A Tour of the Basic Reproductive Number and the Next Generation of Researchers
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ABSTRACT:
SUBMITTER: Callender Highlander H
PROVIDER: S-EPMC7123362 | biostudies-literature | 2020 Jan
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:As highlighted in recent reports published by the Physician-Scientist Workforce Working Group at the National Institutes of Health, the percentage of physicians conducting research has declined over the past decade. Various programs have been put in place to support and develop current medical student interest in research to alleviate this shortage, including The Vanderbilt University School of Medicine Medical Scholars Program (MSP). This report outlines the long-term program goals and short-term outcomes on career development of MSP alumni, to shed light on the effectiveness of research training programs during undergraduate medical training to inform similar programs in the United States. METHODS:MSP alumni were asked to complete an extensive survey assessing demographics, accomplishments, career progress, future career plans, and MSP program evaluation. RESULTS:Fifty-five (81%) MSP alumni responded, among whom 12 had completed all clinical training. The demographics of MSP alumni survey respondents are similar to those of all Vanderbilt medical students and medical students at all other Association of American Medical College (AAMC) medical schools. MSP alumni published a mean of 1.9 peer-reviewed manuscripts (95% CI:1.2, 2.5), and 51% presented at national meetings. Fifty-eight percent of respondents reported that MSP participation either changed their career goals or helped to confirm or refine their career goals. CONCLUSIONS:Results suggest that the MSP program both prepares students for careers in academic medicine and influences their career choices at an early juncture in their training. A longer follow-up period is needed to fully evaluate the long-term outcomes of some participants.
| S-EPMC5753449 | biostudies-literature
Project description:Dissemination and implementation (D&I) research is a relatively young discipline, underscoring the importance of training and career development in building and sustaining the field. As such, D&I research faces several challenges in designing formal training programs and guidance for career development. A cohort of early-stage investigators (ESI) recently involved in an implementation research training program provided a resource for formative data in identifying needs and solutions around career development.Responses outlined fellows' perspectives on the perceived usefulness and importance of, as well as barriers to, developing practice linkages, acquiring additional methods training, academic advancement, and identifying institutional supports. Mentorship was a cross-cutting issue and was further discussed in terms of ways it could foster career advancement in the context of D&I research.Advancing an emerging field while simultaneously developing an academic career offers a unique challenge to ESIs in D&I research. This article summarizes findings from the formative data that outlines some directions for ESIs and provides linkages to the literature and other resources on key points.
| S-EPMC3626831 | biostudies-other
Project description:Reducing health disparities is a national public health priority. Latinos represent the largest racial/ethnic minority group in the United States and suffer disproportionately from poor health outcomes, including cardiovascular disease risk. Academic training programs are an opportunity for reducing health disparities, in part by increasing the diversity of the public health workforce and by incorporating training designed to develop a skill set to address health disparities. This article describes the Training and Career Development Program at the UCLA Center for Population Health and Health Disparities: a multilevel, transdisciplinary training program that uses a community-engaged approach to reduce cardiovascular disease risk in two urban Mexican American communities. Results suggest that this program is effective in enhancing the skill sets of traditionally underrepresented students to become health disparities researchers and practitioners.
| S-EPMC5548049 | biostudies-other
Project description:ProblemDissemination and implementation (D&I) science provides the tools needed to close the gap between known intervention strategies and their effective application. The authors report on the Mentored Training for Dissemination and Implementation Research in Cancer (MT-DIRC) program-a D&I training program for postdoctoral or early-career cancer prevention and control scholars.ApproachMT-DIRC was a 2-year training institute in which fellows attended 2 annual Summer Institutes and other conferences and received didactic, group, and individual instruction; individualized mentoring; and other supports (e.g., pilot funding). A quasi-experimental design compared changes in 3 areas: mentoring, skills, and network composition. To evaluate mentoring and D&I skills, data from fellows on their mentors' mentoring competencies, their perspectives on the importance of and satisfaction with mentoring priority areas, and their self-rated skills in D&I competency domains were collected. Network composition data were collected from faculty and fellows for 3 core social network domains: contact, mentoring, and collaboration. Paired t tests (mentoring), linear mixed models (skills), and descriptive analyses (network composition) were performed.OutcomesMentors were rated as highly competent across all mentoring competencies, and each mentoring priority area showed reductions in gaps between satisfaction and importance between the 6 and 18 months post-first Summer Institute. Fellows' self-rated skills in D&I competencies improved significantly in all domains over time (range: 42.5%-52.9% increase from baseline to 18 months post-first Summer Institute). Mentorship and collaboration networks grew over time, with the highest number of collaboration network ties for scholarly manuscripts (n = 199) in 2018 and for research projects (n = 160) in 2019.Next stepsBuilding on study findings and existing literature, mentored training of scholars is an important approach for building D&I skills and networks, and thus to better applying the vast amount of available intervention evidence to benefit cancer control.
