Factors affecting plant community composition and dynamics in the Ossipee Pine Barrens, New Hampshire

Forty-one 0.25 ha sites were sampled in the Ossipee Pine Barrens to identify and describe tree community types and investigate factors controlling forest composition and dynamics. Every site had three site-time assemblages (STA\u27s) representing past, present, and future trees. Past (1952) vegetation was calculated based on reverse growth estimates of current stems and stumps. Future (2052) vegetation was predicted by current sapling (\u3c10 cm dbh and ≥1 m tall) relative densities. Cluster analysis produced three community types from 121 STA\u27s: pitch pine, mixed pine-hardwoods, and red maple. Pitch pine communities comprised 63% of sites in 1952, but declined since. Mixed pine-hardwoods peaked at 58% in 2002, but were predicted to decline to 37% by 2052 as sites transitioned to red maple. The red maple community only appeared in the future after current saplings replaced aging pitch pine canopies, but the type was predicted to comprise 50% of sites by 2052. Assuming continued fire suppression, pitch pine communities will retain only 12% of sites by 2052. Control over vegetation patterns and successional dynamics by (1) soils, (2) seed source, and (3) disturbance was investigated using field evidence, accounts from residents and forest managers, and dendrochronology. Factors affecting forests since stand formation were analyzed individually and with multivariate techniques. Seed source variables explained the greatest amount of variation in vegetation, followed closely by fire-related disturbance variables and weakly by soil texture. Logging disturbance and soil nutrients were not significant predictors of vegetation in the Ossipee Pine Barrens

Assessing rotation-invariant feature classification for automated wildebeest population counts

Accurate and on-demand animal population counts are the holy grail for wildlife conservation organizations throughout the world because they enable fast and responsive adaptive management policies. While the collection of image data from camera traps, satellites, and manned or unmanned aircraft has advanced significantly, the detection and identification of animals within images remains a major bottleneck since counting is primarily conducted by dedicated enumerators or citizen scientists. Recent developments in the field of computer vision suggest a potential resolution to this issue through the use of rotation-invariant object descriptors combined with machine learning algorithms. Here we implement an algorithm to detect and count wildebeest from aerial images collected in the Serengeti National Park in 2009 as part of the biennial wildebeest count. We find that the per image error rates are greater than, but comparable to, two separate human counts. For the total count, the algorithm is more accurate than both manual counts, suggesting that human counters have a tendency to systematically over or under count images. While the accuracy of the algorithm is not yet at an acceptable level for fully automatic counts, our results show this method is a promising avenue for further research and we highlight specific areas where future research should focus in order to develop fast and accurate enumeration of aerial count data. If combined with a bespoke image collection protocol, this approach may yield a fully automated wildebeest count in the near future

Water, sanitation and hygiene at sex work venues to support menstrual needs

Introduction: Adequate menstrual health and hygiene (MHH) is necessary for women’s health and equity of all menstruators. Female sex workers (FSW) require good MHH to prevent discomfort and exposure to pathogens. No studies have evaluated water, sanitation, and hygiene (WASH) conditions of FSW. We report on a cross-sectional WASH assessment at FSW venues in Kisumu, western Kenya. Methods: Stakeholders identified 77 FSW venues in Kisumu, of which 47 were randomly sampled and visited between April-May 2023. A standardized structured survey of WASH conditions was deployed by trained research staff using Android tablets after proprietor’s consent. WASH scores ranging 0 – 3 were computed based on point each for direct observation of water available, soap available, and acceptable latrine. MHH scores ranging between 0-4 were computed (one point each) for direct observation of: currently available soap and water, locking door on a usable latrine, functional lighting, and a private area for changing clothes or menstrual materials, separate from the latrine(s). WASH and MHH scores were compared by venue type using non-parametric Kruskal-Wallis tests, and non-parametric Spearman rank tests. Results: Full WASH criteria was met by 29.8% of venues; 34.0% had no adequate WASH facilities; 46.8% had no female latrine, and 25.5% provided soap and water in private spaces for women. While 76.6% had menstrual waste disposal only 14 (29.8%) had covered bins. One in 10 venues provided adequate MHM facilities. Poorest WASH facilities were in brothels and in bars, and three-quarters of bars with accommodation had no MHH facilities. Discussion: WASH and MHH services were sub-optimal in the majority of FSW venues, preventing menstrual management safely, effectively, with dignity and privacy. This study highlights the unmet need for MHH support for this population. Poor MHH can deleteriously impact FSW health and wellbeing and compound the stigma and shame associated with their work and ability to stay clean. Acceptable and cost-effective solutions to sustainably improve WASH facilities for these populations are needed

