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1.
Jumpstart Consortium Human Microbiome Project Data Generation Working Group 《PloS one》2012,7(6):e39315
The Human Microbiome Project will establish a reference data set for analysis of the microbiome of healthy adults by surveying multiple body sites from 300 people and generating data from over 12,000 samples. To characterize these samples, the participating sequencing centers evaluated and adopted 16S rDNA community profiling protocols for ABI 3730 and 454 FLX Titanium sequencing. In the course of establishing protocols, we examined the performance and error characteristics of each technology, and the relationship of sequence error to the utility of 16S rDNA regions for classification- and OTU-based analysis of community structure. The data production protocols used for this work are those used by the participating centers to produce 16S rDNA sequence for the Human Microbiome Project. Thus, these results can be informative for interpreting the large body of clinical 16S rDNA data produced for this project. 相似文献
2.
Carsten Nesshöver Marie Vandewalle Heidi Wittmer Estelle V. Balian Esther Carmen Ilse R. Geijzendorffer Christoph Görg Rob Jongman Barbara Livoreil Luis Santamaria Stefan Schindler Josef Settele Isabel Sousa Pinto Katalin Török Jiska van Dijk Allan D. Watt Juliette C. Young Klaus Peter Zulka the KNEU Project Team 《Biodiversity and Conservation》2016,25(7):1215-1233
The absence of a good interface between scientific and other knowledge holders and decision-makers in the area of biodiversity and ecosystem services has been recognised for a long time. Despite recent advancements, e.g. with the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES), challenges remain, particularly concerning the timely provision of consolidated views from different knowledge domains. To address this challenge, a strong and flexible networking approach is needed across knowledge domains and institutions. Here, we report on a broad consultation process across Europe to develop a Network of Knowledge on biodiversity and ecosystem services (NoK), an approach aiming at (1) organising institutions and knowledge holders in an adaptable and responsive framework and (2) informing decision-makers with timely and accurate biodiversity knowledge. The consultation provided a critical analysis of the needs that should be addressed by a NoK and how it could complement existing European initiatives and institutions at the interface between policy and science. Among other functions, the NoK provides consolidated scientific views on contested topics, identification of research gaps to support relevant policies, and horizon scanning activities to anticipate emerging issues. The NoK includes a capacity building component on interfacing activities and contains mechanisms to ensure its credibility, relevance and legitimacy. Such a network would need to ensure credibility, relevance and legitimacy of its work by maximizing transparency and flexibility of processes, quality of outputs, the link to data and knowledge provision, the motivation of experts for getting involved and sound communication and capacity building. 相似文献
3.
Degang Wu Peter Yiqing Li Bangfen Pan Zenia Tiang Jinzhuang Dou Ivanna Williantarra Amadeus Yeremia Pribowo Rizky Nurdiansyah The SG Peranakan Project Roger S Y Foo Chaolong Wang 《Molecular biology and evolution》2021,38(10):4463
The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ∼300–500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ∼5.62% (95% confidence interval [CI]: 4.76–6.49%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.65–1.51%), southern Chinese (0.86%, 0.50–1.23%), and northern Chinese (0.25%, 0.18–0.32%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ∼1,612 (95% CI: 1,345–1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ∼190 (159–213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia. 相似文献
4.
Calmodulin is a small (148 residues), ubiquitous, highly-conserved Ca(2+) binding protein serving as a modulator of many calcium-dependent processes. In this study, we followed, by means of molecular dynamics, the structural stability of the protein when one of its four bound Ca(2+) ions is removed, and compared it to a simulation of the fully Ca(2+) bound protein. We found that the removal of a single Ca(2+) ion from the N-lobe of the protein, which has a lower affinity for the ion, is sufficient to initiate a considerable structural rearrangement. Although the overall structure of the fully 4 Ca(2+) bound protein remained intact in the extended conformation, the Ca(2+)-removed protein changed its conformation into a compact state. The observation that the 3 Ca(2+) loaded protein assumes a compacted solution state is in accord with experimental observation that the NSCP protein, which binds only three Ca(2+) ions, is natively in a compact state. Examination of the folding dynamics reveals a cooperation between the C-lobe, N-lobe, and the interdomain helix that enable the conformation change. The forces driving this conformational change are discussed. 相似文献
5.
