108 research outputs found
Promoting Sustainable Transportation with Campus Car Policies and Public Outreach
In fall of 2016 at California State University Monterey Bay (CSUMB), the Environmental Studies undergraduate program began offering its first group-based capstone course that was based on its first Projects for Sustainable City Year course (ENSTU 471). Capstone projects are a senior-level, project based graduation requirement for an undergraduate degree. The Sustainable City Year projects focused on increasing sustainable transportation at two locations; one in the nearby city of Salinas, California, and one on the CSUMB campus. A majority of the community in Salinas drive which has limited the quality and effectiveness of the shuttle system provided by Monterey-Salinas Transit (MST). Our group seeks to help increase ridership and promote sustainable transportation in this region. At CSUMB, traffic congestion on campus is increasingly problematic as the student body continues to row. The majority of students drive to campus in single passenger vehicles which increases the traffic on campus. Sustainable transportation via buses, bicycling, and carpooling helps decrease traffic congestion. In the following paper, the CSUMB project covers a proposed freshman vehicle restriction policy to encourage sustainable modes of transportation and a bus-bicycle culture. For the Salinas project, we worked directly with MST to encourage common knowledge of bus usage by creating an informational and interactive booklet
A REVIEW OF THE EFFICACY AND ROLE OF THE CARD SORT EXERCISE IN THE TREATMENT OF BIPOLAR DISORDER
The current card sort exercise described by Agius et al. in 2006 provides a tool for patients and their families to characterise the
temporal pattern of occurrence of both stereotyped and idiosyncratic prodromal symptoms that serve as early warning signs
predicting a relapse. This \u27individual relapse signature\u27 is highly specific for bipolar relapse, and aids identification of a relapse
such that patients can be channeled into appropriate early intervention pathways. This review examines the role of the card sort
exercise in the treatment of bipolar disorder, and evaluates the evidence for its efficacy.
Few studies involve the card sort exercise, and those that do paired it with other early therapeutic interventions, such that it
was difficult to assess the true contribution of the card sort exercise alone to outcome measures such as time-to-relapse or
hospitalisation avoidance. We went back to first principles and evaluated the literature concerning various factors necessary for
the card sort exercise to be useful. We concluded that there is good evidence that replicable relapse signatures exist as early
warning signs for bipolar relapse, and that a certain subgroup of patients and their families can reliably use these signs to seek
help and activate therapeutic interventions to abort the relapse episode. Early intervention is both possible and efficacious, which makes early identification of relapse yet more important. The card sort is of less use for depressive relapses, where prodromal symptoms are harder to pinpoint. The card sort exercise is useful in elucidating the relapse signature for each patient, which can then be used in psychoeducation or identification of future relapse episodes. However, more research is needed directly assessing the usefulness of the card sort exercise in helping patients and their families gain insight into the possibility of an imminent relapse
