Predictors of incident herpes simplex virus type 2 infections in young women at risk for unintended pregnancy in San Francisco.

BackgroundYoung women receiving family planning services are at risk for both unintended pregnancy and herpes simplex virus type 2 (HSV-2) infection.MethodsWe performed a secondary analysis using data from a previously published randomized controlled trial evaluating access to emergency contraception on reproductive health outcomes. Women aged 15 to 24 years were recruited from two Planned Parenthood clinics and two community health clinics in San Francisco. Demographic information and sexual history were obtained by interview. HSV-2 seropositivity was determined by fingerstick blood test. New pregnancies were measured by self-report, urine testing and medical chart review. Subjects were evaluated for incident HSV-2 infection and pregnancy at a 6-month follow-up appointment. Women who were pregnant or intending to become pregnant at enrolment were excluded.ResultsAt enrolment 2,104 women were screened for HSV-2 and 170 (8.1%) were seropositive. Eighty-seven percent of initially seronegative women completed the study (n = 1,672) and 73 (4.4%) became HSV-2 seropositive. HSV-2 seroincidence was 7.8 cases per 100 person-years. One hundred and seventeen women (7%) became pregnant and 7 (6%) of these had a seroincident HSV-2 infection during the study. After adjustment for confounders, predictors of incident HSV-2 infection were African American race and having multiple partners in the last six months. Condom use at last sexual encounter was protective.ConclusionHSV-2 seroincidence and the unintended pregnancy rate in young women were high. Providers who counsel women on contraceptive services and sexually transmitted infection prevention could play an expanded role in counselling women about HSV-2 prevention given the potential sequelae in pregnancy. The potential benefit of targeted screening and future vaccination against HSV-2 needs to be assessed in this population

Viral coinfection analysis using a MinHash toolkit

Abstract: Background: Human papillomavirus (HPV) is a common sexually transmitted infection associated with cervical cancer that frequently occurs as a coinfection of types and subtypes. Highly similar sublineages that show over 100-fold differences in cancer risk are not distinguishable in coinfections with current typing methods. Results: We describe an efficient set of computational tools, rkmh, for analyzing complex mixed infections of related viruses based on sequence data. rkmh makes extensive use of MinHash similarity measures, and includes utilities for removing host DNA and classifying reads by type, lineage, and sublineage. We show that rkmh is capable of assigning reads to their HPV type as well as HPV16 lineage and sublineages. Conclusions: Accurate read classification enables estimates of percent composition when there are multiple infecting lineages or sublineages. While we demonstrate rkmh for HPV with multiple sequencing technologies, it is also applicable to other mixtures of related sequences

Effects of relationship context on contraceptive use among young women

OBJECTIVES: To understand how relationship status influences contraceptive use among young people. STUDY DESIGN: Data were collected as part of a longitudinal study on hormonal contraception among unmarried adolescent and young women who wanted to avoid pregnancy for at least one year, recruited at family planning clinics in the San Francisco Bay area. Follow-up surveys were completed at 3, 6, and 12 months. Longitudinal analysis was used to examine whether relationship characteristics, including type and length of sexual relationship are associated with current use of effective contraception. RESULTS: Among women with a partner at baseline, 78%, 70%, and 61% had the same partner at 3, 6, and 12 months follow up, respectively. Women in casual relationships were less likely to use effective contraceptive methods, compared to women in consistent relationships (AOR=0.67, p<0.01). Women in new relationships (0–3 months) were less likely to use effective contraceptive methods (AOR=0.60, p<0.001) compared to women in relationships more than one year in length. Younger women (AOR=0.76, p<0.05), black women (AOR=0.67, p<0.05) and Latina women (AOR=0.73, p<0.05) were also significantly less likely to use effective contraception. These effects remained even after controlling for condom use. CONCLUSIONS: Relationship type and length are independently significantly associated with current effective contraceptive use among adolescent and young women. Women in casual relationships and new relationships were significantly less likely to use effective contraceptive methods. IMPLICATIONS: Family planning providers should discuss women’s relationship context and association with contraceptive use in order to help women think of contraception as a long term personal strategy. Since relationship status affects contraceptive use, providers and programs that aim to reduce unintended pregnancy can consider strategies to create a paradigm shift around contraceptive use that focuses on the woman’s reproductive goals, current life stage, and life goals

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts