Search

We present a genome assembly from an individual Tausonia pullulans (a basidiomycete yeast; Basidiomycota; Tremellomycetes; Cystofilobasidiales; Mrakiaceae). The genome sequence is 23.9 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.82 kilobases in length.

Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.

Abstract Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (Pinteraction = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications.

Rapid antigen testing (RAT) is a cost-effective and time-efficient method of identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and therefore a critical part of infection control strategies. There is no published evidence evaluating the use of RAT during the Omicron wave of the COVID-19 pandemic for asymptomatic patients or its performance between waves. All patients presenting to an Emergency Department over a two-week period without COVID-19 symptoms were screened for SARS-CoV-2 using both the Abbott Panbio RAT as well as the gold standard reverse transcriptase real-time polymerase chain reaction (PCR). The Abbott Panbio RAT sensitivity was 13% (95% CI 0.028, 0.336) for asymptomatic patients. The use of this test in asymptomatic patients during the Omicron wave had a statistically significant reduction in sensitivity compared with two reports of the same test in previous waves (13% vs. 86%, p < 0.0001; 13% vs. 83%, p < 0.0001). As SARS-CoV-2 continues to mutate, the sensitivity of RATs are altered and needs to be continually re-evaluated for each variant of concern if they are to be used as part of an infection control strategy.

We present a genome assembly from an individual Lactarius evosmus (Fruity Milkcap; Basidiomycota; Agaricomycetes; Russulales; Russulaceae). The genome sequence is 57.2 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 61.51 kilobases in length.

Current understanding of Long COVID is limited, in part, due to lack of evidence from population-representative studies. Here, the authors analyse data from ten UK population-based studies and electronic health records, and find wide variation in the frequency of Long COVID between studies but some consistent risk factors.

Tailoring the macroscopic properties of deep eutectic solvents requires knowing how these depend on the local structure and microscopic dynamics. The authors, with computational and experimental tools spanning a wide range of space- and timescales, shed light into the relationship between micro and macroscopic properties in glyceline and ethaline.

Resource development and climate change are increasing concerns regarding safe water for Indigenous people in Canada. A research study was completed to characterize the consumption of water and beverages prepared with water and identify the perception of water consumption in Indigenous communities from the Northwest Territories and Yukon, Canada. As part of a larger research program, data for this study were available from a 24-hour recall dietary survey (n = 162), a health messages survey (n = 150), and an exposure factor survey (n = 63). A focus group was conducted with Elders in an on-the-land camp setting. The consumption of water-based beverages in winter was 0.9 L/day on average, mainly consisting of tea and coffee. Of the 81% of respondents who reported consuming water-based beverages in the previous 24 hours of the survey, 33% drank more bottled water than tap water. About 2% of respondents consumed water from the land (during the winter season). Chlorine smell was the main limiting factor reported to the consumption of tap water. Results from the focus group indicated that Indigenous knowledge might impact both the perception and consumption of water. These findings aim to support public health efforts to enable people to make water their drink of choice.

Frailty is associated with adverse health outcomes and greater healthcare utilization. Less is known about the relationship between frailty and healthcare utilization in Puerto Rico, where high rates of chronic conditions and limited healthcare may put this group at a higher likelihood of using healthcare resources. This study examined the association between pre-frailty and frailty with healthcare utilization at baseline and 4-year follow-up among a cohort of community dwelling Puerto Ricans living on the island. We examined data from 3,040 Puerto Ricans (mean age 70.6 years) from The Puerto Rican Elderly: Health Conditions (PREHCO) study between 2002–2003 and 2006–2007. We used a modified version of the Fried criteria defined as 3 or more of the following: shrinking, weakness, poor energy, slowness, and low physical activity. Pre-frailty was defined as 1–2 components. The number of emergency room visits, hospital stays, and doctor visits within the last year were self-reported. Zero-inflated negative binomial regression models were used for ER visits and hospital stays. Negative binomial models were used for doctor visits. Pre-frailty was associated with a higher rate of doctor visits with a rate ratio of 1.11 (95% CI = 1.01–1.22) at baseline. Frailty was associated with a higher rate of ER visits (1.48, 95% CI = 1.13–1.95), hospital stays (1.69, 95% CI = 1.08–2.65), and doctor visits (1.24, 95% CI = 1.10–1.39) at baseline. Pre-frailty and frailty were not associated with any healthcare outcomes at follow-up. Pre-frailty and frailty are associated with an increased rate of healthcare services cross-sectionally among Puerto Rican adults, which may cause additional burdens on the already pressured healthcare infrastructure on the island.

