Individual herpes simplex virus 1 (HSV-1) particles exit by exocytosis and accumulate at preferential egress sites.

The human pathogen herpes simplex virus 1 (HSV-1) produces a lifelong infection in the majority of the world's population. While the generalities of alpha herpesvirus assembly and egress pathways are known, the precise molecular and spatiotemporal details remain unclear. In order to study this aspect of HSV-1 infection, we engineered a recombinant HSV-1 strain expressing a pH-sensitive reporter, gM-pHluorin. Using a variety of fluorescent microscopy modalities, we can detect individual virus particles undergoing intracellular transport and exocytosis at the plasma membrane. We show that particles exit from epithelial cells individually, not bulk release of many particles at once, as has been reported for other viruses. In multiple cell types, HSV-1 particles accumulate over time at the cell periphery and cell-cell contacts. We show that this accumulation effect is the result of individual particles undergoing exocytosis at preferential sites and that these egress sites can contribute to cell-cell spread. We also show that the viral membrane proteins gE, gI, and US9, which have important functions in intracellular transport in neurons, are not required for preferential egress and clustering in non-neuronal cells. Importantly, by comparing HSV-1 to a related alpha herpesvirus, pseudorabies virus, we show that this preferential exocytosis and clustering effect are cell type dependent, not virus dependent. This preferential egress and clustering appear to be the result of the arrangement of the microtubule cytoskeleton, as virus particles co-accumulate at the same cell protrusions as an exogenous plus end-directed kinesin motor.IMPORTANCEAlpha herpesviruses produce lifelong infections in their human and animal hosts. The majority of people in the world are infected with herpes simplex virus 1 (HSV-1), which typically causes recurrent oral or genital lesions. However, HSV-1 can also spread to the central nervous system, causing severe encephalitis, and might also contribute to the development of neurodegenerative diseases. Many of the steps of how these viruses infect and replicate inside host cells are known in depth, but the final step, exiting from the infected cell, is not fully understood. In this study, we engineered a novel variant of HSV-1 that allows us to visualize how individual virus particles exit from infected cells. With this imaging assay, we investigated preferential egress site formation in certain cell types and their contribution to the cell-cell spread of HSV-1.

The Potential of Cannabichromene (CBC) as a Therapeutic Agent.

There is a growing interest in the use of medicinal plants to treat a variety of diseases, and one of the most commonly used medicinal plants globally is Cannabis sativa The two most abundant cannabinoids (Δ9-tetrahydrocannabinol and cannabidiol) have been governmentally approved to treat selected medical conditions; however, the plant produces over 100 cannabinoids, including cannabichromene (CBC). While the cannabinoids share a common precursor molecule, cannabigerol, they are structurally and pharmacologically unique. These differences may engender differing therapeutic potentials. In this review, we will examine what is currently known about CBC with regards to pharmacodynamics, pharmacokinetics, and receptor profile. We will also discuss the therapeutic areas that have been examined for this cannabinoid, notably antinociceptive, antibacterial, and anti-seizure activities. Finally, we will discuss areas where new research is needed and potential novel medicinal applications for CBC. Significance Statement Cannabichromene (CBC) has been suggested to have disparate therapeutic benefits such as anti-inflammatory, anticonvulsant, antibacterial, and antinociceptive effects. Most of the focus on the medical benefits of cannabinoids has been focused on THC and CBD. The preliminary studies on CBC indicate that this phytocannabinoid may have unique therapeutic potential that warrants further investigation. Following easier access to hemp, CBC products are commercially available over-the-counter and are being widely utilized with little or no evidence of their safety or efficacy.

High Cannabigerol Hemp Extract Moderates Colitis and Modulates the Microbiome in an Inflammatory Bowel Disease Model.

Cannabis sativa L. has a long history of medicinal use, particularly for gastrointestinal diseases. Patients with inflammatory bowel disease (IBD) report using cannabis to manage their symptoms, despite little data to support the use of cannabis or cannabis products to treat the disease. In this study, we use the well-described dextran sodium sulfate (DSS) model of colitis in mice to assess the impact of commercially available, noneuphorigenic, high cannabigerol (CBG) hemp extract (20 mg/mL cannabigerol, 20.7 mg/mL cannabidiol, 1 mg/mL cannabichromene) on IBD activity and the colonic microbiome. Mice were given 2% DSS in drinking water for 5 days, followed by 2 days of regular drinking water. Over the 7 days, mice were dosed daily with either high CBG hemp extract or matched vehicle control. Daily treatment with high CBG hemp extract dramatically reduces the severity of disease at the histological and organismal levels as measured by decreased disease activity index, increased colon length, and decreases in percent colon tissue damage. 16S rRNA gene sequencing of the fecal microbiota reveals high CBG hemp extract treatment results in alterations in the microbiota that may be beneficial for colitis. Finally, using metabolomic analysis of fecal pellets, we find that mice treated with high CBG hemp extract have a normalization of several metabolic pathways, including those involved in inflammation. Taken together, these data suggest that high CBG hemp extracts may offer a novel treatment option for patients. SIGNIFICANCE STATEMENT: Using the dextran sodium sulfate model of colitis, the authors show that treatment with high cannabigerol hemp extract reduces the severity of symptoms associated with colitis. Additionally, they show that treatment modulates both the fecal microbiota and metabolome with potential functional significance.

Stored platelet hemostatic phenotype and function is not altered when donors are on testosterone replacement therapy.

BACKGROUND: Critical shortages in the national blood supply have led to a re-evaluation of previously overlooked donor sources for blood products. As a part of that effort, red blood cells collected from therapeutic phlebotomy of donors on testosterone replacement therapy (TRT) have been conditionally approved for transfusion. However, platelets from TRT donors are not currently approved for use due to limited data on effects of supraphysiologic testosterone on recipient safety and platelet function. The objective of this study was to provide a comprehensive profile of phenotype and function in platelets from TRT and control donors. STUDY DESIGN AND METHODS: Platelets in plasma were collected from TRT and control donors (N = 10 per group; age- and sex-matched) and stored at room temperature for 7 days. On storage Day 1 (D1) and Day 7 (D7), platelet products were analyzed for platelet count, metabolic parameters (i.e., glucose, lactate, mitochondrial function), surface receptor expression, aggregation, thrombin generation, and thrombus formation under physiological flow conditions. RESULTS: TRT donor platelets were not significantly different than control donor platelets in terms of count, surface phenotype, metabolic function, ability to aggregate, thrombin generation, or ability to form occlusive thrombus under arterial flow regimes. Both groups were similar to each other by D7, but had significantly lost hemostatic function compared to D1. DISCUSSION: Platelets derived from donors undergoing TRT have similar phenotypic and functional profiles compared to those derived from control donors. This suggests that therapeutic phlebotomy of TRT donors may provide a useful source for platelet products.

A Cautionary Tale: Digital Clinical Trial Implementation of a Couples-Based HIV Prevention Study among Transgender Women and Their Partners in the United States.

This study investigates baseline differences in couples enrolled in the "It Takes Two" HIV prevention intervention for transgender women and their partners, comparing in-person participation pre-COVID-19 and digital participation during the pandemic. Among 52 couples (40% in-person, 60% digital), bivariate analyses revealed that in-person participants were more likely to be African American, have cisgender male partners, report higher unemployment, incarceration histories, greater relationship stigma, and lower relationship quality. The findings highlight the limitations of digital modalities in engaging transgender women of color and those with structural vulnerabilities. The study emphasizes that reliance on digital methods in HIV research jeopardizes the inclusion of those lacking technological access and literacy, especially communities disproportionately impacted by HIV. Researchers must incorporate hybrid or in-person options and engage communities to ensure equity and inclusion, thus overcoming barriers and ensuring comprehensive population reach in HIV prevention studies.

Empirical legal analysis simplified: reducing complexity through automatic identification and evaluation of legally relevant factors.

This paper investigates the potential for reducing the complexity of AI and Law and empirical legal studies projects through a novel annotation methodology that relies on GPT Family Models to assist human annotators. Improving the speed, cost and quality of annotation could greatly benefit such projects. In modelling types of legal claims, researchers in the fields of empirical legal studies and AI and Law have long relied on manually annotating factors in case texts. To demonstrate our methodology, we employ cases and factors regarding whether a police officer has constitutional authority to detain a motorist on the basis of the officer's suspicion that the motorist is trafficking drugs. Our results demonstrate how recent advances in text analytics can reduce the burden of identifying factors in large numbers of cases and improve machine learning models' predictions of case outcomes. This article is part of the theme issue 'A complexity science approach to law and governance'.