āļāļēāļĢāļŠāļĢāđāļēāļāđāļĨāļ°āļŦāļēāļāļĢāļ°āļŠāļīāļāļāļīāļ āļēāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢ āļāļĨāļīāļāļĢāļ°āļāļąāļāļ§āļīāļŠāļēāļŦāļāļīāļāļāļļāļĄāļāļ
āļāļēāļāļ§āļīāļāļąāļĒāļĄāļĩāļ§āļąāļāļāļļāļāļĢāļ°āļŠāļāļāđāđāļāļ·āđāļ 1) āļŠāļĢāđāļēāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢ āļĢāļ°āļāļąāļāļ§āļīāļŠāļēāļŦāļāļīāļāļāļļāļĄāļāļāđāļāļāļ·āđāļāļāļĩāđāļāļąāļāļŦāļ§āļąāļāļŠāļĢāļ°āđāļāđāļ§ āđāļĨāļ° 2) āļŦāļēāļāļĢāļ°āļŠāļīāļāļāļīāļ āļēāļāļāļēāļĢāļāļģāļāļēāļāļāļĩāđāđāļŦāļĄāļēāļ°āļŠāļĄāļāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢ āļāļđāđāļ§āļīāļāļąāļĒāļāļķāļāđāļāđāļāļāļāđāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢ āđāļĨāļ·āļāļāđāļāđāļ§āļąāļŠāļāļļāđāļāļĢāļāļŠāļĢāđāļēāļāđāļāđāļāļ§āļąāļŠāļāļļāļŠāđāļāļāđāļĨāļŠ SUS 304 āđāļĨāļ°āđāļāđāļĄāļāđāļāļāļĢāđāđāļāļāđāļēāđāļāđāļāļāđāļāļāļģāļĨāļąāļāļāļāļēāļ 1 āđāļĢāļāļĄāđāļē āļāļąāļāļāļģāļĨāļąāļāļāđāļ§āļĒāļāļđāļĨāđāļĨāļĒāđ āļŠāļēāļĒāļāļēāļ āļĢāļāļāļāļ§āļēāļĄāđāļĢāđāļ§āļāļĩāđāđāļāđāļāļ·āļ 846 āļĢāļāļāļāđāļāļāļēāļāļĩ āđāļĨāļ°āđāļĨāļ·āļāļāđāļāđāđāļāļĄāļĩāļāļŦāļąāđāļāđāļāļ 2 āđāļāļĄāļĩāļ āđāļāļĒāđāļāđāļŦāļĨāļąāļāļāļēāļĢāļ§āļīāļĻāļ§āļāļĢāļĢāļĄāļāļēāļĄāļāļĪāļĐāļāļĩāđāļĢāļāđāļāļ·āļāļāļāļēāļāļāļēāļĢāļŦāļĄāļļāļāđāļŦāļ§āļĩāđāļĒāļāđāļāļĄāļĩāļ āļāļĢāļīāļĄāļēāļāļāļēāļĢāļāļĨāļīāļāļāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢāļāļ·āļ 50 āļāļīāđāļĨāļāļĢāļąāļĄ/āļāļąāđāļ§āđāļĄāļ āđāļĨāļ°āđāļāđāļĻāļķāļāļĐāļēāļŦāļēāļāļĢāļ°āļŠāļīāļāļāļīāļ āļēāļāļāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢ āđāļāļĒāļāļēāļĢāļāļāļĨāļāļāļŦāļąāđāļ 10 āļāļĢāļąāđāļ āļāļĢāļąāđāļāļĨāļ° 1,000 āļāļĢāļąāļĄ āļāļĨāļāļēāļĢāļ§āļīāļāļąāļĒāļāļāļ§āđāļē 1) āļāļĨāļāļĩāđāđāļāđāļāļēāļāļāļēāļĢāļŦāļąāđāļāļāļ·āļ āļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢāļĄāļĩāļāļāļēāļāļāļ§āļēāļĄāļĒāļēāļ§āļāđāļģāļāļ§āđāļē 2 āļāļīāđāļ§ āļāļēāļĄāļāļ§āļēāļĄāļāđāļāļāļāļēāļĢāļāļāļāļ§āļīāļŠāļēāļŦāļāļīāļāļāļļāļĄāļāļ āļĢāļ°āļĒāļ°āđāļ§āļĨāļēāđāļāļĨāļĩāđāļĒāļāļĩāđāđāļāđāļŠāļģāļŦāļĢāļąāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢāļāļ·āļ 69.60 āļ§āļīāļāļēāļāļĩ āđāļĨāļ° 2) āļāļĢāļ°āļŠāļīāļāļāļīāļ āļēāļāđāļāļĒāļĢāļ§āļĄāļāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢāđāļāđāļēāļāļąāļ 99.57 % āļāļēāļĢāļ§āļīāđāļāļĢāļēāļ°āļŦāđāļāļļāļāļāļļāđāļĄāļāļļāļāļāļēāļāļāđāļēāļāđāļĻāļĢāļĐāļāļĻāļēāļŠāļāļĢāđāļ§āļīāļĻāļ§āļāļĢāļĢāļĄ āļāđāļāļāļļāļāļāļēāļĢāļŠāļĢāđāļēāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢāđāļāđāļēāļāļąāļ 75,000 āļāļēāļ āđāļĨāļ°āļāđāļāļāļļāļāđāļāļĢāļāļąāļāđāļāđāđāļāđāļāđāļāļāļļāļāļāļēāļĢāļŦāļąāđāļāđāļāđāļēāļāļąāļ 1.13 āļāļēāļ/āļāļīāđāļĨāļāļĢāļąāļĄ āļāļĢāļīāļĄāļēāļāļāļēāļĢāļāļĨāļīāļāđāļāđāļēāļāļąāļ 12,000 āļāļīāđāļĨāļāļĢāļąāļĄ/āđāļāļ·āļāļ āļāļģāļŦāļāđāļēāļĒāļāļīāđāļĨāļāļĢāļąāļĄāļĨāļ° 150 āļāļēāļ āļāļāļ§āđāļēāļāļļāļāļāļļāđāļĄāļāļļāļāđāļāđāļēāļāļąāļ 503 āļāļīāđāļĨāļāļĢāļąāļĄ āļĢāļ°āļĒāļ°āđāļ§āļĨāļēāļāļēāļĢāļāļ·āļāļāļļāļāļāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢ āļŠāļēāļĄāļēāļĢāļāļāļ·āļāļāļļāļāđāļāđāļ āļēāļĒāđāļāļĢāļ°āļĒāļ°āđāļ§āļĨāļēāļāļĢāļ°āļĄāļēāļ 1 āđāļāļ·āļāļ āļāļ°āļāļģāđāļŦāđāļ§āļīāļŠāļēāļŦāļāļīāļāļāļļāļĄāļāļāļāļ°āļĄāļĩāļĢāļēāļĒāđāļāđ 1,800,000 āļāļēāļ/āđāļāļ·āļāļ   āļāļēāļāļ§āļīāļāļąāļĒāļĄāļĩāļ§āļąāļāļāļļāļāļĢāļ°āļŠāļāļāđāđāļāļ·āđāļ 1) āļŠāļĢāđāļēāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢ āļĢāļ°āļāļąāļāļ§āļīāļŠāļēāļŦāļāļīāļāļāļļāļĄāļāļāđāļāļāļ·āđāļāļāļĩāđāļāļąāļāļŦāļ§āļąāļāļŠāļĢāļ°āđāļāđāļ§Â            2) āļŦāļēāļāļĢāļ°āļŠāļīāļāļāļīāļ āļēāļāļāļēāļĢāļāļģāļāļēāļāļāļĩāđāđāļŦāļĄāļēāļ°āļŠāļĄāļāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢ āļāļđāđāļ§āļīāļāļąāļĒāļāļķāļāđāļāđāļāļāļāđāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢ āđāļĨāļ·āļāļāđāļāđāļ§āļąāļŠāļāļļāđāļāļĢāļāļŠāļĢāđāļēāļāđāļāđāļāļ§āļąāļŠāļāļļāļŠāđāļāļāđāļĨāļŠ SUS 304 āđāļĨāļ°āđāļāđāļĄāļāđāļāļāļĢāđāđāļāļāđāļēāđāļāđāļāļāđāļāļāļģāļĨāļąāļāļāļāļēāļ 1 āđāļĢāļāļĄāđāļē āļāļąāļāļāļģāļĨāļąāļāļāđāļ§āļĒāļāļđāļĨāđāļĨāļĒāđ āļŠāļēāļĒāļāļēāļ āļĢāļāļāļāļ§āļēāļĄāđāļĢāđāļ§āļāļĩāđāđāļāđāļāļ·āļ 846 āļĢāļāļāļāđāļāļāļēāļāļĩ āđāļĨāļ°āđāļĨāļ·āļāļāđāļāđāđāļāļĄāļĩāļāļŦāļąāđāļāđāļāļ 2 āđāļāļĄāļĩāļ āđāļāļĒāđāļāđāļŦāļĨāļąāļāļāļēāļĢāļ§āļīāļĻāļ§āļāļĢāļĢāļĄāļāļēāļĄāļāļĪāļĐāļāļĩāđāļĢāļāđāļāļ·āļāļāļāļēāļāļāļēāļĢāļŦāļĄāļļāļāđāļŦāļ§āļĩāđāļĒāļāđāļāļĄāļĩāļ āļāļĢāļīāļĄāļēāļāļāļēāļĢāļāļĨāļīāļāļāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢāļāļ·āļ 50 āļāļīāđāļĨāļāļĢāļąāļĄ/āļāļąāđāļ§āđāļĄāļ āđāļĨāļ°āđāļāđāļĻāļķāļāļĐāļēāļŦāļēāļāļĢāļ°āļŠāļīāļāļāļīāļ āļēāļāļāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢ āđāļāļĒāļāļēāļĢāļāļāļĨāļāļāļŦāļąāđāļ 10 āļāļĢāļąāđāļ āļāļĢāļąāđāļāļĨāļ° 1,000 āļāļĢāļąāļĄ āļāļĨāļāļĩāđāđāļāđāļāļēāļāļāļēāļĢāļŦāļąāđāļāļāļ·āļ āļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢāļĄāļĩāļāļāļēāļāļāļ§āļēāļĄāļĒāļēāļ§āļāđāļģāļāļ§āđāļē 2 āļāļīāđāļ§ āļāļēāļĄāļāļ§āļēāļĄāļāđāļāļāļāļēāļĢāļāļāļāļ§āļīāļŠāļēāļŦāļāļīāļāļāļļāļĄāļāļ āļĢāļ°āļĒāļ°āđāļ§āļĨāļēāđāļāļĨāļĩāđāļĒāļāļĩāđāđāļāđāļŠāļģāļŦāļĢāļąāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢāļāļ·āļ 69.60 āļ§āļīāļāļēāļāļĩ āđāļĨāļ°āļāļĢāļ°āļŠāļīāļāļāļīāļ āļēāļāđāļāļĒāļĢāļ§āļĄāļāļāļāđāļāļĢāļ·āđāļāļāļŦāļąāđāļāļāđāļēāļāļ°āļĨāļēāļĒāđāļāļĢāđāļāđāļēāļāļąāļ 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Evaluating the impact of Brexit on the pharmaceutical industry.
INTRODUCTION: The UK Pharmaceutical Industry is arguably one of the most important industries to consider in the negotiations following the Brexit vote. Providing tens of thousands of jobs and billions in tax revenue and research investment, the importance of this industry cannot be understated. At stake is the global leadership in the sector, which produces some of the field's most influential basic science and translation work. However, interruptions and losses may occur at multiple levels, affecting patients, researchers, universities, companies and government. GOALS: By understanding the current state of pharmaceutical sector, the potential effect of leaving the European Union (EU) on this successful industry can be better understood. This paper aims to address the priorities for negotiations by collating the analyses of professionals in the field, leading companies and non-EU member states. RESEARCH METHODS: A government healthcare policy advisor and Chief Science Officer (CSO) for a major pharmaceutical firm were consulted to scope the paper. In these discussions, five key areas were identified: contribution, legislative