Frailty is associated with adverse health outcomes and greater healthcare utilization. Less is known about the relationship between frailty and healthcare utilization in Puerto Rico, where high rates of chronic conditions and limited healthcare may put this group at a higher likelihood of using healthcare resources. This study examined the association between pre-frailty and frailty with healthcare utilization at baseline and 4-year follow-up among a cohort of community dwelling Puerto Ricans living on the island. We examined data from 3,040 Puerto Ricans (mean age 70.6 years) from The Puerto Rican Elderly: Health Conditions (PREHCO) study between 2002-2003 and 2006-2007. We used a modified version of the Fried criteria defined as 3 or more of the following: shrinking, weakness, poor energy, slowness, and low physical activity. Pre-frailty was defined as 1-2 components. The number of emergency room visits, hospital stays, and doctor visits within the last year were self-reported. Zero-inflated negative binomial regression models were used for ER visits and hospital stays. Negative binomial models were used for doctor visits. Pre-frailty was associated with a higher rate of doctor visits with a rate ratio of 1.11 (95% CI = 1.01-1.22) at baseline. Frailty was associated with a higher rate of ER visits (1.48, 95% CI = 1.13-1.95), hospital stays (1.69, 95% CI = 1.08-2.65), and doctor visits (1.24, 95% CI = 1.10-1.39) at baseline. Pre-frailty and frailty were not associated with any healthcare outcomes at follow-up. Pre-frailty and frailty are associated with an increased rate of healthcare services cross-sectionally among Puerto Rican adults, which may cause additional burdens on the already pressured healthcare infrastructure on the island.

We present a genome assembly from an individual Laetiporus sulphureus (the chicken of the woods fungus; Basidiomycota; Agaricomycetes; Polyporales; Laetiporaceae). The genome sequence is 37.4 megabases in span. The complete assembly is scaffolded into 14 chromosomal pseudomolecules.

BackgroundSex differences in post-stroke cognitive decline have not been systematically evaluated in a nationally representative cohort. We use a quasi-experimental design to investigate sex differences in rate of post-stroke cognitive decline.MethodsUtilizing the event study design, we use the Health and Retirement Study (HRS) data (1996-2016) to evaluate the differences (percentage points [95% Confidence interval]) in the rate of change in cognitive function, measured using the modified version of the Telephone Interview for Cognitive Status (TICS-m) score, before and after incident stroke, and among patients with and without incident stroke. We estimated this event study model for the overall study population and separately fit the same model for male and female participants.ResultsOf 25,872 HRS participants included in our study, 14,459 (55.9%) were females with an overall mean age (SD) of 61.2 (9.3) years. Overall, 2,911 (11.3%) participants reported experiencing incident stroke. Participants with incident stroke (vs. no stroke) had lower baseline TICS-m score (15.6 vs. 16.1). Among participants with incident stroke, the mean pre-stroke TICS-m score was higher than the mean post-stroke TICS-m score (14.9 vs. 12.7). Event study revealed a significant short-term acceleration of cognitive decline for the overall population (4.2 [1.7-6.6] percentage points, p value = 0.001) and among female participants (5.0 [1.7-8.3] percentage points, p value = 0.003). We, however, found no evidence of long-term acceleration of cognitive decline after stroke. Moreover, among males, incident stroke was not associated with significant changes in rate of post-stroke cognitive decline.ConclusionFemales, in contrast to males, experience post-stroke cognitive deficits, particularly during early post-stroke period. Identifying the sex-specific stroke characteristics contributing to differences in post stroke cognitive decline may inform future strategies for reducing the burden of post-stroke cognitive impairment and dementia.

