1,514 results match your criteria coverage linkage


An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome.

Mol Ecol Resour 2021 May 6. Epub 2021 May 6.

Genomics Aotearoa.

We used long read sequencing data generated from Knightia excelsa, a nectar producing Proteaceae tree endemic to Aotearoa (New Zealand), to explore how sequencing data type, volume and workflows can impact final assembly accuracy and chromosome reconstruction. Establishing a high-quality genome for this species has specific cultural importance to Māori and commercial importance to honey producers in Aotearoa. Assemblies were produced by five long read assemblers using data subsampled based on read lengths, two polishing strategies, and two Hi-C mapping methods. Read More

View Article and Full-Text PDF

Two Synthetic 18-Way Outcrossed Populations of Diploid Budding Yeast with Utility for Complex Trait Dissection.

Genetics 2020 Jun;215(2):323-342

Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine, California 92697-2525.

Advanced-generation multiparent populations (MPPs) are a valuable tool for dissecting complex traits, having more power than genome-wide association studies to detect rare variants and higher resolution than F2 linkage mapping. To extend the advantages of MPPs in budding yeast, we describe the creation and characterization of two outbred MPPs derived from 18 genetically diverse founding strains. We carried out de novo assemblies of the genomes of the 18 founder strains, such that virtually all variation segregating between these strains is known, and represented those assemblies as Santa Cruz Genome Browser tracks. Read More

View Article and Full-Text PDF

Contemporary N estimation using temporally-spaced data with linked loci.

Mol Ecol Resour 2021 May 5. Epub 2021 May 5.

Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, United Kingdom.

The contemporary effective population size N is important in many disciplines including population genetics, conservation science and pest management. One of the most popular methods of estimating this quantity uses temporal changes in allele frequency due to genetic drift. A significant assumption of the existing methods is the independence among loci while constructing confidence intervals (C. Read More

View Article and Full-Text PDF

Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of a fruit species.

Hortic Res 2020 May 1;7(1):60. Epub 2020 May 1.

Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Thermi, Thessaloniki, 570001, Greece.

Sweet cherries, Prunus avium L. (Rosaceae), are gaining importance due to their perenniallity and nutritional attributes beneficial for human health. Interestingly, sweet cherry cultivars exhibit a wide range of phenotypic diversity in important agronomic traits, such as flowering time and defense reactions against pathogens. Read More

View Article and Full-Text PDF

COVID-19 vaccine coverage in health-care workers in England and effectiveness of BNT162b2 mRNA vaccine against infection (SIREN): a prospective, multicentre, cohort study.

Lancet 2021 Apr 23. Epub 2021 Apr 23.

Public Health England Colindale, London, UK; The National Institute for Health Research Health Protection Research (NIHR) Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK. Electronic address:

Background: BNT162b2 mRNA and ChAdOx1 nCOV-19 adenoviral vector vaccines have been rapidly rolled out in the UK from December, 2020. We aimed to determine the factors associated with vaccine coverage for both vaccines and documented the vaccine effectiveness of the BNT162b2 mRNA vaccine in a cohort of health-care workers undergoing regular asymptomatic testing.

Methods: The SIREN study is a prospective cohort study among staff (aged ≥18 years) working in publicly-funded hospitals in the UK. Read More

View Article and Full-Text PDF

What gaps remain in the HIV cascade of care? Results of a population-based survey in Nsanje District, Malawi.

PLoS One 2021 22;16(4):e0248410. Epub 2021 Apr 22.

Epicentre, Paris, France.

Introduction: The Malawi Ministry of Health (MoH) has been in collaboration with Médecins sans Frontières (MSF) to increase access to quality HIV care through decentralization of antiretroviral therapy (ART) diagnosis and treatment from hospital to clinics in Nsanje District since 2011. A population-based household survey was implemented to provide information on HIV prevalence and cascade of care to inform and prioritize community-based HIV interventions in the district.

Methods: A cross-sectional survey was conducted between September 2016 and January 2017. Read More

View Article and Full-Text PDF

Finding, treating and retaining persons with HIV in a high HIV prevalence and high treatment coverage country: Results from the Botswana Combination Prevention Project.

PLoS One 2021 21;16(4):e0250211. Epub 2021 Apr 21.

Division of Global HIV/AIDS, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.

Introduction: The scale-up of Universal Test and Treat has resulted in reductions in HIV morbidity, mortality and incidence. However, healthcare system and personal challenges have impacted the levels of treatment coverage achieved. We implemented interventions to improve linkage to care, retention, viral load (VL) coverage and service delivery, and describe the HIV care cascade over the course of the Botswana Combination Prevention Project (BCPP) study. Read More

View Article and Full-Text PDF

Quality of children's death records for regionalized spaces: a methodological route.

Rev Bras Epidemiol 2021 9;24:e210016. Epub 2021 Apr 9.

Postgraduate Program in Decision and Health Models, Universidade Federal da Paraíba - João Pessoa (PB), Brazil.

Objectives: To propose a methodological path to investigate the coverage and information filling of maternal-infant deaths recorded in the Ministry of Health's Mortality Information System for regional spaces.

Methods: Four steps were proposed: 1) Assessment of the completeness of the maternal and child variables, which was measured using the deterministic linkage technique between the Mortality Information System (Sistema de Informações sobre Mortalidade - SIM) and the Live Birth Information System (Sistema de Informações sobre Nascidos Vivos - SINASC); 2) Application of the multiple imputation technique to achieve the total filling of the missing information of the variables; 3) Estimation of death coverage; 4) The Unknown Variable Information Index (Índice de Informação Desconhecida da Variável - IIDV) was measured, which represents the combined effect of data completeness and coverage of deaths. The proposal of the methodological path was exemplified for neonatal deaths in the municipalities of Paraíba that are part of the new classification proposed by the Brazilian Institute of Geography and Statistics (Instituto Brasileiro de Geografia e Estatística - IBGE), as adjacent rural areas, in three triennium periods from 2009 to 2017. Read More

View Article and Full-Text PDF

Using linked administrative health data for palliative and end of life care research in Ireland: potential and challenges.

HRB Open Res 2021 9;4:17. Epub 2021 Feb 9.

School of Medicine, University of Limerick, Limerick, V94 T9PX, Ireland.

: This study aims to examine the potential of currently available administrative health data for palliative and end-of-life care (PEoLC) research in Ireland. Objectives include to i) identify administrative health data sources for PEoLC research ii) describe the challenges and opportunities of using these and iii) estimate  the impact of recent health system reforms and changes to data protection laws. : The 2017 Health Information and Quality Authority catalogue of health and social care datasets was cross-referenced with a recognised list of diseases with associated palliative care needs. Read More

View Article and Full-Text PDF
February 2021

Fine-scale population structure in five rural populations from the Spanish Eastern Pyrenees using high-coverage whole-genome sequence data.

Eur J Hum Genet 2021 Apr 9. Epub 2021 Apr 9.

CNAG-CRG, Centre for Genomic Regulation, C/ Baldiri i Reixach 4, 08028, Barcelona, Spain.

The area of the Spanish Pyrenees is particularly interesting for studying the demographic dynamics of European rural areas given its orography, the main traditional rural condition of its population and the reported higher patterns of consanguinity of the region. Previous genetic studies suggest a gradient of genetic continuity of the area in the West to East axis. However, it has been shown that micro-population substructure can be detected when considering high-quality NGS data and using spatial explicit methods. Read More

View Article and Full-Text PDF

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts.

PLoS Pathog 2021 04 7;17(4):e1009499. Epub 2021 Apr 7.

Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.

Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. Read More

View Article and Full-Text PDF

Interest in Sexually Transmitted Infections: Analysis of Web Search Data Terms in Eleven Large German Cities from 2015 to 2019.

Int J Environ Res Public Health 2021 03 9;18(5). Epub 2021 Mar 9.

Department of Dermatology and Allergy, School of Medicine, Technical University of Munich, 80802 Munich, Germany.