Analysis of Bacterial vaginosis, the vaginal microbiome, and sexually transmitted infections following the provision of menstrual cups in Kenyan schools: results of a nested study within a cluster randomized controlled trial

Abstract Background: Non-hygienic products for managing menstruation are reported to cause reproductive tract infections. Menstrual cups are a potential solution. We assessed whether menstrual cups would reduce Bacterial vaginosis (BV), vaginal microbiome (VMB), and sexually transmitted infections (STIs) as studies have not evaluated this. Methods and Findings: A cluster-randomized controlled trial was performed in 96 Kenyan secondary schools, randomized (1:1:1:1) to control, menstrual cup, cash transfer, or menstrual cup plus cash transfer. This sub-study assessing the impact of menstrual cups on BV, VMB, and STIs, included 6 schools from the control (3) and menstrual cup only (3) groups, both receiving BV and STI testing and treatment at each visit. Self-collected vaginal swabs were used to measure VMB (16S rRNA gene amplicon sequencing), BV (Nugent score), and STIs. STIs were a composite of Chlamydia trachomatis and Neisseria gonorrhoeae (nucleic acid amplification test)¸ and Trichomonas vaginalis (rapid immunochromatographic assay). Participants were not masked and were followed for 30 months. The primary outcome was diagnosis of BV; secondary outcomes were VMB and STIs. Intention to treat blinded analyses used mixed effects generalized linear regressions, with random effects term for school. The study was conducted between May 2, 2018, and Feb 7, 2021. 436 participants were included: 213 cup, 223 control. There were 289 BV diagnoses: 162 among control participants and 127 among intervention participants (odds ratio 0.76 [95% CI 0.59–0.98]; p=0.038). The occurrence of Lactobacillus crispatus dominated VMB was higher among cup group participants (odds ratio 1.37 [95% CI 1.06–1.75]), as was the mean relative abundance of Lactobacillus crispatus (3.95% [95% CI 1.92–5.99]). There was no effect of intervention on STIs (relative risk 0.82 [95% CI 0.50–1.35]). The primary limitations of this study were insufficient power for sub-group analyses, and generalizability of findings to non-school and other global settings. Conclusions: Menstrual cups with BV and STI testing and treatment benefitted adolescent schoolgirls through lower occurrence of BV and higher L. crispatus compared with only BV and STI testing and treatment during the 30 months of a cluster-randomized menstrual cup intervention. ClinicalTrials.gov, NCT03051789

High Prevalence of Lactobacillus crispatus Dominated Vaginal Microbiome Among Kenyan Secondary School Girls: Negative Effects of Poor Quality Menstrual Hygiene Management and Sexual Activity

The vaginal microbiome (VMB) impacts numerous health outcomes, but evaluation among adolescents is limited. We characterized the VMB via 16S rRNA gene amplicon sequencing, and its association with Bacterial vaginosis (BV) and sexually transmitted infections (STIs; chlamydia, gonorrhea, trichomoniasis) among 436 schoolgirls in Kenya, median age 16.9 years. BV and STI prevalence was 11.2% and 9.9%, respectively, with 17.6% of girls having any reproductive tract infection. Three community state types (CST) accounted for 95% of observations: CST-I L.crispatus-dominant (N=178, BV 0%, STI 2.8%, sexually active 21%); CST-III L.iners-dominant (N=152, BV 3.3%, STI 9.7%, sexually active 35%); CST-IV G.vaginalis-dominant (N=83, BV 51.8%, STI 25.3%, sexually active 43%). In multivariable adjusted analyses, sexually active girls had increased odds of CST-III and CST-IV, and use of cloth to manage menses had 1.72-fold increased odds of CST-IV vs. CST-I. The predominance of L.crispatus-dominated VMB, substantially higher than observed in prior studies of young adult and adult women in sub-Saharan Africa, indicates that non-optimal VMB can be an acquired state. Interventions to maintain or re-constitute L.crispatus dominance should be considered even in adolescents