Holly L Neibergs Christopher M Seabury Andrzej J Wojtowicz Zeping Wang Erik Scraggs Jennifer N Kiser Mahesh Neupane James E Womack Alison Van Eenennaam Gerald Robert Hagevoort Terry W Lehenbauer Sharif Aly Jessica Davis Jeremy F Taylor The Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team 《BMC genomics》2014,15(1)
Background
Bovine respiratory disease complex (BRDC) is an infectious disease of cattle that is caused by a combination of viral and/or bacterial pathogens. Selection for cattle with reduced susceptibility to respiratory disease would provide a permanent tool for reducing the prevalence of BRDC. The objective of this study was to identify BRDC susceptibility loci in pre-weaned Holstein calves as a prerequisite to using genetic improvement as a tool for decreasing the prevalence of BRDC. High density SNP genotyping with the Illumina BovineHD BeadChip was conducted on 1257 male and 757 female Holstein calves from California (CA), and 767 calves identified as female from New Mexico (NM). Of these, 1382 were classified as BRDC cases, and 1396 were classified as controls, with all phenotypes assigned using the McGuirk health scoring system. During the acquisition of blood for DNA isolation, two deep pharyngeal and one mid-nasal diagnostic swab were obtained from each calf for the identification of bacterial and viral pathogens. Genome-wide association analyses were conducted using four analytical approaches (EIGENSTRAT, EMMAX-GRM, GBLUP and FvR). The most strongly associated SNPs from each individual analysis were ranked and evaluated for concordance. The heritability of susceptibility to BRDC in pre-weaned Holstein calves was estimated.Results
The four statistical approaches produced highly concordant results for 373 top ranked SNPs that defined 126 chromosomal regions for the CA population. Similarly, in NM, 370 SNPs defined 138 genomic regions that were identified by all four approaches. When the two populations were combined (i.e., CA + NM) and analyzed, 324 SNPs defined 116 genomic regions that were associated with BRDC across all analytical methods. Heritability estimates for BRDC were 21% for both CA and NM as individual populations, but declined to 13% when the populations were combined.Conclusions
Four analytical approaches utilizing both single and multi-marker association methods revealed common genomic regions associated with BRDC susceptibility that can be further characterized and used for genomic selection. Moderate heritability estimates were observed for BRDC susceptibility in pre-weaned Holstein calves, thereby supporting the application of genomic selection to reduce the prevalence of BRDC in U.S. Holsteins.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1164) contains supplementary material, which is available to authorized users. 相似文献6.
P B Jacklin J A Roberts P Wallace A Haines R Harrison J A Barber S G Thompson L Lewis R Currell S Parker P Wainwright the Virtual Outreach Project Group 《BMJ (Clinical research ed.)》2003,327(7406):84
Objectives To test the hypotheses that, compared with conventional outpatient consultations, joint teleconsultation (virtual outreach) would incur no increased costs to the NHS, reduce costs to patients, and reduce absences from work by patients and their carers.Design Cost consequences study alongside randomised controlled trial.Setting Two hospitals in London and Shrewsbury and 29 general practices in inner London and Wales.Participants 3170 patients identified; 2094 eligible for inclusion and willing to participate. 1051 randomised to virtual outreach and 1043 to standard outpatient appointments.Main outcome measures NHS costs, patient costs, health status (SF-12), time spent attending index consultation, patient satisfaction.Results Overall six months costs were greater for the virtual outreach consultations (£724 per patient) than for conventional outpatient appointments (£625): difference in means £99 ($162; €138) (95% confidence interval £10 to £187, P=0.03). If the analysis is restricted to resource items deemed “attributable” to the index consultation, six month costs were still greater for virtual outreach: difference in means £108 (£73 to £142, P < 0.0001). In both analyses the index consultation accounted for the excess cost. Savings to patients in terms of costs and time occurred in both centres: difference in mean total patient cost £8 (£5 to £10, P < 0.0001). Loss of productive time was less in the virtual outreach group: difference in mean cost £11 (£10 to £12, P < 0.0001).Conclusion The main hypothesis that virtual outreach would be cost neutral is rejected, but the hypotheses that costs to patients and losses in productivity would be lower are supported. 相似文献
7.
R. I. M. Dunbar A. H. Korstjens and J. Lehmann British Academy Centenary Research Project 《Biological reviews of the Cambridge Philosophical Society》2009,84(3):413-429
Conventional approaches to population biology emphasise the roles of climatic conditions, nutrient flow and predation as constraints on population dynamics. We argue here that this focus has obscured the role of time as a crucial constraint on species' abilities to survive in some habitats. Time constraints may be particularly intrusive both for species that live in intensely bonded groups (where the need to devote time to social interaction may ultimately limit the size of group that a species can maintain in a particular habitat) and for taxa that face constraints on the length of the active day. We use a linear programming approach that allows us to specify both how time allocations to different activities are influenced by local environmental and climatic variables and how these in turn limit group size and population density. The linear programming approach identifies the realizable niche space within which a species can maintain coherent groups that are larger than the minimum viable group size (or density). This approach thus allow us to understand better why a given taxon can survive in some habitats but not others, as well as the demographic stress that a population may face. In addition, they also allow us to evaluate the implications of both past and future climate change for a taxon's ability to cope with particular habitats. 相似文献
8.