Changes in opioid prescribing and prescription drug monitoring program utilization following electronic health record integration-Massachusetts, 2018.

OBJECTIVE: In this study, we explored key prescription drug monitoring program-related outcomes among clinicians from a broad cohort of Massachusetts healthcare facilities following prescription drug monitoring program (PDMP) and electronic health record (EHR) data integration. METHODS: Outcomes included seven-day rolling averages of opioids prescribed, morphine milligram equivalents (MMEs) prescribed, and PDMP queries. We employed a longitudinal study design to analyze PDMP data over a 15-month study period which allowed for six and a half months of pre- and post-integration observations surrounding a two-month integration period. We used longitudinal mixed effects models to examine the effect of EHR integration on each of the key outcomes. RESULTS: Following EHR integration, PDMP queries increased both through the web-based portal and in total (0.037, [95% CI = 0.017, 0.057] and 0.056, [95% CI = 0.035, 0.077]). Both measures of clinician opioid prescribing declined throughout the study period; however, no significant effect following EHR integration was observed. These results were consistent when our analysis was applied to a subset consisting only of continuous PDMP users. CONCLUSIONS: Our results support EHR integration contributing to PDMP utilization by clinicians but do not support changes in opioid prescribing behavior.

Racial/ethnic differences in the association between transgender-related U.S. state policies and self-rated health of transgender women.

BACKGROUND: Policy protections for transgender adults in the United States are consistently associated with positive health outcomes. However, studies over-represent non-Latinx White transgender people and obscure variation in policies' intended goals. This study examined racial differences in the relationship between transgender-related policies and transgender women's self-rated health. Guided by Critical Race Theory, we hypothesized that policies conferring access to resources (e.g., healthcare) would be associated with better self-rated health among all participants while policies signifying equality (e.g., nondiscrimination laws) would be associated with better self-rated health only for White participants. METHODS: Using cross-sectional data collected between March 2018-December 2020 from 1566 transgender women, we analyzed 7 state-level 'access policies,' 5 'equality policies,' and sum indices of each. Participants represented 29 states, and 54.7% were categorized as people of color. We fit a series of multilevel ordinal regression models predicting self-rated health by each policy. Multivariate models were adjusted for relevant covariates at the individual- and state-level. We then tested moderation by race/ethnicity using interaction terms and generated stratified predicted probability plots. RESULTS: In bivariate models, 4 access policies, 2 equality policies, and both indices were associated with better self-rated health, but associations did not persist in adjusted models. Results from the multivariable models including interaction terms indicated that policies concerning private insurance coverage of gender-affirming care, private insurance nondiscrimination, credit nondiscrimination, and both indices were statistically significantly associated with better self-rated health for White participants and worse self-rated health for participants of color. CONCLUSIONS: The policies included in this analysis do not mitigate racism's effects on access to resources, indicating they may be less impactful for transgender women of color than White transgender women. Future research and policy advocacy efforts promoting transgender women's health must center racial equity as well as transgender people of color's priorities.

How Have Patient Out-of-pocket Costs for Common Outpatient Orthopaedic Foot and Ankle Surgical Procedures Changed Over Time? A Retrospective Study From 2010 to 2020.