Purposes The relationship between body mass index (BMI) and frailty in older Mexican Americans has not been previously studied. The objective of this study was to examine the relationship between BMI and frailty among non-frail older Mexican Americans at baseline over 18 years of follow up. Methods Longitudinal population-based study of 1,648 non-institutionalized Mexican Americans aged ≥ 67 years from the Hispanic Established Population for the Epidemiologic Study of the Elderly (1995/96-2012/13). Frailty phenotype was defined as meeting three or more of the following: unintentional weight loss of >10 pounds, weakness, self-reported exhaustion, low physical activity, and slow walking speed. BMI (kg/m2) was classified as underweight (Results Participants with underweight or obesity category II/ morbid obesity had greater odds of frailty over time compared to those with normal weight (OR = 2.39, 95% CI = 1.29–4.44 and OR = 1.62, 95% CI = 1.07–2.44, respectively) after controlling for all covariates. Participants with BMIs in the overweight or category I obesity were at lower odds of frailty over time. Conclusions Mexican American older adults with BMIs in the underweight or obesity category II/morbid obesity were at higher odds of frailty over time. This indicates that maintaining a healthy weight in this population may prevent future frailty.

PurposesThe relationship between body mass index (BMI) and frailty in older Mexican Americans has not been previously studied. The objective of this study was to examine the relationship between BMI and frailty among non-frail older Mexican Americans at baseline over 18 years of follow up.MethodsLongitudinal population-based study of 1,648 non-institutionalized Mexican Americans aged ≥ 67 years from the Hispanic Established Population for the Epidemiologic Study of the Elderly (1995/96-2012/13). Frailty phenotype was defined as meeting three or more of the following: unintentional weight loss of >10 pounds, weakness, self-reported exhaustion, low physical activity, and slow walking speed. BMI (kg/m2) was classified as underweight (ResultsParticipants with underweight or obesity category II/ morbid obesity had greater odds of frailty over time compared to those with normal weight (OR = 2.39, 95% CI = 1.29-4.44 and OR = 1.62, 95% CI = 1.07-2.44, respectively) after controlling for all covariates. Participants with BMIs in the overweight or category I obesity were at lower odds of frailty over time.ConclusionsMexican American older adults with BMIs in the underweight or obesity category II/morbid obesity were at higher odds of frailty over time. This indicates that maintaining a healthy weight in this population may prevent future frailty.

Genome-wide association studies (GWAS) of neuroimaging data pose a significant computational burden because of the need to correct for multiple testing in both the genetic and the imaging data. Here, Ganjgahi et al. develop WLS-REML which significantly reduces computation running times in brain imaging GWAS.

The impacts of changes in climate are often most readily observed through the effects of extremes in local weather, effects that often propagate through multiple ecosystem levels. Precise effects of any extreme weather event depend not only on the type of event and its timing, but also on the ecosystem affected. Here the cascade of effects following the arrival of an atmospheric river (directed by record-breaking Storm Desmond) across terrestrial, freshwater and coastal zones is quantified, using the Burrishoole system on the Atlantic coast of Ireland as a natural observatory. We used a network of high-frequency in-situ sensors to capture in detail the effects of an unprecedented period of rainfall, high wind speeds and above-average winter air temperatures on catchment and estuarine dynamics. In the main freshwater lake, water clarity decreased and acidity increased during Storm Desmond. Surface heat input, due to a warm and moist above-lake air mass, was rapidly distributed throughout the water column. River discharge into the downstream coastal basin was estimated to be the highest on record (since 1976), increasing the buoyancy flux by an order of magnitude and doubling the water column stratification stability. Entrainment of salt into the outflowing freshwater plume exported resident salt from the inner estuarine basin, resulting in net salt loss. Here, the increased stratification markedly reinforced isolation of the bottom waters, promoting deoxygenation. Measurements of current between the inner estuarine basin and the adjacent coastal waters indicated a 20-fold increase in the volume of seaward flowing low-salinity water, as a result of storm rainfall over the watershed. Storm impacts spanned the full catchment-to-coast continuum and these results provide a glimpse into a potential future for hydrological systems where these severe hydroclimatic events are expected to occur more frequently.

BACKGROUND:Older adults with Alzheimer's disease and related dementias (ADRD) are high-risk to experience hospitalizations and emergency room (ER) admissions. Mexican-Americans have a high prevalence of ADRD, but there is limited information on the healthcare use of older Mexican-Americans with ADRD. We used data from a cohort of older Mexican-Americans that has been linked with Medicare files to investigate differences in hospitalizations, ER admissions, and physician visits according to ADRD diagnosis. We also identify sociodemographic, health, and functional characteristics that may contribute to differences in healthcare utilization between Mexican-American Medicare beneficiaries with and without an ADRD diagnosis. METHODS AND FINDINGS:Data came from the Hispanic Established Populations for the Epidemiological Study of the Elderly that has been linked with Medicare Master Beneficiary Summary Files, Medicare Provider Analysis and Review files, Outpatient Standard Analytic files, and Carrier files. The final analytic sample included 1048 participants. Participants were followed for two years (eight quarters) after their survey interview. Generalized estimating equations were used to estimate the probability for one or more hospitalizations, ER admissions, and physician visits at each quarter. ADRD was associated with higher odds for hospitalizations (OR = 1.65, 95%CI = 1.29-2.11) and ER admissions (OR = 1.57, 95%CI = 1.23-1.94) but not physician visits (OR = 1.23, 95%CI = 0.91-1.67). The odds for hospitalizations (OR = 1.24, 95%CI = 0.97-1.60) and ER admissions (OR = 1.27, 95%CI = 1.01-1.59) were reduced after controlling for limitations in activities of daily living and comorbidities. CONCLUSIONS:Mexican-American Medicare beneficiaries with ADRD had significantly higher odds for one or more hospitalizations and ER admissions but similar physician visits compared to beneficiaries without ADRD. Functional limitations and comorbidities contributed to the higher hospitalizations and ER admissions for older Mexican-Americans with ADRD.

The design of efficient and stable oxygen evolution catalysts has implications for water splitting and metal-air battery technology. Here, the authors fabricate double perovskite nanofibers and demonstrate the favourable effects of co-doping and nanostructuring on oxygen evolution performance.

In 2015, we conducted a cross-sectional, Internet-based, U.S. nationally representative probability survey of 2,021 adults (975 men, 1,046 women) focused on a broad range of sexual behaviors. Individuals invited to participate were from the GfK KnowledgePanel®. The survey was titled the 2015 Sexual Exploration in America Study and survey completion took about 12 to 15 minutes. The survey was confidential and the researchers never had access to respondents' identifiers. Respondents reported on demographic items, lifetime and recent sexual behaviors, and the appeal of 50+ sexual behaviors. Most (>80%) reported lifetime masturbation, vaginal sex, and oral sex. Lifetime anal sex was reported by 43% of men (insertive) and 37% of women (receptive). Common lifetime sexual behaviors included wearing sexy lingerie/underwear (75% women, 26% men), sending/receiving digital nude/semi-nude photos (54% women, 65% men), reading erotic stories (57% of participants), public sex (≥43%), role-playing (≥22%), tying/being tied up (≥20%), spanking (≥30%), and watching sexually explicit videos/DVDs (60% women, 82% men). Having engaged in threesomes (10% women, 18% men) and playful whipping (≥13%) were less common. Lifetime group sex, sex parties, taking a sexuality class/workshop, and going to BDSM parties were uncommon (each

BackgroundPeste des petits ruminants (PPR) is a contagious disease listed by the World Organisation for Animal health (OIE) as being a specific hazard. It affects sheep, goats, and wild ungulates, and is prevalent throughout the developing world particularly Asia, the Middle East, and Africa. PPR has been targeted for eradication by 2030 by the Food and Agriculture Organization of the United Nations (FAO) and the OIE, after the successful eradication of the related disease, rinderpest in cattle. PPR was first reported in 1942 in the Ivory Coast in Western Africa and has since extended its range in Asia, the Middle East, and Africa posing an immediate threat of incursion into Europe, South East Asia and South Africa. Although robust vaccines are available, the use of these vaccines in a systematic and rational manner is not widespread, resulting in this devastating disease becoming an important neglected tropical disease in the developing world.MethodologyWe isolated and characterized the PPR virus from an outbreak in Cheraga, northern Algeria, during October 2015 by analyzing the partial N-gene sequence in comparison with other viruses from the Maghreb region. As well as sequencing the full length viral genome and performing real-time RT-PCR on clinical samples. Maximum-likelihood and Bayesian temporal and phylogeographic analyses were performed to assess the persistence and spread of PPRV circulation from Eastern Africa in the Maghreb region of North Africa.ConclusionsRecent PPR outbreaks in Cheraga, in the northern part of Algiers (October 2015) and North-West Morocco (June, 2015) highlight that PPRV has spread to the northern border of North Africa and may pose a threat of introduction to Europe. Phylogeographic analysis suggests that lineage IV PPRV has spread from Eastern Africa, most likely from the Sudan 2000 outbreak, into Northern Africa resulting in the 2008 Moroccan outbreak. Maximum-likelihood and Bayesian analysis shows that these North African viruses cluster closely together suggesting the existence of continual regional circulation. Considering the same virus is circulating in Algeria, Morocco and Tunisia, implementation of a common Maghreb PPR eradication strategy would be beneficial for the region.

As bisexual individuals in the United States (U.S.) face significant health disparities, researchers have posited that these differences may be fueled, at least in part, by negative attitudes, prejudice, stigma, and discrimination toward bisexual individuals from heterosexual and gay/lesbian individuals. Previous studies of individual and social attitudes toward bisexual men and women have been conducted almost exclusively with convenience samples, with limited generalizability to the broader U.S. POPULATION:Our study provides an assessment of attitudes toward bisexual men and women among a nationally representative probability sample of heterosexual, gay, lesbian, and other-identified adults in the U.S. Data were collected from the 2015 National Survey of Sexual Health and Behavior (NSSHB), via an online questionnaire with a probability sample of adults (18 years and over) from throughout the U.S. We included two modified 5-item versions of the Bisexualities: Indiana Attitudes Scale (BIAS), validated sub-scales that were developed to measure attitudes toward bisexual men and women. Data were analyzed using descriptive statistics, gamma regression, and paired t-tests. Gender, sexual identity, age, race/ethnicity, income, and educational attainment were all significantly associated with participants' attitudes toward bisexual individuals. In terms of responses to individual scale items, participants were most likely to "neither agree nor disagree" with all attitudinal statements. Across sexual identities, self-identified other participants reported the most positive attitudes, while heterosexual male participants reported the least positive attitudes. As in previous research on convenience samples, we found a wide range of demographic characteristics were related with attitudes toward bisexual individuals in our nationally-representative study of heterosexual, gay/lesbian, and other-identified adults in the U.S. In particular, gender emerged as a significant characteristic; female participants' attitudes were more positive than male participants' attitudes, and all participants' attitudes were generally more positive toward bisexual women than bisexual men. While recent population data suggest a marked shift in more positive attitudes toward gay men and lesbian women in the general population of the U.S., the largest proportions of participants in our study reported a relative lack of agreement or disagreement with all affective-evaluative statements in the BIAS scales. Findings document the relative lack of positive attitudes toward bisexual individuals among the general population of adults in the U.S. and highlight the need for developing intervention approaches to promote more positive attitudes toward bisexual individuals, targeted toward not only heterosexual but also gay/lesbian individuals and communities.

Chironomidae (Diptera) are among the most diverse and widespread aquatic insects, with roughly 5,500 described species. However, prior to the present work, no species of Chironomidae had been documented from the island of Hispaniola. Collections of non-biting midges, with emphasis on the lotic fauna, were made in the Dominican Republic during July of 2015. In total, 578 specimens belonging to 27 genera and at least 44 species within the subfamilies Chironominae (20 taxa), Orthocladiinae (16 taxa) and Tanypodinae (8 taxa) were found. The subfamilies Chironominae and Orthocladiinae predominated. Polypedilum was the most widespread and diverse genus of Chironominae. Metriocnemus were collected in bromeliad tanks. The chironomid fauna in Dominican Republic includes multiple genera with worldwide distributions, including Holarctic and Neotropical components.

The South African local government sector has undergone changes in the post-apartheid era as policy makers have sought to improve basic services provided to disadvantaged local communities. While scholars have considered various dimensions of the reform program, little effort has been directed at evaluating the effectiveness and efficiency dimensions of the changes in service provision, with some notable exceptions (van der Westhuizen and Dollery, 2009; Krugell, et al., 2010). This article seeks to contribute to this literature by evaluating the efficiency with which municipalities have provided (Reconstruction and Development Program) RDP water, RDP sanitation RDP electricity and RDP refuse removal, using Data Envelopment Analysis techniques (DEA) applied to panel data from 2006/2007 to 2008/2009 for 231 local municipalities and 46 district municipalities. Keywords: Data warehousing, Systems thinking, Prescriptive theory, Descriptive theory, Interpretative research. Disciplines: Information technology, systems theory, data warehousing, hermeneutics

A high percentage of patients with the myeloproliferative disorder polycythemia vera (PV) harbor a Val617→Phe activating mutation in the Janus kinase 2 (JAK2) gene, and both cell culture and mouse models have established a functional role for this mutation in the development of this disease. We describe the properties of MRLB-11055, a highly potent inhibitor of both the WT and V617F forms of JAK2, that has therapeutic efficacy in erythropoietin (EPO)-driven and JAK2V617F-driven mouse models of PV. In cultured cells, MRLB-11055 blocked proliferation and induced apoptosis in a manner consistent with JAK2 pathway inhibition. MRLB-11055 effectively prevented EPO-induced STAT5 activation in the peripheral blood of acutely dosed mice, and could prevent EPO-induced splenomegaly and erythrocytosis in chronically dosed mice. In a bone marrow reconstituted JAK2V617F-luciferase murine PV model, MRLB-11055 rapidly reduced the burden of JAK2V617F-expressing cells from both the spleen and the bone marrow. Using real-time in vivo imaging, we examined the kinetics of disease regression and resurgence, enabling the development of an intermittent dosing schedule that achieved significant reductions in both erythroid and myeloid populations with minimal impact on lymphoid cells. Our studies provide a rationale for the use of non-continuous treatment to provide optimal therapy for PV patients.

South Africa has experienced immense changes in the post- apartheid era and coordinated local public policy has sought to expand and improve the level of basic services provided to previously disadvantaged people. Local government has played a pivotal role in this process and has been subjected to intense reform in an effort to enhance its effective- ness and broaden its range of activities. While a number of scholars have examined the administrative, political and social dimensions of the local government reform program, little attention has focused on the economic efficiency of service delivery. This paper seeks to remedy this neglect by evaluating the productive efficiency with which municipal councils have delivered electricity, domestic waste removal, sanitation and water in line with their new responsibilities using Data Envelopment Analysis (DEA) techniques applied to cross-sectional data covering the period 2006/2007 for 231 local municipalities and 46 district municipalities.