Biology subjects

Campbell, E.

Publications and source records attributed to Campbell, E..

6 recordsLinked to original sources

bioRxiv2018

Beyond financial conflicts of interest: Institutional oversight of faculty consulting agreements at schools of medicine and public health

ImportanceApproximately one-third of U.S. life sciences faculty engage in industry consulting. Despite reports that consulting contracts often impinge on faculty and university interests, institutional approaches to regulating consulting agreements are largely unknown.\n\nObjectiveTo investigate the nature of institutional oversight of faculty consulting contracts at U.S. schools of medicine and public health.\n\nDesignStructured telephone interviews with institutional administrators. Questions included the nature of oversight for faculty consulting agreements, if any, and views about consulting as a private versus institutional matter. Interviews were analyzed using a structured coding scheme.\n\nSettingAll accredited schools of medicine and public health in the U.S.\n\nParticipantsAdministrators responsible for faculty affairs were identified via internet searches and telephone and email follow-up. The 118 administrators interviewed represented 73% of U.S. schools of medicine and public health, and 75% of those invited to participate.\n\nInterventionStructured, 15-30 minute telephone interviews.\n\nMain outcomes and measuresPrevalence and type of institutional oversight; responses to concerning provisions in consulting agreements; perceptions of institutional oversight.\n\nResultsOne third of institutions (36%) required faculty to submit at least some agreements for institutional review and 36% reviewed contracts upon request, while 35% refused to review contracts. Among institutions with review, there was wide variation the issues covered. The most common topic was intellectual property rights (64%), while only 23% looked at publication rights and 19% for inappropriately broad confidentiality provisions. Six in ten administrators reported they had no power to prevent faculty from signing consulting agreements. Although most respondents identified institutional risks from consulting relationships, many maintained that consulting agreements are \"private.\"\n\nConclusions and relevanceOversight of faculty consulting agreements at U.S. schools of medicine and public health is inconsistent across institutions and usually not robust. The interests at stake suggest the need for stronger oversight.

scientific communication and education↗

bioRxiv2018

CliqueSNV: Scalable Reconstruction of Intra-Host Viral Populations from NGS Reads

Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to promptly adjust the patient's treatment plan preventing potential disease complications. Minority haplotypes can be identified using next-generation sequencing (NGS), but sequencing noise hinders accurate identification. The elimination of sequencing noise is a non-trivial task that still remains open. Here we propose CliqueSNV based on extracting pairs of statistically linked mutations from noisy reads. This effectively reduces sequencing noise and enables identifying minority haplotypes with the frequency below the sequencing error rate. We comparatively assess the performance of CliqueSNV using an in vitro mixture of nine haplotypes that were derived from the mutation profile of an existing HIV patient. We show that CliqueSNV can accurately assemble viral haplotypes with frequencies as low as 0.1% and maintains consistent performance across short and long bases sequencing platforms.

bioinformatics↗

bioRxiv2018

Cost-effectiveness of telephone-based weight loss support for patients with knee osteoarthritis: a pragmatic randomised controlled trial

BackgroundTelephone-based support offers a promising option to provide widely accessible and cost-effective weight loss care to the people with knee osteoarthritis who are overweight. While telephone-based interventions targeting weight loss are used routinely in the general populations, the cost-effectiveness of referring patients with knee osteoarthritis to these is unknown. The aim of this study was to assess the cost-effectiveness of referral to a telephone-based weight management and healthy lifestyle service for patients with knee osteoarthritis, who are overweight or obese, compared to usual care. MethodsWe randomised 120 patients with knee osteoarthritis to an intervention or usual care control group in a 1:1 ratio. Participants in the intervention group received a referral to an existing non-disease specific 6-month telephone-based weight management and healthy lifestyle service. The primary outcome of the study was quality-adjusted life years (QALYs). Secondary outcomes included pain intensity, disability, weight, and body mass index (BMI). Costs included intervention costs, healthcare utilisation costs (healthcare services and medication use) and absenteeism costs due to knee pain. The primary cost-effectiveness analysis was performed from the societal perspective. ResultsMean cost differences between groups (intervention minus control) were, $454 (95%CI: -2735 to 4206) for healthcare costs, $-36, (95%CI: -73 to 2) for medication costs, and $-13 (95%CI: -225 to 235) for absenteeism costs. The total mean difference in societal costs was $1022 (95%CI: -2201 to 4771). For all outcomes, the probability of the intervention being cost-effective compared with usual care was less than 0.33 at all willingness-to-pay values. ConclusionFrom a societal perspective, telephone-based weight loss support, provided using an existing non-disease specific 6-month weight management and healthy lifestyle service was not cost-effective in comparison with usual care for overweight and obese patients with knee osteoarthritis for QALYs, pain intensity, disability, weight, and BMI.