Jared M. Baeten Renee Heffron Lara Kidoguchi Nelly R. Mugo Elly Katabira Elizabeth A. Bukusi Stephen Asiimwe Jessica E. Haberer Jennifer Morton Kenneth Ngure Nulu Bulya Josephine Odoyo Edna Tindimwebwa Craig Hendrix Mark A. Marzinke Norma C. Ware Monique A. Wyatt Susan Morrison Harald Haugen Andrew Mujugira Deborah Donnell Connie Celum Partners Demonstration Project Team 《PLoS medicine》2016,13(8)
BackgroundAntiretroviral-based interventions for HIV-1 prevention, including antiretroviral therapy (ART) to reduce the infectiousness of HIV-1 infected persons and pre-exposure prophylaxis (PrEP) to reduce the susceptibility of HIV-1 uninfected persons, showed high efficacy for HIV-1 protection in randomized clinical trials. We conducted a prospective implementation study to understand the feasibility and effectiveness of these interventions in delivery settings.ConclusionsIntegrated delivery of time-limited PrEP until sustained ART use in African HIV-1-serodiscordant couples was feasible, demonstrated high uptake and adherence, and resulted in near elimination of HIV-1 transmission, with an observed HIV incidence of <0.5% per year compared to an expected incidence of >5% per year. 相似文献
9.
Avila-Ríos S García-Morales C Garrido-Rodríguez D Ormsby CE Hernández-Juan R Andrade-Villanueva J González-Hernández LA Torres-Escobar I Navarro-Álvarez S Reyes-Terán G;Mexican HIV Molecular Epidemiology Project Group 《PloS one》2011,6(11):e27812
Background
Transmitted drug resistance (TDR) remains an important concern for the management of HIV infection, especially in countries that have recently scaled-up antiretroviral treatment (ART) access.Methodology/Principal Findings
We designed a study to assess HIV diversity and transmitted drug resistance (TDR) prevalence and trends in Mexico. 1655 ART-naïve patients from 12 Mexican states were enrolled from 2005 to 2010. TDR was assessed from plasma HIV pol sequences using Stanford scores and the WHO TDR surveillance mutation list. TDR prevalence fluctuations over back-projected dates of infection were tested. HIV subtype B was highly prevalent in Mexico (99.9%). TDR prevalence (Stanford score>15) in the country for the study period was 7.4% (95% CI, 6.2∶8.8) and 6.8% (95% CI, 5.7∶8.2) based on the WHO TDR surveillance mutation list. NRTI TDR was the highest (4.2%), followed by NNRTI (2.5%) and PI (1.7%) TDR. Increasing trends for NNRTI (p = 0.0456) and PI (p = 0.0061) major TDR mutations were observed at the national level. Clustering of viruses containing minor TDR mutations was observed with some apparent transmission pairs and geographical effects.Conclusions
TDR prevalence in Mexico remains at the intermediate level and is slightly lower than that observed in industrialized countries. Whether regional variations in TDR trends are associated with differences in antiretroviral drug usage/ART efficacy or with local features of viral evolution remains to be further addressed. 相似文献10.
The Mountain Gorilla Veterinary Project Employee Health GroupEmail author 《EcoHealth》2004,1(4):351-361
Humans and gorillas share 97% of their genetic makeup which means the risk of disease transmission between the two is potentially high. Humans with high exposure and whose exposure-related activity can most easily be managed are park conservation personnel. In June 2001, the Morris Animal Foundations Mountain Gorilla Veterinary Project initiated a health program for all employees working in Rwandas Parc National des Volcans in collaboration with in-country government and nongovernmental agencies. The goal is to improve the health of conservation personnel and reduce the risk of zoonotic disease transmission between employees and the parks mountain gorillas. Employees annually receive a clinical examination and laboratory testing, and provide a clinical history, In 2002, analyses were performed on the dataset of 127 employees to identify potential risk factors associated with positive laboratory tests. Considering all fecal tests combined, 70.1% were positive for one or more pathogenic organisms. A high percentage (> 80%) tested positive on viral antibody titer testing for various communicable diseases including measles, chickenpox, and hepatitis. On multivariate analysis, the main risk factor for testing positive for any pathogenic organism was use of a pit latrine at home. Vaccination against childhood communicable diseases and improved human waste disposal could be critical control points for preventing disease transmission to mountain gorillas. Program results have been shared with local health officials to aid in their efforts to improve village health and sanitation standards, and with park employers as a basis for ongoing employee health education.The Mountain Gorilla Veterinary Project 2002 Employee Health Group members are listed in Appendix 1. by area of contribution. 相似文献