Selvaraj, Kangusamy Boopathi, Ramesh Paranjape, Sanjay Mehendale
BACKGROUND AND OBJECTIVES: Respondent-driven sampling (RDS) is widely used to sample hidden populations and RDS data are analyzed using specially designed RDS analysis tool (RDSAT). RDSAT estimates parameters such as proportions. Analysis with RDSAT requires separate weight assignment for individual variables even in a single individual; hence, regression analysis is a problem. RDS-analyst is another advanced software that can perform three methods of estimates, namely, successive sampling method, RDS I and RDS II...
September 2016: Indian Journal of Medical Research
https://www.readbyqxmd.com/read/28135296/genome-wide-association-of-copy-number-polymorphisms-and-kidney-function
#14
Man Li, Jacob Carey, Stephen Cristiano, Katalin Susztak, Josef Coresh, Eric Boerwinkle, Wen Hong L Kao, Terri H Beaty, Anna Köttgen, Robert B Scharpf
Genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) have identified more than 50 loci associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. However, significant SNPs account for a small proportion of eGFR variability. Other forms of genetic variation have not been comprehensively evaluated for association with eGFR. In this study, we assess whether changes in germline DNA copy number are associated with GFR estimated from serum creatinine, eGFRcrea...
2017: PloS One
https://www.readbyqxmd.com/read/28133644/aggressive-periodontitis-the-unsolved-mystery
#15
Danielle Clark, Maria Febbraio, Liran Levin
Aggressive periodontal disease is an oral health mystery. Our current understanding of this disease is that specific bacteria invade the oral cavity and the host reacts with an inflammatory response leading to mass destruction of the alveolar bone. Aggressive periodontal disease is typically observed in a population under the age of 30 and occurs so rapidly that it is difficult to treat. Unfortunately, the consequence of this disease frequently involves tooth extractions. As a result, the aftermath is chewing disability and damage to self-esteem due to an altered self-image...
2017: Quintessence International
https://www.readbyqxmd.com/read/28127765/hidden-survival-heterogeneity-of-three-common-eider-populations-in-response-to-climate-fluctuations
#16
L Guéry, S Descamps, R Pradel, S A Hanssen, K E Erikstad, G W Gabrielsen, H G Gilchrist, J Bêty
1.Understanding how individuals and populations respond to fluctuations in climatic conditions is critical to explain and anticipate changes in ecological systems. Most such studies focus on climate impacts on single populations without considering inter- and intra-population heterogeneity. However, comparing geographically dispersed populations limits the risk of faulty generalizations and helps to improve ecological and demographic models. 2.We aimed to determine whether differences in migration tactics among and within populations would induce inter- or intra-population heterogeneity in survival in relation to winter climate fluctuations...
January 26, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28126110/a-comparison-of-network-sampling-designs-for-a-hidden-population-of-drug-users-random-walk-vs-respondent-driven-sampling
#17
David C Bell, Elizabeth B Erbaugh, Tabitha Serrano, Cheryl A Dayton-Shotts, Isaac D Montoya
Both random walk and respondent-driven sampling (RDS) exploit social networks and may reduce biases introduced by earlier methods for sampling from hidden populations. Although RDS has become much more widely used by social researchers than random walk (RW), there has been little discussion of the tradeoffs in choosing RDS over RW. This paper compares experiences of implementing RW and RDS to recruit drug users to a network-based study in Houston, Texas. Both recruitment methods were implemented over comparable periods of time, with the same population, by the same research staff...
February 2017: Social Science Research
https://www.readbyqxmd.com/read/28125022/pediatric-exercise-testing-value-and-implications-of-peak-oxygen-uptake
#18
REVIEW
Paolo T Pianosi, Robert I Liem, Robert G McMurray, Frank J Cerny, Bareket Falk, Han C G Kemper
Peak oxygen uptake (peak V ˙ O 2 ) measured by clinical exercise testing is the benchmark for aerobic fitness. Aerobic fitness, estimated from maximal treadmill exercise, is a predictor of mortality in adults. Peak V ˙ O 2 was shown to predict longevity in patients aged 7-35 years with cystic fibrosis over 25 years ago. A surge of exercise studies in young adults with congenital heart disease over the past decade has revealed significant prognostic information. Three years ago, the first clinical trial in children with pulmonary arterial hypertension used peak V ˙ O 2 as an endpoint that likewise delivered clinically relevant data...
January 24, 2017: Children
https://www.readbyqxmd.com/read/28122953/single-step-blup-with-varying-genotyping-effort-in-open-pollinated-picea-glauca
#19
Blaise Ratcliffe, Omnia Gamal El-Dien, Eduardo P Cappa, Ilga Porth, Jaroslav Klapste, Charles Chen, Yousry El-Kassaby
Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters as well as rankings of selection candidates using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities (tree height and wood density) were assessed at various levels of family genotyping efforts (0, 25, 50, 75, 100%) from a population of white spruce (Picea glauca) consisting of 1,694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada...
January 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28118860/genetic-relatedness-analysis-reveals-the-cotransmission-of-genetically-related-plasmodium-falciparum-parasites-in-thi%C3%A3-s-senegal
#20
Wesley Wong, Allison D Griggs, Rachel F Daniels, Stephen F Schaffner, Daouda Ndiaye, Amy K Bei, Awa B Deme, Bronwyn MacInnis, Sarah K Volkman, Daniel L Hartl, Daniel E Neafsey, Dyann F Wirth
BACKGROUND: As public health interventions drive parasite populations to elimination, genetic epidemiology models that incorporate population genomics can be powerful tools for evaluating the effectiveness of continued intervention. However, current genetic epidemiology models may not accurately simulate the population genetic profile of parasite populations, particularly with regard to polygenomic (multi-strain) infections. Current epidemiology models simulate polygenomic infections via superinfection (multiple mosquito bites), despite growing evidence that cotransmission (a single mosquito bite) may contribute to polygenomic infections...
January 24, 2017: Genome Medicine
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