Vaginal Microbial Network Analysis Reveals Novel Taxa Relationships among Adolescent and Young Women with Incident Sexually Transmitted Infection Compared with Those Remaining Persistently Negative Over a 30-Month Period

A non-optimal vaginal microbiome (VMB) is typically diverse with a paucity of Lactobacillus cris-patus, and is often associated with Bacterial vaginosis (BV) and sexually transmitted infections (STIs). Although compositional characterization of the VMB is well-characterized, especially for BV, knowledge remains limited on how different groups of bacteria relate to incident STIs, espe-cially among adolescents. In this study, we compared the VMB (measured via 16S ribosomal RNA gene amplicon sequencing) of Kenyan secondary school girls with incident STIs (composite of chlamydia, gonorrhea, trichomoniasis) to those who remained persistently negative for STIs and BV over 30 months of follow-up. We applied microbial network analysis to identify key taxa (i.e., those with greatest connectedness in terms of linkages to other taxa), as measured by betweenness and eigenvector centralities, and sub-groups of clustered taxa. VMB networks of those who re-mained persistently negative reflected greater connectedness compared to the VMB from partic-ipants with STI. Taxa with highest centralities were not correlated with relative abundance and differed between those with and without STI. Subject level analyses indicated that sociodemo-graphic (e.g., age, socioeconomic status) and behavioral (e.g., sexual activity) factors contribute to microbial network structure, and may be of relevance when designing interventions to improve VMB health

Genetic variants associated with fasting glucose and insulin concentrations in an ethnically diverse population: results from the Population Architecture using Genomics and Epidemiology (PAGE) study

Background: Multiple genome-wide association studies (GWAS) within European populations have implicated common genetic variants associated with insulin and glucose concentrations. In contrast, few studies have been conducted within minority groups, which carry the highest burden of impaired glucose homeostasis and type 2 diabetes in the U.S. Methods: As part of the 'Population Architecture using Genomics and Epidemiology (PAGE) Consortium, we investigated the association of up to 10 GWAS-identified single nucleotide polymorphisms (SNPs) in 8 genetic regions with glucose or insulin concentrations in up to 36,579 non-diabetic subjects including 23,323 European Americans (EA) and 7,526 African Americans (AA), 3,140 Hispanics, 1,779 American Indians (AI), and 811 Asians. We estimated the association between each SNP and fasting glucose or log-transformed fasting insulin, followed by meta-analysis to combine results across PAGE sites. Results: Overall, our results show that 9/9 GWAS SNPs are associated with glucose in EA (p = 0.04 to 9 × 10-15), versus 3/9 in AA (p= 0.03 to 6 × 10-5), 3/4 SNPs in Hispanics, 2/4 SNPs in AI, and 1/2 SNPs in Asians. For insulin we observed a significant association with rs780094/GCKR in EA, Hispanics and AI only. Conclusions: Generalization of results across multiple racial/ethnic groups helps confirm the relevance of some of these loci for glucose and insulin metabolism. Lack of association in non-EA groups may be due to insufficient power, or to unique patterns of linkage disequilibrium

Genetic Determinants of Lipid Traits in Diverse Populations from the Population Architecture using Genomics and Epidemiology (PAGE) Study

For the past five years, genome-wide association studies (GWAS) have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE) study was established in 2008 to characterize GWAS–identified variants in diverse population-based studies. We genotyped 49 GWAS–identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG) levels in self-identified European American (∼20,000), African American (∼9,000), American Indian (∼6,000), Mexican American/Hispanic (∼2,500), Japanese/East Asian (∼690), and Pacific Islander/Native Hawaiian (∼175) adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92%) SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05) and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG) in European Americans generalized to African Americans (48%, 61%, and 57%), American Indians (45%, 64%, and 77%), and Mexican Americans/Hispanics (57%, 56%, and 86%). Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms