Measuring and mitigating PCR bias in microbiota datasets.
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ABSTRACT:
SUBMITTER: Silverman JD
PROVIDER: S-EPMC8284789 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:IntroductionSimulation is a valuable and novel tool in the expanding approach to racism and bias education for medical practitioners. We present a simulation case focused on identifying and addressing the implicit bias of a consultant to teach bias mitigation skills and limit harm to patients and families.MethodsLearners were presented with a case of a classic toddler's fracture in an African American child. The learners interacted with an orthopedic resident who insisted on child welfare involvement, with nonspecific and increasingly biased concerns about the child/family. The learners were expected to identify that this case was not concerning for nonaccidental trauma and that the orthopedic resident was demonstrating bias. They were expected to communicate with both the resident and the parent effectively to defuse the situation and prevent harm from reaching the family. A debrief and an anonymous survey followed the case.ResultsSeventy-five learners participated, including pediatric and emergency medicine residents, fellows, attendings, and medical students. After the case, the majority of learners expressed confidence that they could recognize racial bias in the care of a patient (90%), ensure patient care was not influenced by racial bias (88%), and utilize a tool to frame a concern about bias (79%).DiscussionParticipants felt that this simulation was relevant and effective and overall left the experience feeling confident in their abilities to identify and manage racially biased patient care. This anti-racist simulation offers an important skill-building opportunity that has been well received by learners.
| S-EPMC10507144 | biostudies-literature
Project description:BackgroundThe lung allocation system in the U.S. prioritizes lung transplant candidates based on estimated pre- and post-transplant survival via the Lung Allocation Scores (LAS). However, these models do not account for selection bias, which results from individuals being removed from the waitlist due to receipt of transplant, as well as transplanted individuals necessarily having survived long enough to receive a transplant. Such selection biases lead to inaccurate predictions.MethodsWe used a weighted estimation strategy to account for selection bias in the pre- and post-transplant models used to calculate the LAS. We then created a modified LAS using these weights, and compared its performance to that of the existing LAS via time-dependent receiver operating characteristic (ROC) curves, calibration curves, and Bland-Altman plots.ResultsThe modified LAS exhibited better discrimination and calibration than the existing LAS, and led to changes in patient prioritization.ConclusionsOur approach to addressing selection bias is intuitive and can be applied to any organ allocation system that prioritizes patients based on estimated pre- and post-transplant survival. This work is especially relevant to current efforts to ensure more equitable distribution of organs.
| S-EPMC8454078 | biostudies-literature
Project description:Ideological media bias is increasingly central to the study of politics. Yet, past literature often assumes that the ideological bias of any outlet, at least in the short term, is static and exogenous to the political process. We challenge this assumption. We use longitudinal data from the Stanford Cable News Analyzer (2010 to 2021), which reports the screen time of various political actors on cable news, and quantify the partisan leaning of those actors using their past campaign donation behavior. Using one instantiation of media bias-the mean ideology of political actors on a channel, i.e., visibility bias-we examine weekly, within-day, and program-level estimates of media bias. We find that media bias is highly dynamic even in the short term and that the heightened polarization between TV channels over time was mostly driven by the prime-time shows.
| S-EPMC9371639 | biostudies-literature
Project description:Student evaluations of teaching are widely believed to contain gender bias. In this study, we conduct a randomized experiment with the student evaluations of teaching in four classes with large enrollments, two taught by male instructors and two taught by female instructors. In each of the courses, students were randomly assigned to either receive the standard evaluation instrument or the same instrument with language intended to reduce gender bias. Students in the anti-bias language condition had significantly higher rankings of female instructors than students in the standard treatment. There were no differences between treatment groups for male instructors. These results indicate that a relatively simple intervention in language can potentially mitigate gender bias in student evaluation of teaching.
| S-EPMC6519786 | biostudies-literature
Project description:As transposon sequencing (TnSeq) assays have become prolific in the microbiology field, it is of interest to scrutinize their potential drawbacks. TnSeq results are determined by counting transposon insertions following the PCR-based enrichment and subsequent deep sequencing of transposon insertions. Here we explore the possibility that PCR amplification of transposon insertions in a TnSeq library skews the results by introducing bias into the detection and/or enumeration of insertions. We compared the detection and frequency of mapped insertions when altering the number of PCR cycles in the enrichment step. In addition, we devised and validated a novel, PCR-free TnSeq method where the insertions are enriched via CRISPR/Cas9-targeted transposon cleavage and subsequent Oxford Nanopore sequencing. These PCR-based and PCR-free experiments demonstrate that, overall, PCR amplification does not significantly bias the results of the TnSeq assay insofar as insertions in the majority of genes represented in our library were similarly detected regardless of PCR cycle number and whether or not PCR amplification was employed. However, the detection of a small subset of genes which had been previously described as essential is indeed sensitive to the number of PCR cycles. We conclude that PCR-based enrichment of transposon insertions in a TnSeq assay is reliable but researchers interested in profiling essential genes should carefully weigh the number of amplification cycles employed in their library preparation protocols. In addition, we present a PCR-free TnSeq alternative that is comparable to traditional PCR-based methods although the latter remain superior owing to their accessibility and high sequencing depth.
2020-12-21 | GSE162988 | GEO
Project description:Investigating PCR bias in TnSeq
| PRJNA684144 | ENA
Project description:PCR-Bias in multi-template PCR: validation data
| PRJEB77604 | ENA
Project description:Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved priming sites, (2) increasing PCR template concentration, (3) reducing PCR cycle number or (4) avoiding locus specific amplification by directly sequencing genomic DNA. Amplification bias is reduced considerably by degenerate primers or targeting amplicons with conserved priming sites. Surprisingly, a reduction of PCR cycles did not have a strong effect on amplification bias. The association of taxon abundance and read count was actually less predictable with fewer cycles. Even a complete exclusion of locus specific amplification did not exclude bias. Copy number variation of the target loci may be another explanation for read abundance differences between taxa, which would affect amplicon based and PCR free methods alike. As read abundance biases are taxon specific and predictable, the application of correction factors allows abundance estimates.
| S-EPMC5732254 | biostudies-literature
Project description:We amplified DNA fragments randomly sheared from PER1 BAC library with four different PCR cycles (3, 6, 12, and 18 cycles). We report the effect of Gibbs free energy bias to coverage significantly increases with additional number of PCR cycles, especially for fragments with high Gibbs free energy (usually corresponding to low GC content).
2020-05-06 | GSE149914 | GEO
Project description:While several methods have been proposed to assess the influence of continuous visual cues in parallel numerosity estimation, the impact of temporal magnitudes on sequential numerosity judgments has been largely ignored. To overcome this issue, we extend a recently proposed framework that makes it possible to separate the contribution of numerical and non-numerical information in numerosity comparison by introducing a novel stimulus space designed for sequential tasks. Our method systematically varies the temporal magnitudes embedded into event sequences through the orthogonal manipulation of numerosity and two latent factors, which we designate as "duration" and "temporal spacing". This allows us to measure the contribution of finer-grained temporal features on numerosity judgments in several sensory modalities. We validate the proposed method on two different experiments in both visual and auditory modalities: results show that adult participants discriminated sequences primarily by relying on numerosity, with similar acuity in the visual and auditory modality. However, participants were similarly influenced by non-numerical cues, such as the total duration of the stimuli, suggesting that temporal cues can significantly bias numerical processing. Our findings highlight the need to carefully consider the continuous properties of numerical stimuli in a sequential mode of presentation as well, with particular relevance in multimodal and cross-modal investigations. We provide the complete code for creating sequential stimuli and analyzing participants' responses.
| S-EPMC11362239 | biostudies-literature