Incidence of sexually transmitted infections (STIs) such as chlamydia, gonorrhea, and syphilis has increased in recent years in the US and in European countries. In order to implement effective educational programs, the interests of target populations have to be identified. Since the internet is an important source of information-gathering on health issues, this study investigates web search data in large German cities related to STIs. Read More

View Article and Full-Text PDF

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing.

BMC Genomics 2021 Mar 29;22(1):222. Epub 2021 Mar 29.

Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.

Background: The larvacean Oikopleura dioica is an abundant tunicate plankton with the smallest (65-70 Mbp) non-parasitic, non-extremophile animal genome identified to date. Currently, there are two genomes available for the Bergen (OdB3) and Osaka (OSKA2016) O. dioica laboratory strains. Read More

View Article and Full-Text PDF

Predicting HIV Incidence in the SEARCH Trial: A Mathematical Modeling Study.

J Acquir Immune Defic Syndr 2021 Mar 23. Epub 2021 Mar 23.

University of California, Berkeley, Berkeley, USA Institute for Disease Modeling, Bellevue, USA University of Massachusetts Amherst, Amherst, USA University of California, San Francisco, San Francisco, USA Makerere University Joint AIDS Program, Kampala, Uganda Makerere University, Kampala, Uganda.

Background: The SEARCH study provided community-based HIV and multi-disease testing and antiretroviral therapy (ART) to 32 communities in East Africa and reported no statistically significant difference in three-year HIV incidence. We used mathematical modelling to estimate the effect of control arm viral suppression and community mixing on SEARCH trial outcomes.

Setting: Uganda and Kenya. Read More

View Article and Full-Text PDF

Asymmetric Core-Shell Gold Nanoparticles and Controllable Assemblies for SERS Ratiometric Detection of MicroRNA.

Angew Chem Int Ed Engl 2021 Mar 26. Epub 2021 Mar 26.

MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China.

Janus nanogap gold nanoparticles (JAuNNPs) with varying proportions of Au shell coverage of (ca. 100/75/50/25 %) are presented. The internal nanogap between the partial Au shell and core caused asymmetric optical behavior; tunability depends on the degree of Au shell coverage and structural asymmetry. Read More

View Article and Full-Text PDF

A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas.

Gigascience 2021 Mar;10(3)

The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.

Background: The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Read More

View Article and Full-Text PDF

Multi-source financing for tuberculosis treatment in China: key issues and challenges.

Infect Dis Poverty 2021 Mar 10;10(1):17. Epub 2021 Mar 10.

Department of Epidemiology, School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China.

Background: The End Tuberculosis (TB) Strategy of the World Health Organization highlights the need for patient-centered care and social protection measures that alleviate the financial hardships faced by many TB patients. In China, TB treatments are paid for by earmarked government funds, social health insurance, medical assistance for the poor, and out-of-pocket payments from patients. As part of Phase III of the China-Gates TB project, this paper introduces multi-source financing of TB treatment in the three provinces of China and analyzes the challenges of moving towards universal coverage and its implications of multi-sectoral engagement for TB care. Read More

View Article and Full-Text PDF

Dissecting Quantitative Trait Loci for Spot Blotch Resistance in South Asia Using Two Wheat Recombinant Inbred Line Populations.

Front Plant Sci 2021 4;12:641324. Epub 2021 Mar 4.

International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.

Spot blotch (SB) disease causes significant yield loss in wheat production in the warm and humid regions of the eastern Gangetic plains (EGP) of South Asia (SA). Most of the cultivated varieties in the eastern part of SA are affected by SB under favorable climatic conditions. To understand the nature of SB resistance and map the underlying resistant loci effective in SA, two bi-parental mapping populations were evaluated for 3 years, i. Read More

View Article and Full-Text PDF

Selective Gas-Phase Functionalization of SiO and SiN Surfaces with Hydrocarbons.

Langmuir 2021 Apr 17;37(13):3960-3969. Epub 2021 Mar 17.

Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States.

Selective functionalization of dielectric surfaces is required for area-selective atomic layer deposition and etching. We have identified precursors for the selective gas-phase functionalization of plasma-deposited SiO and SiN surfaces with hydrocarbons. The corresponding reaction mechanism of the precursor molecules with the two surfaces was studied using in situ surface infrared spectroscopy. Read More

View Article and Full-Text PDF

Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia).

