National trends in reported past year opioid misuse among black women.

BACKGROUND: The opioid crisis within the United States has been widely studied; however, some gaps within the literature still exist. There is limited information on trends in opioid misuse as it relates to income among a national sample of Black Women. Given the recent increase in opioid overdose deaths in Black Americans and the vulnerability of women who misuse opioids, research in this population is important. OBJECTIVE: The objective of this study is to evaluate trends of past year opioid misuse (PYOM) among Black women by income over the study period. METHODS: A cross-sectional study among adult aged Black women captured in the National Survey on Drug Use and Health (NSDUH) from 2015 to 2019 was conducted. Descriptive statistics for all study variables was conducted. Weighted logistic regression analyses were conducted to evaluate predictors of PYOM. A stratified analysis was also conducted to examine possible differences between income strata on predictors of PYOM. RESULTS: A total of 15,196 Black women were included in the study (16,008,921 weighted visits). Among the women included, 41.5% were age 50+, 57.7% were unemployed, 63.8% reported very good/good health, 59.5% had past year alcohol use, 44.1% had never been married, 39.1% received government assistance, and 90.1% resided in a metro area. An estimated 3.14% of Black women reported PYOM. Findings from the regression analysis showed that Black women who were between 18 and 25, had past year major depressive episode, had alcohol use, illicit drug use, and who received government assistance had significantly greater odds of PYOM. Those reporting an excellent general health rating and higher education had significantly lower odds of PYOM. Income was not associated with PYOM in this study. CONCLUSION: Overall, income was not found to be a significant predictor of PYOM. However, income was found to modify the effects of major depressive episode and alcohol use on PYOM, especially among Black women who reported earning ≥$75,000/year. These findings suggest that high-earning Black women may be just as at risk for opioid misuse as low-earning Black women. Further studies are warranted to explore these effects among other gender/racial groups to determine if this trend is unique to Black women.

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs.

Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources.

Cassava (Manihot esculenta Crantz) is a food and industrial storage root crop with substantial potential to contribute to managing risk associated with climate change due to its inherent resilience and in providing a biodegradable option in manufacturing. In Africa, cassava production is challenged by two viral diseases, cassava brown streak disease (CBSD) and cassava mosaic disease. Here we detect quantitative trait loci (QTL) associated with CBSD in a biparental mapping population of a Tanzanian landrace, Nachinyaya and AR37-80, phenotyped in two locations over three years. The purpose was to use the information to ultimately facilitate either marker-assisted selection or adjust weightings in genomic selection to increase the efficiency of breeding. Results from this study were considered in relation to those from four other biparental populations, of similar genetic backgrounds, that were phenotyped and genotyped simultaneously. Further, we investigated the co-localization of QTL for CBSD resistance across populations and the genetic relationships of parents based on whole genome sequence information. Two QTL on chromosome 4 for resistance to CBSD foliar symptoms and one on each of chromosomes 11 and 18 for root necrosis were of interest. Of significance within the candidate genes underlying the QTL on chromosome 4 are Phenylalanine ammonia-lyase (PAL) and Cinnamoyl-CoA reductase (CCR) genes and three PEPR1-related kinases associated with the lignin pathway. In addition, a CCR gene was also underlying the root necrosis-resistant QTL on chromosome 11. Upregulation of key genes in the cassava lignification pathway from an earlier transcriptome study, including PAL and CCR, in a CBSD-resistant landrace compared to a susceptible landrace suggests a higher level of basal lignin deposition in the CBSD-resistant landrace. Earlier RNAscope® in situ hybridisation imaging experiments demonstrate that cassava brown streak virus (CBSV) is restricted to phloem vessels in CBSV-resistant varieties, and phloem unloading for replication in mesophyll cells is prevented. The results provide evidence for the involvement of the lignin pathway. In addition, five eukaryotic initiation factor (eIF) genes associated with plant virus resistance were found within the priority QTL regions.

Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research.

Research increasingly relies on interrogating large-scale data resources. The NIH National Heart, Lung, and Blood Institute developed the NHLBI BioData CatalystⓇ (BDC), a community-driven ecosystem where researchers, including bench and clinical scientists, statisticians, and algorithm developers, find, access, share, store, and compute on large-scale datasets. This ecosystem provides secure, cloud-based workspaces, user authentication and authorization, search, tools and workflows, applications, and new innovative features to address community needs, including exploratory data analysis, genomic and imaging tools, tools for reproducibility, and improved interoperability with other NIH data science platforms. BDC offers straightforward access to large-scale datasets and computational resources that support precision medicine for heart, lung, blood, and sleep conditions, leveraging separately developed and managed platforms to maximize flexibility based on researcher needs, expertise, and backgrounds. Through the NHLBI BioData Catalyst Fellows Program, BDC facilitates scientific discoveries and technological advances. BDC also facilitated accelerated research on the coronavirus disease-2019 (COVID-19) pandemic.

The 2022 human monkeypox outbreak: Clinical review and management guidance.