BACKGROUND: Out-of-pocket (OOP) costs can be substantial financial burdens for patients and may even cause patients to delay or forgo necessary medical procedures. Although overall healthcare costs are rising in the United States, recent trends in patient OOP costs for foot and ankle orthopaedic surgical procedures have not been reported. Fully understanding patient OOP costs for common orthopaedic surgical procedures, such as those performed on the foot and ankle, might help patients and professionals make informed decisions regarding treatment options and demonstrate to policymakers the growing unaffordability of these procedures. QUESTIONS/PURPOSES: (1) How do OOP costs for common outpatient foot and ankle surgical procedures for commercially insured patients compare between elective and trauma surgical procedures? (2) How do these OOP costs compare between patients enrolled in various insurance plan types? (3) How do these OOP costs compare between surgical procedures performed in hospital-based outpatient departments and ambulatory surgical centers (ASCs)? (4) How have these OOP costs changed over time? METHODS: This was a retrospective, comparative study drawn from a large, longitudinally maintained database. Data on adult patients who underwent elective or trauma outpatient foot or ankle surgical procedures between 2010 and 2020 were extracted using the MarketScan Database, which contains well-delineated cost variables for all patient claims, which are particularly advantageous for assessing OOP costs. Of the 1,031,279 patient encounters initially identified, 41% (427,879) met the inclusion criteria. Demographic, procedural, and financial data were recorded. The median patient age was 50 years (IQR 39 to 57); 65% were women, and more than half of patients were enrolled in preferred provider organization insurance plans. Approximately 75% of surgical procedures were classified as elective (rather than trauma), and 69% of procedures were performed in hospital-based outpatient departments (rather than ASCs). The primary outcome was OOP costs incurred by the patient, which were defined as the sum of the deductible, coinsurance, and copayment paid for each episode of care. Monetary data were adjusted to 2020 USD. A general linear regression, the Kruskal-Wallis test, and the Wilcoxon-Mann-Whitney test were used for analysis, as appropriate. Alpha was set at 0.05. RESULTS: For foot and ankle indications, trauma surgical procedures generated higher median OOP costs than elective procedures (USD 942 [IQR USD 150 to 2052] versus USD 568 [IQR USD 51 to 1426], difference of medians USD 374; p < 0.001). Of the insurance plans studied, high-deductible health plans had the highest median OOP costs. OOP costs were lower for procedures performed in ASCs than in hospital-based outpatient departments (USD 645 [IQR USD 114 to 1447] versus USD 681 [IQR USD 64 to 1683], difference of medians USD 36; p < 0.001). This trend was driven by higher coinsurance for hospital-based outpatient departments than for ASCs (USD 391 [IQR USD 0 to 1136] versus USD 337 [IQR USD 0 to 797], difference of medians USD 54; p < 0.001). The median OOP costs for common outpatient foot and ankle surgical procedures increased by 102%, from USD 450 in 2010 to USD 907 in 2020. CONCLUSION: Rapidly increasing OOP costs of common foot and ankle orthopaedic surgical procedures warrant a thorough investigation of potential cost-saving strategies and initiatives to enhance healthcare affordability for patients. In particular, measures should be taken to reduce underuse of necessary care for patients enrolled in high-deductible health plans, such as shorter-term deductible timespans and placing additional regulations on the implementation of these plans. Moreover, policymakers and physicians could consider finding ways to increase the proportion of procedures performed at ASCs for procedure types that have been shown to be equally safe and effective as in hospital-based outpatient departments. Future studies should extend this analysis to publicly insured patients and further investigate the health and financial effects of high-deductible health plans and ASCs, respectively. LEVEL OF EVIDENCE: Level III, economic and decision analysis.

Correlating Severity of Pulmonary Hypertension by Echocardiogram with Mortality in Premature Infants with Bronchopulmonary Dysplasia.

OBJECTIVE: Bronchopulmonary dysplasia (BPD) is the most common complication of preterm birth. Infants with BPD are at increased risk for pulmonary hypertension (PH). Cardiac catheterization is the gold standard for diagnosing PH, but cardiac catheterization is challenging to perform in small, sick, premature infants. The utility of echocardiography for diagnosing PH and predicting outcomes in extremely premature infants has not been clearly defined. Therefore, we sought to use predefined criteria to diagnose PH by echocardiogram and relate PH severity to mortality in extremely premature infants with BPD. STUDY DESIGN: Echocardiograms from 46 infants born ≤28 weeks' postmenstrual age with a diagnosis of BPD were assessed for PH by three pediatric cardiologists using predefined criteria, and survival times among categories of PH patients were compared. A total of 458 echocardiograms were reviewed, and 15 (33%) patients were found to have at least moderate PH. Patients with at least moderate PH had similar demographic characteristics to those with no/mild PH. RESULTS: Ninety percent of infants without moderate to severe PH survived to hospital discharge, compared with 67% of infants with at least moderate PH (p = 0.048). Patients with severe PH had decreased survival to hospital discharge (38%) compared with moderate (100%) and no/mild PH (90%) groups. Kaplan-Meier survival curves also differed among PH severity groups (Wilcoxon p < 0.001). CONCLUSION: Using predefined criteria for PH, premature infants with BPD can be stratified into PH severity categories. Patients diagnosed with severe PH by echocardiogram have significantly reduced survival. KEY POINTS: · A composite score definition of PH by echocardiogram showed high inter- and intrarater reliability.. · Infants with severe PH by echocardiogram had decreased survival rates.. · Early diagnosis of PH by echocardiogram dictates treatment which may improve outcomes..

Remarkably Low KIR and HLA Diversity in Amerindians Reveals Signatures of Strong Purifying Selection Shaping the Centromeric KIR Region.

The killer-cell immunoglobulin-like receptors (KIR) recognize human leukocyte antigen (HLA) molecules to regulate the cytotoxic and inflammatory responses of natural killer cells. KIR genes are encoded by a rapidly evolving gene family on chromosome 19 and present an unusual variation of presence and absence of genes and high allelic diversity. Although many studies have associated KIR polymorphism with susceptibility to several diseases over the last decades, the high-resolution allele-level haplotypes have only recently started to be described in populations. Here, we use a highly innovative custom next-generation sequencing method that provides a state-of-art characterization of KIR and HLA diversity in 706 individuals from eight unique South American populations: five Amerindian populations from Brazil (three Guarani and two Kaingang); one Amerindian population from Paraguay (Aché); and two urban populations from Southern Brazil (European and Japanese descendants from Curitiba). For the first time, we describe complete high-resolution KIR haplotypes in South American populations, exploring copy number, linkage disequilibrium, and KIR-HLA interactions. We show that all Amerindians analyzed to date exhibit the lowest numbers of KIR-HLA interactions among all described worldwide populations, and that 83-97% of their KIR-HLA interactions rely on a few HLA-C molecules. Using multiple approaches, we found signatures of strong purifying selection on the KIR centromeric region, which codes for the strongest NK cell educator receptors, possibly driven by the limited HLA diversity in these populations. Our study expands the current knowledge of KIR genetic diversity in populations to understand KIR-HLA coevolution and its impact on human health and survival.

CpG methylation patterns in placenta and neonatal blood are differentially associated with neonatal inflammation.

BACKGROUND: Infants born extremely premature are at increased risk for health complications later in life for which neonatal inflammation may be a contributing biological driver. Placental CpG methylation provides mechanistic information regarding the relationship between prenatal epigenetic programming, prematurity, neonatal inflammation, and later-in-life health. METHODS: We contrasted CpG methylation in the placenta and neonatal blood spots in relation to neonatal inflammation in the Extremely Low Gestational Age Newborn (ELGAN) cohort. Neonatal inflammation status was based on the expression of six inflammation-related proteins, assessed as (1) day-one inflammation (DOI) or (2) intermittent or sustained systemic inflammation (ISSI, inflammation on ≥2 days in the first 2 postnatal weeks). Epigenome-wide CpG methylation was assessed in 354 placental samples and 318 neonatal blood samples. RESULTS: Placental CpG methylation displayed the strongest association with ISSI (48 CpG sites) but was not associated with DOI. This was in contrast to CpG methylation in blood spots, which was associated with DOI (111 CpG sites) and not with ISSI (one CpG site). CONCLUSIONS: Placental CpG methylation was strongly associated with ISSI, a measure of inflammation previously linked to later-in-life cognitive impairment, while day-one neonatal blood methylation was associated with DOI. IMPACT: Neonatal inflammation increases the risk of adverse later-life outcomes, especially in infants born extremely preterm. CpG methylation in the placenta and neonatal blood spots were evaluated in relation to neonatal inflammation assessed via circulating proteins as either (i) day-one inflammation (DOI) or (ii) intermittent or sustained systemic inflammation (ISSI, inflammation on ≥2 days in the first 2 weeks). Tissue specificity was observed in epigenetic-inflammatory relationships: placental CpG methylation was associated with ISSI, neonatal blood CpG methylation was associated with DOI. Supporting the placental origins of disease framework, placental epigenetic patterns are associated with a propensity for ISSI in neonates.

Following Transplantation for Acute Myelogenous Leukemia, Donor KIR Cen B02 Better Protects against Relapse than KIR Cen B01.

In the treatment of acute myelogenous leukemia with allogeneic hematopoietic cell transplantation, we previously demonstrated that there is a greater protection from relapse of leukemia when the hematopoietic cell transplantation donor has either the Cen B/B KIR genotype or a genotype having two or more KIR B gene segments. In those earlier analyses, KIR genotyping could only be assessed at the low resolution of gene presence or absence. To give the analysis greater depth, we developed high-resolution KIR sequence-based typing that defines all the KIR alleles and distinguishes the expressed alleles from those that are not expressed. We now describe and analyze high-resolution KIR genotypes for 890 donors of this human transplant cohort. Cen B01 and Cen B02 are the common CenB haplotypes, with Cen B02 having evolved from Cen B01 by deletion of the KIR2DL5, 2DS3/5, 2DP1, and 2DL1 genes. We observed a consistent trend for Cen B02 to provide stronger protection against relapse than Cen B01 This correlation indicates that protection depends on the donor having inhibitory KIR2DL2 and/or activating KIR2DS2, and is enhanced by the donor lacking inhibitory KIR2DL1, 2DL3, and 3DL1. High-resolution KIR typing has allowed us to compare the strength of the interactions between the recipient's HLA class I and the KIR expressed by the donor-derived NK cells and T cells, but no clinically significant interactions were observed. The trend observed between donor Cen B02 and reduced relapse of leukemia points to the value of studying ever larger transplant cohorts.

Structural Needs, Substance Use, and Mental Health Among Transgender and Nonbinary Young Adults in the San Francisco Bay Area: Findings from the Phoenix Study.

Transgender and nonbinary (trans) young adults report high rates of substance use and adverse mental health outcomes; however, few studies have examined how social, economic, and legal factors may contribute to health inequities in this population. Guided by the structural vulnerability framework, this study sought to explore structural needs and whether these needs were associated with substance use and mental health outcomes among trans young adults. Between 2019 and 2021, 215 trans young adults aged 18-29 from San Francisco Bay Area were recruited into a longitudinal study. Baseline data were used to examine bivariate and multivariable associations between structural needs and substance use and mental health outcomes. There were bivariate differences in the number of structural needs by education, income source, incarceration history, and ethnicity, and the number of unmet structural needs was associated with education and income source. After adjusting for sociodemographics, the number of structural needs was associated with daily marijuana use (AOR 1.29, 95% CI: 1.10-1.49) and suicidal ideation (AOR 1.24, 95% CI: 1.06-1.45), and the number of unmet structural needs was associated with daily marijuana use (AOR 1.30, 95% CI: 1. 10-1.55) and depressive symptoms (ß 2.00, 95% CI: 1.00-3.00). Additionally, both numbers of structural needs and unmet structural needs mediated the relationship between income source (traditional employment vs. other income only) and depressive symptoms (TIE ß 2.51, 95% CI: 0.99-4.04; ß 1.37, 95% CI: 0.23-2.52, respectively). Findings highlight a need for multisector efforts to address structural vulnerabilities among trans young adults.

Structural vulnerability as a conceptual framework for transgender health research: findings from a community needs assessment of transgender women of colour in Detroit.

The concept of structural vulnerability explains how systems of oppression drive health inequities by reducing access to survival resources (e.g. food, housing) for marginalised populations. Indicators of structural vulnerability such as housing instability, violent victimisation and poverty are often interconnected and result from intersectional oppression. We sought to demonstrate the utility of the structural vulnerability framework for transgender health research by examining patterns of structural vulnerability indicators among transgender women of colour in Detroit. We conducted latent class analysis and tested associations between classes and mental health and substance use outcomes. Membership to the Lowest Vulnerability class was negatively associated with post-traumatic stress disorder (PTSD) (aOR = 0.10, 95% CI: 0.02-0.59). High Economic Vulnerability membership was associated with daily marijuana use (aOR = 4.61, 95% CI: 1.31-16.16). Complex Multi-Vulnerability membership was associated with PTSD (aOR = 9.75, 95% CI: 2.55-37.29), anxiety (aOR = 4.12, 95% CI: 1.22-13.97), suicidality (aOR = 6.20, 95% CI: 1.39-27.70), and club drug use (aOR = 4.75, 95% CI: 1.31-17.29). Substantively different findings emerged when testing relationships between each indicator and each outcome, highlighting the value of theoretically grounded quantitative approaches to understanding health inequities. Community-driven interventions and policy changes that reduce structural vulnerability may improve mental health and substance use outcomes among structurally vulnerable trans women of colour.

When are environmental DNA early detections of invasive species actionable?

Environmental DNA (eDNA) sampling provides sensitive early detection capabilities for recently introduced taxa. However, natural resource managers struggle with how to integrate eDNA results into an early detection rapid response program because positive eDNA detections are not always indicative of an eventual infestation. We used a structured decision making (SDM) framework to evaluate appropriate response actions to hypothetical eDNA early detections of an introduced aquatic plant in Sebago Lake (Maine, USA). The results were juxtaposed to a recent study that used a similar SDM approach to evaluate response actions to hypothetical eDNA early detections of introduced mussels in Jordanelle Reservoir (Utah, USA). We found that eDNA early detections were not actionable in Sebago Lake because the plant's invasion potential was spatially constrained and the current management activities provided acceptable levels of mitigation. In Jordanelle Reservoir, eDNA detections were actionable due to high invasion potential and analyses supported management actions to contain the invasion. The divergent outcomes of the two case studies are related to the unique attributes of the habitats and species, highlighting the utility of the SDM approach when considering an eDNA monitoring program. We use these two case studies to present a general SDM framework and a set of heuristics that can be efficiently applied to eDNA early detection rapid response scenarios and other instances associated with indeterminant eDNA detections, especially when there is an imperative to make decisions as quickly as possible.

Decomposing the spatial and temporal effects of climate on bird populations in northern European mountains.

The relationships between species abundance or occurrence versus spatial variation in climate are commonly used in species distribution models to forecast future distributions. Under "space-for-time substitution", the effects of climate variation on species are assumed to be equivalent in both space and time. Two unresolved issues of space-for-time substitution are the time period for species' responses and also the relative contributions of rapid- versus slow reactions in shaping spatial and temporal responses to climate change. To test the assumption of equivalence, we used a new approach of climate decomposition to separate variation in temperature and precipitation in Fennoscandia into spatial, temporal, and spatiotemporal components over a 23-year period (1996-2018). We compiled information on land cover, topography, and six components of climate for 1756 fixed route surveys, and we modeled annual counts of 39 bird species breeding in the mountains of Fennoscandia. Local abundance of breeding birds was associated with the spatial components of climate as expected, but the temporal and spatiotemporal climatic variation from the current and previous breeding seasons were also important. The directions of the effects of the three climate components differed within and among species, suggesting that species can respond both rapidly and slowly to climate variation and that the responses represent different ecological processes. Thus, the assumption of equivalent species' response to spatial and temporal variation in climate was seldom met in our study system. Consequently, for the majority of our species, space-for-time substitution may only be applicable once the slow species' responses to a changing climate have occurred, whereas forecasts for the near future need to accommodate the temporal components of climate variation. However, appropriate forecast horizons for space-for-time substitution are rarely considered and may be difficult to reliably identify. Accurately predicting change is challenging because multiple ecological processes affect species distributions at different temporal scales.

Differential placental CpG methylation is associated with chronic lung disease of prematurity.