BMC Genomics 2021 Mar 16;22(1):190. Epub 2021 Mar 16.

College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.

Background: The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers.

Results: Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Read More

View Article and Full-Text PDF

Hybrid Approach to Estimation of Underreporting of Tuberculosis Case Notification in High-Burden Settings With Weak Surveillance Infrastructure: Design and Implementation of an Inventory Study.

JMIR Public Health Surveill 2021 Mar 15;7(3):e22352. Epub 2021 Mar 15.

KNCV TB Foundation, Koninklijke Centrale Vereniging tot bestrijding der Tuberculose (KNCV), The Hague, Netherlands.

Background: The greatest risk of infectious disease undernotification occurs in settings with limited capacity to detect it reliably. World Health Organization guidance on the measurement of misreporting is paradoxical, requiring robust, independent systems to assess surveillance rigor. Methods are needed to estimate undernotification in settings with incomplete, flawed, or weak surveillance systems. Read More

View Article and Full-Text PDF

Accurate, ultra-low coverage genome reconstruction and association studies in Hybrid Swarm mapping populations.

G3 (Bethesda) 2021 Apr;11(4)

Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.

Genetic association studies seek to uncover the link between genotype and phenotype, and often utilize inbred reference panels as a replicable source of genetic variation. However, inbred reference panels can differ substantially from wild populations in their genotypic distribution, patterns of linkage-disequilibrium, and nucleotide diversity. As a result, associations discovered using inbred reference panels may not reflect the genetic basis of phenotypic variation in natural populations. Read More

View Article and Full-Text PDF

Characterization of axolotl lampbrush chromosomes by fluorescence in situ hybridization and immunostaining.

Exp Cell Res 2021 Apr 3;401(2):112523. Epub 2021 Mar 3.

Carnegie Institution for Science, Baltimore, MD, USA. Electronic address:

The lampbrush chromosomes (LBCs) in oocytes of the Mexican axolotl (Ambystoma mexicanum) were identified some time ago by their relative lengths and predicted centromeres, but they have never been associated completely with the mitotic karyotype, linkage maps or genome assembly. We identified 9 of the axolotl LBCs using RNAseq to identify actively transcribed genes and 13 BAC (bacterial artificial clone) probes containing pieces of active genes. Using read coverage analysis to find candidate centromere sequences, we developed a centromere probe that localizes to all 14 centromeres. Read More

View Article and Full-Text PDF

Formative assessment to identify perceived benefits and barriers of HIV oral self-testing among female sex workers, service providers, outreach workers, and peer educators to inform scale-up in Kenya.

AIDS Care 2021 Mar 3:1-8. Epub 2021 Mar 3.

Centers for Disease Control and Prevention, Nairobi, Kenya.

In Kenya, HIV prevalence estimates among female sex workers (FSWs) are almost five times higher than among women in the general population. However, only 68% of infected FSWs are aware of their HIV-positive status. We aimed to identify perceived benefits, opportunities, and barriers of HIV self-testing (HIVST) in improving testing coverage among FSWs. Read More

View Article and Full-Text PDF

Chromosome level reference of Atlantic halibut Hippoglossus hippoglossus provides insight into the evolution of sexual determination systems.

Mol Ecol Resour 2021 Mar 2. Epub 2021 Mar 2.

Biology Department, Dalhousie University, Halifax, NS, Canada.

Changes in the genetic mechanisms that control sexual determination have occurred independently across the tree of life, and with exceptional frequency in teleost fishes. To investigate the genomic changes underlying the evolution of sexual determination, we sequenced a chromosome-level genome, multitissue transcriptomes, and reduced representation population data for the Atlantic halibut (Hippoglossus hippoglossus), which has an XY/XX sex determination mechanism and has recently diverged (0.9-3. Read More

View Article and Full-Text PDF

[Administrative data linkage and its usefulness in public health: the case of EcuadorVinculação de dados administrativos e sua utilização em saúde pública: o caso do Equador].

Rev Panam Salud Publica 2021 26;45:e9. Epub 2021 Feb 26.

Manitoba Centre for Health Policy, Department of Community Health Sciences, Rady Faculty of Health Sciences, University of Manitoba WinnipegManitoba Canada Manitoba Centre for Health Policy, Department of Community Health Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.

The objective of this article is to describe the characteristics of addressing the linkage of administrative databases and the uses of such linkages in public health research, and also to discuss the opportunities and challenges for implementation in Ecuador. The linkage of databases makes it possible to integrate a person's data that may be scattered across different subsectors such as health, education, justice, immigration, and social programs. It also facilitates research that can inform more efficient management of social and health programs and policies. Read More

View Article and Full-Text PDF
February 2021

Suitability of databases in the Asia-Pacific for collaborative monitoring of vaccine safety.

Pharmacoepidemiol Drug Saf 2021 Feb 26. Epub 2021 Feb 26.

Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia.

Introduction: Information regarding availability of electronic healthcare databases in the Asia-Pacific region is critical for planning vaccine safety assessments particularly, as COVID-19 vaccines are introduced. This study aimed to identify data sources in the region, potentially suitable for vaccine safety surveillance. This manuscript is endorsed by the International Society for Pharmacoepidemiology (ISPE). Read More

View Article and Full-Text PDF
February 2021

Estimating pneumococcal vaccine coverage among Australian Indigenous children and children with medically at-risk conditions using record linkage.

Vaccine 2021 Mar 20;39(12):1727-1735. Epub 2021 Feb 20.

School of Population Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; The University of Sydney Northern Clinical School, Women and Babies Research, St Leonards, NSW, Australia; Northern Sydney Local Health District, Kolling Institute, St Leonards, NSW, Australia; National Centre for Immunisation Research and Surveillance, Westmead, NSW, Australia.

Background: Risk-based recommendations are common for pneumococcal vaccines but little is known about their uptake. In Australia, pneumococcal conjugate vaccine (PCV) was funded only for Aboriginal or Torres Strait Islander (Indigenous) children and those with underlying medical conditions in 2001, and then there were different booster dose recommendations depending on risk after the introduction of universal PCV vaccination in 2005.

Methods: We measured coverage of PCV dose 3 and additional PCV and 23-valent pneumococcal polysaccharide vaccine (PPV23) doses by risk group among children born in July 2001-December 2012 in two Australian states using linked immunisation and hospitalisation data (available until December 2013). Read More

View Article and Full-Text PDF

Barriers to HIV and Hepatitis C care for people who inject drugs in Colombia.

AIDS Care 2021 Feb 22:1-6. Epub 2021 Feb 22.

School of Medicine, New York University, New York, USA.

People who inject drugs (PWIDs) are a key population targeted in global efforts to increase HIV and Hepatitis C virus (HCV) diagnosis, linkage to care, and treatment retention. Colombia has experienced a significant increase in the incidence of HIV and HCV attributed to the alarming rise in injection drug use. The primary aim of this study was to identify factors influencing access to HIV and HCV care among PWIDs. Read More

View Article and Full-Text PDF
February 2021

National Health Insurance Fund's relationship to retail drug outlets: a Tanzania case study.

J Pharm Policy Pract 2021 Feb 17;14(1):21. Epub 2021 Feb 17.

Management Sciences for Health/Medicines, Technologies, and Pharmaceutical Services Program, Arlington, USA.

Background: Achieving universal health coverage will require robust private sector engagement; however, as many low- and middle-income countries launch prepayment schemes to achieve universal health coverage, few are covering products from retail drug outlets (pharmacies and drug shops). This case study aims to characterize barriers and facilitators related to incorporating retail drug outlets into national prepayment schemes based on the experience of the Tanzanian National Health Insurance Fund's (NHIF) certification of pharmacies and accredited drug dispensing outlets.

Methods: We reviewed government documents and interviewed 26 key informants including retail outlet owners and dispensers and central and district government authorities representing eight districts overall. Read More

View Article and Full-Text PDF
February 2021