The Community Land Trust: Preserving Affordable Housing Stock in Orange County, North Carolina

Orange County, North Carolina, located in the state's booming Research Triangle region, is increasingly becoming an area in which only the affluent can afford to live, threatening the economic, racial and cultural diversity that is needed for a healthy society. In response to the county's dwindling supply of affordable housing, area activists and governments together established the Community Land Trust in Orange County (CLTOC), incorporated in 1999. Two years later, CLTOC is now beginning to realize its goal of creating housing that will remain permanently affordable for generations

An agricultural community’s perspectives on COVID-19 testing to support safe school reopening

IntroductionSchool-based COVID-19 testing may be an effective strategy for reducing transmission in schools and keeping schools open. The study objective was to examine community perspectives on school-based COVID-19 testing as a mitigation strategy to support safe school reopening.MethodsWe conducted a qualitative study in Yakima County, an agricultural region of Washington state, where over half of residents are Hispanic/Latino. From June to July 2021, we interviewed 18 students (13 years old, on average) and 19 school employees, and conducted four focus groups (2 in Spanish, 2 in English) with 26 parents. We audio-recorded the semi-structured interviews and focus group discussions which were then transcribed. We used an inductive, constant comparison approach to code the transcripts and conducted a thematic analysis to generate themes.ResultsWe identified four main themes. Students, parents, and school employees desired a return to in-person learning (Theme 1). Schools implemented numerous COVID-19 mitigation strategies (e.g., masking) to facilitate a safe return to school but felt that adding testing would not be feasible due to a lack of resources and overworked staff (Theme 2). Parents and school employees’ familiarity with COVID-19 testing procedures influenced their support for testing (Theme 3). Parents and school employees felt there were inadequate resources for individuals who test positive for COVID-19 (Theme 4).DiscussionSchools require adequate resources and medical personnel to implement COVID-19 testing. Individuals also need resources after testing positive, including physical space to isolate, financial resources for those without paid time off, and delivery of food and other necessities to households in rural communities

Soil Change: Impacts and Responses

Peer reviewe

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

Nutrient Losses from Unlined Bedded Swine Hoop Structures and an Associated Windrow Composting Site

Mass balance analysis of livestock manure management systems can offer important insight into the flows and losses of nutrients and potential pollutants. This study describes the objectives, design, and two years of results from a field study examining the nutrient losses from bedded swine structures and an associated composting site. Nutrient mass balances have been completed on three groups of pigs in naturally ventilated hoop structures, along with the corresponding three composting trials at the outdoor windrow composting site. Soil core nutrient analysis and mass balances on nutrients in the swine production system and composting piles have been used to assess losses to the environment. The mass balance analysis of deep bedded hoop structures identified significant N losses from the bedded pack (54 ± 6% of the excreted manure; 3.9 kg/pig) but negligible P losses in the hoop. Both N and P losses at the compost site were significant (19 ± 10% and 21 ± 21% of the excreted manure respectively). After losses in both the hoop and the composting process, the nutrient quantities remaining were 1.9 ± 0.4 kg N/pig and 1.0 ± 0.3 kg P/pig. 10% or less of the N losses from the hoop accumulated in the top 1.2 m of soil, and that net accumulation was entirely in the first year. Most N losses within the hoop structure appear to be in gaseous forms, e.g. N 2 , N 2 O, and NH 3 . Improved management of these gaseous losses in bedded livestock systems will be important to making these systems environmentally sustainable. Although soil sample variability precluded a direct correlation between nitrogen losses and soil accumulation at the composting site, high apparent soil accumulations did indicate that a considerable fraction of the N losses observed at the composting site are being leaching into the soil. Design and management strategies to mitigate this leaching loss are likely to be necessary for manure composting facilities in humid regions located near vulnerable groundwater resources.This conference presentation is published as Garrison, Mark V., Tom L. Richard, Sonia M. Tiquia, and Mark S. Honeyman. "Nutrient losses from unlined bedded swine hoop structures and an associated windrow composting site." ASABE Paper No. 012238. ASABE Annual International Meeting, July 30-August 1, 2001. DOI: 10.13031/2013.4202. Posted with permission.</p

Examination Stress as an Ecological Inducer of Cortisol and Psychological Responses to Stress in Undergraduate Students

The purpose of the present study was to investigate basic methodological issues related to the usage of an examination stress protocol in studies of psychoneuroendocrinology. In the present study, 57 undergraduate students served as participants. All subjects provided salivary samples and completed psychological inventories during a low examination stress period and again during a high examination stress period. Salivary samples were analyzed for cortisol. Three major findings were observed. First, the examination stress protocol proved to be an effective trigger of elevations in both psychological measures of stress and in cortisol levels. Second, sex differences were observed in cortisol levels, such that males showed an elevation in cortisol during the high examination stress session whereas females did not. Finally, no significant correlations were observed between elevations in psychological measures of stress and elevations in cortisol levels. These findings suggest that the examination stress protocol used in the present study effectively elevated both psychological stress and cortisol levels. Furthermore, these findings suggest that there are biological differences in how males and females respond to stress. Finally, no evidence was found to suggest a relationship between psychological and hormonal levels of stress. Together, these findings suggest the need to better define and consider the implications of both the specific measures of stress being used and individual differences in the subject samples in psychoendocrine studies

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

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

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

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.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 (VAFPeer reviewe