BACKGROUND: Chronic lung disease (CLD) is the most common pulmonary morbidity in extremely preterm infants. It is unclear to what extent prenatal exposures influence the risk of CLD. Epigenetic variation in placenta DNA methylation may be associated with differential risk of CLD, and these associations may be dependent upon sex. METHODS: Data were obtained from a multi-center cohort of infants born extremely preterm (<28 weeks' gestation) and an epigenome-wide approach was used to identify associations between placental DNA methylation and CLD (n = 423). Associations were evaluated using robust linear regression adjusting for covariates, with a false discovery rate of 0.05. Analyses stratified by sex were used to assess differences in methylation-CLD associations. RESULTS: CLD was associated with differential methylation at 49 CpG sites representing 46 genes in the placenta. CLD was associated with differential methylation of probes within genes related to pathways involved in fetal lung development, such as p53 signaling and myo-inositol biosynthesis. Associations between CpG methylation and CLD differed by sex. CONCLUSIONS: Differential placental methylation within genes with key roles in fetal lung development may reflect complex cell signaling between the placenta and fetus which mediate CLD risk. These pathways appear to be distinct based on fetal sex. IMPACT: In extremely preterm infants, differential methylation of CpG sites within placental genes involved in pathways related to cell signaling, oxidative stress, and trophoblast invasion is associated with chronic lung disease of prematurity. DNA methylation patterns associated with chronic lung disease were distinctly based on fetal sex, suggesting a potential mechanism underlying dimorphic phenotypes. Mechanisms related to fetal hypoxia and placental myo-inositol signaling may play a role in fetal lung programming and the developmental origins of chronic lung disease. Continued research of the relationship between the placental epigenome and chronic lung disease could inform efforts to ameliorate or prevent this condition.

US Black-White Differences in Mortality Risk Among Transgender and Cisgender People in Private Insurance, 2011-2019.

Objectives. To compare survival by gender and race among transgender and cisgender people enrolled in private insurance in the United States between 2011 and 2019. Methods. We examined Optum's Clinformatics Data Mart Database. We identified transgender enrollees using claims related to gender-affirming care. Our analytic sample included those we identified as transgender and a 10% random sample of cisgender enrollees. We limited our sample to those 18 years or older who were non-Hispanic Black or White. We identified 18 033 transgender and more than 4 million cisgender enrollees. We fit Kaplan-Meier survival curves and calculated standardized mortality ratios while adjusting for census region. Results. Black transfeminine and nonbinary people assigned male sex at birth were 2.73 times more likely to die than other Black transgender people and 2.38 and 3.34 times more likely than Black cisgender men and women, respectively; similar results were found when White transfeminine and nonbinary people assigned male sex at birth were compared with White cisgender cohorts. Conclusions. Our findings highlight glaring inequities in mortality risks among Black transfeminine and nonbinary people assigned male sex at birth and underscore the need to monitor mortality risks in transgender populations and address the social conditions that increase these risks. (Am J Public Health. 2022;112(10):1507-1514. https://doi.org/10.2105/AJPH.2022.306963).

High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING.

The killer-cell immunoglobulin-like receptor (KIR) complex on chromosome 19 encodes receptors that modulate the activity of natural killer cells, and variation in these genes has been linked to infectious and autoimmune disease, as well as having bearing on pregnancy and transplant outcomes. The medical relevance and high variability of KIR genes makes short-read sequencing an attractive technology for interrogating the region, providing a high-throughput, high-fidelity sequencing method that is cost-effective. However, because this gene complex is characterized by extensive nucleotide polymorphism, structural variation including gene fusions and deletions, and a high level of homology between genes, its interrogation at high resolution has been thwarted by bioinformatic challenges, with most studies limited to examining presence or absence of specific genes. Here, we present the PING (Pushing Immunogenetics to the Next Generation) pipeline, which incorporates empirical data, novel alignment strategies and a custom alignment processing workflow to enable high-throughput KIR sequence analysis from short-read data. PING provides KIR gene copy number classification functionality for all KIR genes through use of a comprehensive alignment reference. The gene copy number determined per individual enables an innovative genotype determination workflow using genotype-matched references. Together, these methods address the challenges imposed by the structural complexity and overall homology of the KIR complex. To determine copy number and genotype determination accuracy, we applied PING to European and African validation cohorts and a synthetic dataset. PING demonstrated exceptional copy number determination performance across all datasets and robust genotype determination performance. Finally, an investigation into discordant genotypes for the synthetic dataset provides insight into misaligned reads, advancing our understanding in interpretation of short-read sequencing data in complex genomic regions. PING promises to support a new era of studies of KIR polymorphism, delivering high-resolution KIR genotypes that are highly accurate, enabling high-quality, high-throughput KIR genotyping for disease and population studies.