A5021345648- Fiscal Policy and Economic Growth
- Genomics and Phylogenetic Studies
- Biochemical and Molecular Research
- Economic Growth and Productivity
- Antimicrobial Resistance in Staphylococcus
- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- Local Government Finance and Decentralization
- Fiscal Policies and Political Economy
- Monetary Policy and Economic Impact
- Bacterial Identification and Susceptibility Testing
- Corporate Taxation and Avoidance
- Evolution and Genetic Dynamics
- Salmonella and Campylobacter epidemiology
- Antibiotic Resistance in Bacteria
- Viral gastroenteritis research and epidemiology
- Bacterial Genetics and Biotechnology
- HIV/AIDS drug development and treatment
- Escherichia coli research studies
- Innovation Policy and R&D
- Firm Innovation and Growth
- Health disparities and outcomes
- Clostridium difficile and Clostridium perfringens research
- Psychological Well-being and Life Satisfaction
- Gut microbiota and health
University of Oxford
2016-2025
University of Minnesota
2014-2025
Federal Reserve Bank of San Francisco
2014-2024
Wellcome Centre for Ethics and Humanities
2024
Leeds Teaching Hospitals NHS Trust
2005-2024
Open Data Institute
2017-2023
University of Illinois Chicago
2007-2023
Library of Virginia
2023
University of Virginia
2023
Boston University
2023
BackgroundTuberculosis incidence in the UK has risen past decade. Disease control depends on epidemiological data, which can be difficult to obtain. Whole-genome sequencing detect microevolution within Mycobacterium tuberculosis strains. We aimed estimate genetic diversity of related M strains Midlands and investigate how this measurement might used community outbreaks.MethodsIn a retrospective observational study, we Illumina technology sequence genomes from an archive frozen cultures....
Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference simultaneously detect recombination bacterial genomes and account for phylogenetic reconstruction. ClonalFrameML can analyse hundreds matter hours, demonstrate its usefulness on simulated real datasets. We find evidence hotspots associated with mobile elements...
It has been thought that Clostridium difficile infection is transmitted predominantly within health care settings. However, endemic spread hampered identification of precise sources and the assessment efficacy interventions.
Abstract The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection drug resistance in clinical samples, and improvements global surveillance. Here we show how de Bruijn graph representation bacterial diversity can be used identify species profiles isolates. We implement this method Staphylococcus aureus Mycobacterium tuberculosis a software package (‘Mykrobe predictor’) that takes raw sequence data as input, generates clinician-friendly report within 3 minutes...
Campylobacter jejuni is the leading cause of bacterial gastro-enteritis in developed world. It thought to infect 2-3 million people a year US alone, at cost economy excess $4 billion. C. widespread zoonotic pathogen that carried by animals farmed for meat and poultry. A connection with contaminated food recognized, but also commonly found wild water sources. Phylogenetic studies have suggested genotypes pathogenic humans bear greatest resemblance non-livestock isolates. Moreover, seasonal...
Nature Communications 6: Article number: 10063 (2015); Published: 21 December 2015; Updated: 20 April 2016 In Supplementary Data 3 of this Article, one the Staphylococcus aureus accession codes is incorrect, as follows: SRR2101499 should be ERR1197981.
Campylobacter species cause a high proportion of bacterial gastroenteritis cases and are significant burden on health care systems economies worldwide; however, the relative contributions various possible sources infection in humans unclear.National-scale genotyping was used to quantify importance human infection. Multilocus sequence types were determined for 5674 isolates obtained from campylobacteriosis Scotland July 2005 through September 2006 999 3417 contemporaneous samples potential...
<b><i>Background: </i></b>The relationship between serum potassium, mortality, and conditions commonly associated with dyskalemias, such as heart failure (HF), chronic kidney disease (CKD), and/or diabetes mellitus (DM) is largely unknown. <b><i>Methods:</i></b> We reviewed electronic medical record data from a geographically diverse population (<i>n</i> = 911,698) receiving care, determined the distribution of an index potassium...