| S-EPMC7769184 | biostudies-literature
Project description:The basic reproductive number (R0) is a function of contact rates among individuals, transmission probability, and duration of infectiousness. We sought to determine the association between population density and R0 of SARS-CoV-2 across U.S. counties. We conducted a cross-sectional analysis using linear mixed models with random intercept and fixed slopes to assess the association of population density and R0, and controlled for state-level effects using random intercepts. We also assessed whether the association was differential across county-level main mode of transportation percentage as a proxy for transportation accessibility, and adjusted for median household income. The median R0 among the United States counties was 1.66 (IQR: 1.35-2.11). A population density threshold of 22 people/km2 was needed to sustain an outbreak. Counties with greater population density have greater rates of transmission of SARS-CoV-2, likely due to increased contact rates in areas with greater density. An increase in one unit of log population density increased R0 by 0.16 (95% CI: 0.13 to 0.19). This association remained when adjusted for main mode of transportation and household income. The effect of population density on R0 was not modified by transportation mode. Our findings suggest that dense areas increase contact rates necessary for disease transmission. SARS-CoV-2 R0 estimates need to consider this geographic variability for proper planning and resource allocation, particularly as epidemics newly emerge and old outbreaks resurge.
| S-EPMC8059825 | biostudies-literature
Project description:BackgroundA copy number variation (CNV) is a difference between genotypes in the number of copies of a genomic region. Next generation sequencing (NGS) technologies provide sensitive and accurate tools for detecting genomic variations that include CNVs. However, statistical approaches for CNV identification using NGS are limited. We propose a new methodology for detecting CNVs using NGS data. This method (henceforth denoted by m-HMM) is based on a hidden Markov model with emission probabilities that are governed by mixture distributions. We use the Expectation-Maximization (EM) algorithm to estimate the parameters in the model.ResultsA simulation study demonstrates that our proposed m-HMM approach has greater power for detecting copy number gains and losses relative to existing methods. Furthermore, application of our m-HMM to DNA sequencing data from the two maize inbred lines B73 and Mo17 to identify CNVs that may play a role in creating phenotypic differences between these inbred lines provides results concordant with previous array-based efforts to identify CNVs.ConclusionsThe new m-HMM method is a powerful and practical approach for identifying CNVs from NGS data.
| S-EPMC4021345 | biostudies-literature
Project description:The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals. falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. A modified Bayesian information criterion is used to guide model selection for determining the number of copy number events. Falcon is evaluated on in silico spike-in data and applied to the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allows us to draw detailed conclusions regarding the clonal history of the individual's colon cancer.
| S-EPMC4344483 | biostudies-literature
Project description:BackgroundThe aim of this study was to evaluate the effectiveness of the Arthritis Research UK funded graduate internship scheme for podiatrists and to explore the experiences of interns and mentors.MethodsNine new graduates completed the internship programme (July 2006-June 2010); six interns and two mentors participated in this study. The study was conducted in three phases. Phase 1: quantitative survey of career and research outcomes for interns. Phase 2 and 3: qualitative asynchronous interviews through email to explore the experiences of interns and mentors. Interpretive phenomenological analysis (IPA) of coded transcripts identified recurring themes.ResultsResearch outputs included ten peer reviewed publications with authorial contributions from interns, 23 conference abstract presentations and one subsequent 'Jewel in the Crown' award at the British Society for Rheumatology Conference. Career progression includes two National Institute for Health research (NIHR) PhD fellowships, two Arthritis Research UK PhD fellowships, one NIHR Master of Research fellowship and one specialist rheumatology clinical post. Two interns are members of NIHR and professional body committees.Seven important themes arose from the qualitative phases: perceptions of the internship pre-application; internship values; maximising personal and professional development; psychosocial components of the internship; the role of mentoring and networking; access to research career pathways; perceptions of future developments for the internship programme. The role of mentorship and the peer support network have had benefits that have persisted beyond the formal period of the scheme.ConclusionsThe internship model appears to have been perceived to have been valuable to the interns' careers and may have contributed significantly to the broader building of capacity in clinical research in foot and ankle rheumatology. We believe the model has potential to be transferable across health disciplines and on national and international scales.
| S-EPMC3637456 | biostudies-literature
Project description:Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ~55.6-Mbp sequence--476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (~52%, ?(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.
| S-EPMC3317159 | biostudies-literature
Project description:Despite their importance in gene innovation and phenotypic variation, duplicated regions have remained largely intractable owing to difficulties in accurately resolving their structure, copy number and sequence content. We present an algorithm (mrFAST) to comprehensively map next-generation sequence reads, which allows for the prediction of absolute copy-number variation of duplicated segments and genes. We examine three human genomes and experimentally validate genome-wide copy number differences. We estimate that, on average, 73-87 genes vary in copy number between any two individuals and find that these genic differences overwhelmingly correspond to segmental duplications (odds ratio = 135; P < 2.2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology.
| S-EPMC2875196 | biostudies-literature