clinical trials↗

bioRxiv2018

Would an RRS by any other name sound as RAD?

Sampling markers throughout a genome with restriction enzymes emerged in the 2000s as reduced representation shotgun sequencing (RRS). Rapid advances in sequencing technology have since spurred modifications of RRS, giving rise to many derivatives with unique names, such as RADseq. But naming conventions have often been more creative than consistent, with unclear criteria for recognition as a unique method resulting in a proliferation of names characterized by ambiguity. We conducted a literature review to assess methodological and etymological relationships among 36 restriction enzyme-based methods, as well as rates of correct referencing of commonly-used methods. We identify several instances of methodological convergence or misattribution in the literature, and note that many published derivatives have modified only minor elements of parent protocols. We urge greater restraint in naming derivative methods, to strike a better balance between clarity, recognition of scientific innovation, and correct attribution.

genomics↗

bioRxiv2017

Effects of species invasion on population dynamics, vital rates, and life histories of the native species

Invasions occurring in natural environments provide the opportunity to study how vital rates change and life histories evolve in the presence of a competing species. In this work, we estimate differences in reproductive traits, individual growth trajectories, survival, life histories, and population dynamics between a native species living in allopatry and in sympatry with an invasive species of the same taxonomic Family. We used as a model system marble trout Salmo marmoratus (native species) and rainbow trout Oncorhynchus mykiss (non-native) living in the Idrijca River (Slovenia). An impassable waterfall separates the stream in two sectors only a few hundred meters apart: a downstream sector in which marble trout live in sympatry with rainbow trout and a upstream sector in which marble trout live in allopatry. We used an overarching modeling approach that uses tag-recapture and genetic data (> 2,500 unique marble and rainbow trout were sampled and SNP-genotyped) to reconstruct pedigrees, test for synchrony of population dynamics, and model survival and growth while accounting for individual heterogeneity in performance. The population dynamics of the two marble trout populations and of rainbow trout were overall synchronous. We found higher prevalence of younger parents, higher mortality, and lower population density in marble trout living in sympatry with rainbow trout than in marble trout living in allopatry. There were no differences in the average individual growth trajectories between the two marble trout populations. Faster life histories of marble trout living in sympatry with rainbow trout are consistent with predictions of life-history theory.

ecology↗

bioRxiv2017

A toolbox of immunoprecipitation-grade monoclonal antibodies against human transcription factors.

A key component to overcoming the reproducibility crisis in biomedical research is the development of readily available, rigorously validated and renewable protein affinity reagents. As part of the NIH Protein Capture Reagents Program (PCRP), we have generated a collection of 1406 highly validated, immunoprecipitation (IP) and/or immunoblotting (IB) grade, mouse monoclonal antibodies (mAbs) to 736 human transcription factors. We used HuProt human protein microarrays to identify mAbs that recognize their cognate targets with exceptional specificity. Using an integrated production and validation pipeline, we validated these mAbs in multiple experimental applications, and have distributed them to the Developmental Studies Hybridoma Bank (DSHB) and several commercial suppliers. This study allowed us to perform a meta-analysis that identified critical variables that contribute to the generation of high quality mAbs. We find that using full-length antigens for immunization, in combination with HuProt analysis, provides the highest overall success rates. The efficiencies built into this pipeline ensure substantial cost savings compared to current standard practices.

biochemistry↗