Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Evolution and Reproducibility of Simulation Modeling in Epidemiology and Health Policy Over Half a Century

Abstract Simulation models are increasingly being used to inform epidemiologic studies and health policy, yet there is great variation in their transparency and reproducibility. In this review, we provide an overview of applications of simulation models in health policy and epidemiology, analyze the use of best reporting practices, and assess the reproducibility of the models using predefined, categorical criteria. We identified and analyzed 1,613 applicable articles and found exponential growth in the number of studies over the past half century, with the highest growth in dynamic modeling approaches. The largest subset of studies focused on disease policy models (70%), within which pathological conditions, viral diseases, neoplasms, and cardiovascular diseases account for one-third of the articles. Model details were not reported in almost half of the studies. We also provide in-depth analysis of modeling best practices, reporting quality and reproducibility of models for a subset of 100 articles (50 highly cited and 50 randomly selected from the remaining articles). Only 7 of 26 in-depth evaluation criteria were satisfied by more than 80% of samples. We identify areas for increased application of simulation modeling and opportunities to enhance the rigor and documentation in the conduct and reporting of simulation modeling in epidemiology and health policy.</jats:p

Weather, air pollution, and SARS-CoV-2 transmission: a global analysis

BACKGROUND: Understanding how environmental factors affect SARS-CoV-2 transmission could inform global containment efforts. Despite high scientific and public interest and multiple research reports, there is currently no consensus on the association of environmental factors and SARS-CoV-2 transmission. To address this research gap, we aimed to assess the relative risk of transmission associated with weather conditions and ambient air pollution. METHODS: In this global analysis, we adjusted for the delay between infection and detection, estimated the daily reproduction number at 3739 global locations during the COVID-19 pandemic up until late April, 2020, and investigated its associations with daily local weather conditions (ie, temperature, humidity, precipitation, snowfall, moon illumination, sunlight hours, ultraviolet index, cloud cover, wind speed and direction, and pressure data) and ambient air pollution (ie, PM2·5, nitrogen dioxide, ozone, and sulphur dioxide). To account for other confounding factors, we included both location-specific fixed effects and trends, controlling for between-location differences and heterogeneities in locations' responses over time. We built confidence in our estimations through synthetic data, robustness, and sensitivity analyses, and provided year-round global projections for weather-related risk of global SARS-CoV-2 transmission. FINDINGS: Our dataset included data collected between Dec 12, 2019, and April 22, 2020. Several weather variables and ambient air pollution were associated with the spread of SARS-CoV-2 across 3739 global locations. We found a moderate, negative relationship between the estimated reproduction number and temperatures warmer than 25°C (a decrease of 3·7% [95% CI 1·9-5·4] per additional degree), a U-shaped relationship with outdoor ultraviolet exposure, and weaker positive associations with air pressure, wind speed, precipitation, diurnal temperature, sulphur dioxide, and ozone. Results were robust to multiple assumptions. Independent research building on our estimates provides strong support for the resulting projections across nations. INTERPRETATION: Warmer temperature and moderate outdoor ultraviolet exposure result in a slight reduction in the transmission of SARS-CoV-2; however, changes in weather or air pollution alone are not enough to contain the spread of SARS-CoV-2 with other factors having greater effects. FUNDING: None

The impacts of biosecurity measures on Campylobacter contamination in broiler houses and slaughterhouses in the Netherlands : A simulation modelling approach

