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Busy machines
Bursting with bright illustrations of tractors, trucks, diggers and emergency vehicles, busy little people will love exploring this big book of busy machines. With engaging text, action-packed scenes and delightful characters throughout, there's plenty for vehicle fans to look at, talk about and discover on every page.
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Improving visualization of the cervix during pelvic exams: A simulation using a physical model of the speculum and human vagina as a steppingstone to reducing disparities in gynecological cancers
Pelvic exams are frequently complicated by collapse of the lateral vaginal walls, obstructing the view of the cervix. To overcome this, physicians frequently repurpose a glove or a condom as a sheath placed over the speculum blades to retract the lateral vaginal walls. Despite their regular use in clinical practice, little research has been done comparing the relative efficacy of these methods. Better visualization of the cervix can benefit patients by decreasing examination-related discomfort, improving cancer screening accuracy, and preventing the need to move the examination to the operating room under general anesthesia. This study presents a physical model that simulates vaginal pressure being exerted around a speculum. Using it, we conduct controlled experiments comparing the efficacy of different condom types, glove materials, glove sizes, and techniques to place gloves on the speculum. The results show that the best sheath is the middle finger of nitrile-material gloves. They provide adequate lateral wall retraction without significantly restricting the opening of the speculum. In comparison, condoms provide a smaller amount of retraction due to loosely fitting the speculum. They may still be a reasonable option for a different speculum size. However, vinyl-material gloves are an impractical option for sheaths; they greatly restrict speculum opening, occasionally even breaking the speculum, which overcome its retraction benefits. Glove size, condom brand, and condom material (latex vs polyisoprene) had minimal impact. This study serves as a guide for clinicians as they use easily accessible tools to perform difficult pelvic exams. We recommend that physicians consider nitrile gloves as the preferred option for a sheath around a speculum. Additionally, this study demonstrates proof-of-concept of a physical model that quantitatively describes different materials on their ability to improve cervical access. This model can be used in future research with more speculum and material combinations, including with materials custom-designed for vaginal retraction.
Journal Article
DADA2: High-resolution sample inference from Illumina amplicon data
DADA2 is an open-source software package that denoises and removes sequencing errors from Illumina amplicon sequence data to distinguish microbial sample sequences differing by as little as a single nucleotide.
We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (
https://github.com/benjjneb/dada2
). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected
Lactobacillus crispatus
variants.
Journal Article
Changes in Mental Health and Treatment, 1997–2017
Mental health outcomes have shown dramatic changes over the past half-century, yet these trends are still underexplored. I utilize an age-period-cohort analysis of the National Health Interview Survey from 1997 to 2017 (N = 627,058) to disentangle trends in mental health outcomes in the United States over time. Specifically, I leverage the contrast between reported psychological distress and rates of mental health treatment to isolate which has changed, how, and for whom. There is little evidence that psychological distress is worsening over time. Yet, treatment seeking has increased over the past 20 years. The increase in treatment seeking is best modeled as a period effect, providing initial evidence that the historical context has influenced responses to mental health over time for Americans of all ages and birth cohorts. I conclude with potential mechanisms and implications for future mental health research.
Journal Article
Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar
Purpose:
Data sharing through ClinVar offers a unique opportunity to identify interpretation differences between laboratories. As part of a ClinGen initiative, four clinical laboratories (Ambry, GeneDx, Partners Healthcare Laboratory for Molecular Medicine, and University of Chicago Genetic Services Laboratory) collaborated to identify the basis of interpretation differences and to investigate if data sharing and reassessment resolve interpretation differences by analyzing a subset of variants.
Methods:
ClinVar variants with submissions from at least two of the four participating laboratories were compared. For a subset of identified differences, laboratories documented the basis for discordance, shared internal data, independently reassessed with the American College of Medical Genetics and Genomics–Association for Molecular Pathology (ACMG-AMP) guidelines, and then compared interpretations.
Results:
At least two of the participating laboratories interpreted 6,169 variants in ClinVar, of which 88.3% were initially concordant. Laboratories reassessed 242/724 initially discordant variants, of which 87.2% (211) were resolved by reassessment with current criteria and/or internal data sharing; 12.8% (31) of reassessed variants remained discordant owing to differences in the application of the ACMG-AMP guidelines.
Conclusion:
Participating laboratories increased their overall concordance from 88.3 to 91.7%, indicating that sharing variant interpretations in ClinVar—thereby allowing identification of differences and motivation to resolve those differences—is critical to moving toward more consistent variant interpretations.
Genet Med
advance online publication 09 March 2017
Journal Article
Millimeter-scale topography facilitates coral larval settlement in wave-driven oscillatory flow
Larval settlement in wave-dominated, nearshore environments is the most critical life stage for a vast array of marine invertebrates, yet it is poorly understood and virtually impossible to observe in situ . Using a custom-built flume tank that mimics the oscillatory fluid flow over a shallow coral reef, we isolated the effect of millimeter-scale benthic topography and showed that it increases the settlement of slow-swimming coral larvae by an order of magnitude relative to flat substrates. Particle tracking velocimetry of flow fields revealed that millimeter-scale ridges introduced regions of flow recirculation that redirected larvae toward the substrate surface and decreased the local fluid speed, effectively increasing the window of time for larvae to settle. Regions of recirculation were quantified using the Q -criterion method of vortex identification and correlated with the settlement locations of larvae for the first time. In agreement with experiments, computational fluid dynamics modeling and agent-based larval simulations also showed significantly higher settlement onto ridged substrates. Additionally, in contrast to previous reports on the effect of micro-scale substrate topography, we found that these topographies did not produce key hydrodynamic features linked to increased settlement. These findings highlight how physics-based substrate design can create new opportunities to increase larval recruitment for ecosystem restoration.
Journal Article