Whole-genome sequencing (WGS) could potentially provide a single platform for extracting all the information required to predict an organism's phenotype. However, its ability accurate predictions has not yet been demonstrated in large independent studies of specific organisms. In this study, we aimed develop genotypic prediction method antimicrobial susceptibilities. The whole genomes 501 unrelated Staphylococcus aureus isolates were sequenced, and assembled interrogated using BLASTn panel...
Escherichia colisequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of lineage, antimicrobial elements it, remain unclearly defined. This study largest worldwide collection (n= 215) sequenced ST131E. coliisolates to date demonstrates that clonal...
The proliferation of R&D tax incentives among U.S. states in recent decades raises two questions: (i) Are these effective increasing in-state R&D? (ii) How much any increase is due to being drawn away from other states? This paper answers “yes” and “nearly all.” estimates an augmented factor demand model using state panel data 1981 2004. I estimate that the long-run elasticity with respect user cost about –2.5, while its out-of-state costs +2.5, suggesting a zero-sum game states.
The control of Clostridium difficile infections is an international clinical challenge. incidence C in England declined by roughly 80% after 2006, following the implementation national policies; we tested two hypotheses to investigate their role this decline. First, if infection declines were driven reductions use particular antibiotics, then caused resistant isolates should decline faster than that susceptible across multiple genotypes. Second, improvements hospital control, transmitted...
Analysis of "big data" frequently involves statistical comparison millions competing hypotheses to discover hidden processes underlying observed patterns data, for example, in the search genetic determinants disease genome-wide association studies (GWAS). Controlling familywise error rate (FWER) is considered strongest protection against false positives but makes it difficult reach multiple testing-corrected significance threshold. Here, I introduce harmonic mean p-value (HMP), which...
The recent widespread emergence of carbapenem resistance in Enterobacteriaceae is a major public health concern, as carbapenems are therapy last resort against this family common bacterial pathogens. Resistance genes can mobilize via various mechanisms, including conjugation and transposition; however, the importance mobility short-term evolution, such within nosocomial outbreaks, unknown. Using combination short- long-read whole-genome sequencing 281 blaKPC-positive isolates from single...
Whole-genome sequencing offers new insights into the evolution of bacterial pathogens and etiology disease. Staphylococcus aureus is a major cause bacteria-associated mortality invasive disease carried asymptomatically by 27% adults. Eighty percent bacteremias match strain. However, role evolutionary change in pathogen during progression from carriage to incompletely understood. Here we use high-throughput genome discover genetic changes that accompany transition nasal fatal bloodstream...
We quantify how sensitive is migration by star scientists to changes in personal and business tax differentials across states. uncover large, stable, precisely estimated effects of corporate taxes on scientists' patterns. The long-run elasticity mobility relative 1.8 for income taxes, 1.9 state tax, −1.7 the investment credit. While there are many other factors that drive when innovative individuals companies decide locate, enough firms workers margin matter. (JEL H24, H25, H71, H73, J44, J61, R32)
Phylogeographic methods aim to infer migration trends and the history of sampled lineages from genetic data. Applications phylogeography are broad, in context pathogens include reconstruction transmission histories origin emergence outbreaks. inference based on bottom-up population genetics models is computationally expensive, as a result faster alternatives evolution discrete traits have become popular. In this paper, we show that rates root locations trait extremely unreliable sensitive...
To investigate the prospects of newly available benchtop sequencers to provide rapid whole-genome data in routine clinical practice. Next-generation sequencing has potential resolve uncertainties surrounding route and timing person-to-person transmission healthcare-associated infection, which been a major impediment optimal management.
Generation time varies widely across organisms and is an important factor in the life cycle, history evolution of organisms. Although doubling (DT) has been estimated for many bacteria laboratory, it nearly impossible to directly measure natural environment. However, estimate can be obtained by measuring rate at which accumulate mutations per year wild they mutate generation laboratory. If we assume mutation same that all are neutral, assumption show not very important, then DT dividing...
The sequencing and comparative analysis of a collection bacterial genomes from single species or lineage interest can lead to key insights into its evolution, ecology epidemiology. tool choice for such study is often build phylogenetic tree, more specifically when possible dated phylogeny, in which the dates all common ancestors are estimated. Here, we propose new Bayesian methodology construct phylogenies designed genomics. Unlike previous methods aimed at building phylogenies, consider...