Intestinal campylobacteriosis, caused by Campylobacter ingestion, is the most reported zoonosis in the EU; it is societally costly and can lead to more severe sequelae. To reduce Campylobacter infections, biosecurity measures at both farms and slaughterhouses are warranted. However, the potential improvements achieved by these interventions have not been quantified. We used a systems science approach to develop a simulation model, synthesizing information from interviews with stakeholders in the Dutch broiler production industry and the current literature. The model includes both farms and slaughterhouses in a “system of systems,” helping to clarify the complexity of interrelated components of these systems and analyse the impact of various interventions. Insects, transportation crates, farm personnel, and catchers were identified as potential Campylobacter sources and modelled as elements of feedback loops. Insect control, farm hygiene, visitor control, thinning, and transportation control interventions were analysed. The model was shown to accurately describe the seasonality of Campylobacter, which supports its validity. Model simulation revealed that insect control interventions had the strongest impacts, followed by combined farm hygiene and visitor control, and combined thinning and transportation control. Insect control interventions alone reduced the peak percentage of contaminated chickens from 51% to 26% and the peak percentage of highly contaminated (>1000 CFU/g) neck samples of chicken carcasses from 13% to 8%. Implementing all interventions concurrently reduced the peak percentages of contaminated chickens to 5% and highly contaminated chicken neck samples to 2%. These results suggest that multiple biosecurity measures must be implemented to reduce Campylobacter contamination

The impacts of biosecurity measures on Campylobacter contamination in broiler houses and slaughterhouses in the Netherlands: A simulation modelling approach

Intestinal campylobacteriosis, caused by Campylobacter ingestion, is the most reported zoonosis in the EU; it is societally costly and can lead to more severe sequelae. To reduce Campylobacter infections, biosecurity measures at both farms and slaughterhouses are warranted. However, the potential improvements achieved by these interventions have not been quantified. We used a systems science approach to develop a simulation model, synthesizing information from interviews with stakeholders in the Dutch broiler production industry and the current literature. The model includes both farms and slaughterhouses in a “system of systems,” helping to clarify the complexity of interrelated components of these systems and analyse the impact of various interventions. Insects, transportation crates, farm personnel, and catchers were identified as potential Campylobacter sources and modelled as elements of feedback loops. Insect control, farm hygiene, visitor control, thinning, and transportation control interventions were analysed. The model was shown to accurately describe the seasonality of Campylobacter, which supports its validity. Model simulation revealed that insect control interventions had the strongest impacts, followed by combined farm hygiene and visitor control, and combined thinning and transportation control. Insect control interventions alone reduced the peak percentage of contaminated chickens from 51% to 26% and the peak percentage of highly contaminated (&gt;1000 CFU/g) neck samples of chicken carcasses from 13% to 8%. Implementing all interventions concurrently reduced the peak percentages of contaminated chickens to 5% and highly contaminated chicken neck samples to 2%. These results suggest that multiple biosecurity measures must be implemented to reduce Campylobacter contamination.Policy Analysi

Limited disease progression in endocrine surgery patients with treatment delays due to COVID-19.

BackgroundThe COVID-19 pandemic profoundly impacted the delivery of care and timing of elective surgical procedures. Most endocrine-related operations were considered elective and safe to postpone, providing a unique opportunity to assess clinical outcomes under protracted treatment plans.MethodsAmerican Association of Endocrine Surgeon members were surveyed for participation. A Research Electronic Data Capture survey was developed and distributed to 27 institutions to assess the impact of COVID-19-related delays. The information collected included patient demographics, primary diagnosis, resumption of care, and assessment of disease progression by the surgeon.ResultsTwelve out of 27 institutions completed the survey (44.4%). Of 850 patients, 74.8% (636) were female; median age was 56 (interquartile range, 44-66) years. Forty percent (34) of patients had not been seen since their original surgical appointment was delayed; 86.2% (733) of patients had a delay in care with women more likely to have a delay (87.6% vs 82.2% of men, χ2&nbsp;= 3.84, P&nbsp;= .05). Median duration of delay was 70 (interquartile range, 42-118) days. Among patients with a delay in care, primary disease site included thyroid (54.2%), parathyroid (37.2%), adrenal (6.5%), and pancreatic/gastrointestinal neuroendocrine tumors (1.3%). In addition, 4.0% (26) of patients experienced disease progression and 4.1% (24) had a change from the initial operative plan. The duration of delay was not associated with disease progression (P&nbsp;= .96) or a change in operative plan (P&nbsp;= .66).ConclusionAlthough some patients experienced disease progression during COVID-19 delays to endocrine disease-related care, most patients with follow-up did not. Our analysis indicated that temporary delay may be an acceptable course of action in extreme circumstances for most endocrine-related surgical disease