processes, regulatory processes, research and outcomes, commercial risk. Multiple search engines were utilised for selecting relevant material, predominantly PubMed and Google Scholar. To supplement this information, Government documents were located using the "GOV.UK" publications tool, and interviews and commentaries were found through the Google News search function. CONCLUSION: With thorough investigation of the literature, we propose four foundations in the advancement of negotiations. These prioritise: negotiation of 'associated country' status, bilaterally favourable trade agreements, minimal interruption to regulatory bodies and special protection for the movement of workforce in the life sciences industry
Negative affect, stress, and smoking in college students: unique associations independent of alcohol and marijuana use
a b s t r a c t a r t i c l e i n f o Introduction: Stress and negative affect (NA) figure prominently in theoretical models of smoking initiation, maintenance and relapse, yet few studies have examined these associations among college students. Further complicating examination of these associations, smoking often occurs in the context of other substance use (e.g., alcohol, marijuana) in college populations. Thus, it remains unclear whether stress and NA are associated with cigarette use among college students, and if so, whether these associations are evident after controlling for effects of other substance use. The goals of this study were: a) to examine whether several aspects of stress (objective events, subjective experiences) and NA (sad mood, general emotional distress) were associated with cigarette smoking among college students and b) whether associations remained after accounting for alcohol and marijuana use. Sample: A large sample of college freshmen (N = 633) followed longitudinally over 35 weeks via internet assessments. Results: Results of hierarchical linear modeling demonstrated that measures of subjective stress and NA were positively related to cigarette use, whereas measures of objective stressful events were negatively related to cigarette use. When alcohol and marijuana use were added to the models, associations between smoking and stress/NA were diminished. Associations between NA and smoking remained significant; however, associations between subjective stress/stressful events and smoking were no longer significant. Conclusions: This is the first study to comprehensively examine links between subjective and objective measures of stress and smoking behavior among college students while also considering the influence of other substance use. Negative affect was the most robust correlate of smoking among college students. Subjective and objective stress do not appear to be strongly associated with college smoking above and beyond alcohol and marijuana use. Stress may not be an important etiological factor for relatively low levels of cigarette use among college students. Given that relations between NA/stress and cigarette smoking were diminished when concurrent alcohol and marijuana use was considered, it is imperative for future studies of college students to consider other substance use
Need for recovery amongst emergency physicians in the UK and Ireland: a cross-sectional survey.
OBJECTIVES: To determine the need for recovery (NFR) among emergency physicians and to identify demographic and occupational characteristics associated with higher NFR scores. DESIGN: Cross-sectional electronic survey. SETTING: Emergency departments (EDs) (n=112) in the UK and Ireland. PARTICIPANTS: Emergency physicians, defined as any registered physician working principally within the ED, responding between June and July 2019. MAIN OUTCOME MEASURE: NFR Scale, an 11-item self-administered questionnaire that assesses how work demands affect intershift recovery. RESULTS: The median NFR Score for all 4247 eligible, consented participants with a valid NFR Score was 70.0 (95% CI: 65.5 to 74.5), with an IQR of 45.5-90.0. A linear regression model indicated statistically significant associations between gender, health conditions, type of ED, clinical grade, access to annual and study leave, and time spent working out-of-hours. Groups including male physicians, consultants, general practitioners (GPs) within the ED, those working in paediatric EDs and those with no long-term health condition or disability had a lower NFR Score. After adjusting for these characteristics, the NFR Score increased by 3.7 (95% CI: 0.3 to 7.1) and 6.43 (95% CI: 2.0 to 10.8) for those with difficulty accessing annual and study leave, respectively. Increased percentage of out-of-hours work increased NFR Score almost linearly: 26%-50% out-of-hours work=5.7 (95% CI: 3.1 to 8.4); 51%-75% out-of-hours work=10.3 (95% CI: 7.6 to 13.0); 76%-100% out-of-hours work=14.5 (95% CI: 11.0 to 17.9). CONCLUSION: Higher NFR scores were observed among emergency physicians than reported in any other profession or population to date. While out-of-hours working is unavoidable, the linear relationship observed suggests that any reduction may result in NFR improvement. Evidence-based strategies to improve well-being such as proportional out-of-hours working and improved access to annual and study leave should be carefully considered and implemented where feasible
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Psychological distress and trauma in doctors providing frontline care during the COVID-19 pandemic in the United Kingdom and Ireland: a prospective longitudinal survey cohort study.
OBJECTIVES: The psychological impact of the COVID-19 pandemic on doctors is a significant concern. Due to the emergence of multiple pandemic waves, longitudinal data on the impact of COVID-19 are vital to ensure an adequate psychological care response. The primary aim was to assess the prevalence and degree of psychological distress and trauma in frontline doctors during the acceleration, peak and deceleration of the COVID-19 first wave. Personal and professional factors associated with psychological distress are also reported. DESIGN: A prospective online three-part longitudinal survey. SETTING: Acute hospitals in the UK and Ireland. PARTICIPANTS: Frontline doctors working in emergency medicine, anaesthetics and intensive care medicine during the first wave of the COVID-19 pandemic in March 2020. PRIMARY OUTCOME MEASURES: Psychological distress and trauma measured using the General Health Questionnaire-12 and the Impact of Events-Revised. RESULTS: The initial acceleration survey distributed across networks generated a sample of 5440 doctors. Peak and deceleration response rates from the original sample were 71.6% (n=3896) and 56.6% (n=3079), respectively. Prevalence of psychological distress was 44.7% (n=1334) during the acceleration, 36.9% (n=1098) at peak and 31.5% (n=918) at the deceleration phase. The prevalence of trauma was 23.7% (n=647) at peak and 17.7% (n=484) at deceleration. The prevalence of probable post-traumatic stress disorder was 12.6% (n=343) at peak and 10.1% (n=276) at deceleration. Worry of family infection due to clinical work was the factor most strongly associated with both distress (R2=0.06) and trauma (R2=0.10). CONCLUSION: Findings reflect a pattern of elevated distress at acceleration and peak, with some natural recovery. It is essential that policymakers seek to prevent future adverse effects through (a) provision of vital equipment to mitigate physical and psychological harm, (b) increased awareness and recognition of signs of psychological distress and (c) the development of clear pathways to effective psychological care. TRIAL REGISTRATION NUMBER: ISRCTN10666798
Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.We thank four reviewers and the handling editor for helpful comments on previous versions of our manuscript. We are grateful to the members of the DrosEU and DrosRTEC consortia for their long-standing support, collaboration, and for discussion. DrosEU was funded by a Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB). M.K. was supported by the Austrian Science Foundation (grant no. FWF P32275); J.G. by the European Research Council (ERC) under the European Unionâs Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900) and by the Spanish Ministry of Science and Innovation (BFU-2011-24397); T.F. by the Swiss National Science Foundation (SNSF grants PP00P3_133641, PP00P3_165836, and 31003A_182262) and a Mercator Fellowship from the German Research Foundation (DFG), held as a EvoPAD Visiting Professor at the Institute for Evolution and Biodiversity, University of MÞnster; AOB by the National Institutes of Health (R35 GM119686); M.K. by Academy of Finland grant 322980; V.L. by Danish Natural Science Research Council (FNU) (grant no. 4002-00113B); FS Deutsche Forschungsgemeinschaft (DFG) (grant no. STA1154/4-1), Project 408908608; J.P. by the Deutsche Forschungsgemeinschaft Projects 274388701 and 347368302; A.U. by FPI fellowship (BES-2012-052999); ET Israel Science Foundation (ISF) (grant no. 1737/17); M.S.V., M.S.R. and M.J. by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178); A.P., K.E. and M.T. by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200007); and TM NSERC grant RGPIN-2018-05551. The authors acknowledge Research Computing at The University of Virginia for providing computational resources and technical support that have contributed to the results reported within this publication (https://rc.virginia.edu, last accessed September 6, 2021)
Drosophila evolution over space and time (DEST):A new population genomics resource
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations inâ>â20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.DrosEU is funded by a Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB). MK (M. Kapun) was supported by the Austrian Science Foundation (grant no. FWF P32275); JG by the European Research Council (ERC) under the European Unionâs Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900) and by the Spanish Ministry of Science and Innovation (BFU-2011-24397); TF by the Swiss National Science Foundation (SNSF grants PP00P3_133641, PP00P3_165836, and 31003A_182262) and a Mercator Fellowship from the German Research Foundation (DFG), held as a EvoPAD Visiting Professor at the Institute for Evolution and Biodiversity, University of MÞnster; AOB by the National Institutes of Health (R35 GM119686); MK (M. Kankare) by Academy of Finland grant 322980; VL by Danish Natural Science Research Council (FNU) grant 4002-00113B; FS Deutsche Forschungsgemeinschaft (DFG) grant STA1154/4-1, Project 408908608; JP by the Deutsche Forschungsgemeinschaft Projects 274388701 and 347368302; AU by FPI fellowship (BES-2012-052999); ET Israel Science Foundation (ISF) grant 1737/17; MSV, MSR and MJ by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178); AP, KE and MT by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200007); and TM NSERC grant RGPIN-2018-05551.Peer reviewe
Corrigendum to: Drosophila Evolution over Space and Time (DEST): a New Population Genomics Resource
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations inâ>â20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.DrosEU is funded by a Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB). MK (M. Kapun) was supported by the Austrian Science Foundation (grant no. FWF P32275); JG by the European Research Council (ERC) under the European Unionâs Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900) and by the Spanish Ministry of Science and Innovation (BFU-2011-24397); TF by the Swiss National Science Foundation (SNSF grants PP00P3_133641, PP00P3_165836, and 31003A_182262) and a Mercator Fellowship from the German Research Foundation (DFG), held as a EvoPAD Visiting Professor at the Institute for Evolution and Biodiversity, University of MÞnster; AOB by the National Institutes of Health (R35 GM119686); MK (M. Kankare) by Academy of Finland grant 322980; VL by Danish Natural Science Research Council (FNU) grant 4002-00113B; FS Deutsche Forschungsgemeinschaft (DFG) grant STA1154/4-1, Project 408908608; JP by the Deutsche Forschungsgemeinschaft Projects 274388701 and 347368302; AU by FPI fellowship (BES-2012-052999); ET Israel Science Foundation (ISF) grant 1737/17; MSV, MSR and MJ by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178); AP, KE and MT by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200007); and TM NSERC grant RGPIN-2018-05551.Peer reviewe
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