PURPOSE: The objective of this clinical review is to provide an overview of antiviral therapies for monkeypox treatment and summarize the role of vaccines in monkeypox prevention. SUMMARY: The human monkeypox virus is a double-stranded DNA virus of the Orthopoxvirus genus of the Poxviridae family. The estimated case fatality rate for monkeypox ranges between 0% and 11%. The first human monkeypox infection was reportedly due to an unidentified animal reservoir. Per the Centers for Disease Control and Prevention, isolation and infection control procedures should be followed in the care of those infected with monkeypox virus. Monkeypox virus infection symptoms include rash, fever, chills, headache, muscle aches, backache, and fatigue that may progress to exhaustion. Severe complications such as encephalitis, pneumonia, and retropharyngeal abscess could appear in immunocompromised or critically ill patients. There are currently no specific Food and Drug Administration (FDA)-approved therapies for monkeypox. As with most viral infections, supportive care is the backbone of monkeypox clinical management. However, therapies effective for smallpox, such as cidofovir, brincidofovir, and tecovirimat, have previously been reported to be effective in the management of monkeypox. Pre- and postexposure prophylaxis to prevent monkeypox transmission are recommended in the US for those at high risk for disease transmission. CONCLUSION: There are no FDA-approved treatments for monkeypox infection. Surveillance and detection of monkeypox among high-risk populations should be implemented to help understand the epidemiology of this disease.

New insights into Xenopus sex chromosome genomics from the Marsabit clawed frog X. borealis.

In many groups, sex chromosomes change frequently but the drivers of their rapid evolution are varied and often poorly characterized. With an aim of further understanding sex chromosome turnover, we investigated the polymorphic sex chromosomes of the Marsabit clawed frog, Xenopus borealis, using genomic data and a new chromosome-scale genome assembly. We confirmed previous findings that 54.1 Mb of chromosome 8L is sex-linked in animals from east Kenya and a laboratory strain, but most (or all) of this region is not sex-linked in natural populations from west Kenya. Previous work suggests possible degeneration of the Z chromosomes in the east population because many sex-linked transcripts of this female heterogametic population have female-biased expression, and we therefore expected this chromosome to not be present in the west population. In contrast, our simulations support a model where most or all of the sex-linked portion of the Z chromosome from the east acquired autosomal segregation in the west, and where much genetic variation specific to the large sex-linked portion of the W chromosome from the east is not present in the west. These recent changes are consistent with the hot-potato model, wherein sex chromosome turnover is favoured by natural selection if it purges a (minimally) degenerate sex-specific sex chromosome, but counterintuitively suggest natural selection failed to purge a Z chromosome that has signs of more advanced and possibly more ancient regulatory degeneration. These findings highlight complex evolutionary dynamics of young, rapidly evolving Xenopus sex chromosomes and set the stage for mechanistic work aimed at pinpointing additional sex-determining genes in this group.

Chromosome evolution and the genetic basis of agronomically important traits in greater yam.

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

Spatial ecology, activity patterns, and habitat use by giant pythons (Simalia amethistina) in tropical Australia.

Although giant snakes are abundant in some tropical forests, their ecology is far less well-known than for smaller species of snakes in cooler climates. Information on spatial ecology can clarify management issues such as the sizes and types of habitats needed for conservation. We radio-tracked 27 scrub pythons (Simalia amethistina; snout-vent lengths 2.02 to 3.70 m) in Cape York, near the northeastern tip of Australia, for a mean period of 426 days (up to 1001 days) per snake. Home ranges were larger in males than females (means 0.60 vs. 0.28 km2) and overlapped considerably among individuals. All snakes used rainforest habitat, but seasonal shifts into open woodland were common. Snakes were active primarily by night, with larger snakes hunting less of the time overall, and more often by day. Hunting behaviour was seen more often during the wet season than the dry season. Average daily displacement was < 10 m, typically involving a shift from diurnal refuge to nocturnal ambush-site. A reliance on sit-and-wait predation results in small home ranges and limited movements, despite the large body size of this species.

Long-term Survival after Hematopoietic Cell Transplant for Sickle Cell Disease Compared to the United States Population.

Hematopoietic cell transplant for sickle cell disease is curative but is associated with life threatening complications most of which occur within the first 2 years after transplantation. In the current era with interest in gene therapy and gene editing we felt it timely to report on sickle cell disease transplant recipients who were alive for at least 2-year after transplantation, not previously reported. Our objectives were to (1) report the conditional survival rates of patients who were alive for 2 or more years after transplantation (2) identify risk factors for death beyond 2 years after transplantation and (3) compare all-cause mortality risks to those of an age-, sex- and race-matched general population in the United States. By limiting to 2-year survivors, we exclude deaths that occur as a direct consequence of the transplantation procedure. De-identified records of 1149 patients were reviewed from a publicly available data source and 950 patients were eligible (https://picsure.biodatacatalyst.nhlbi.nih.gov). All analyses were performed in this secure cloud environment using the available statistical software package(s). The validity of the public database was confirmed by reproducing results from an earlier publication. Conditional survival estimates were obtained using the Kaplan-Meier method for the sub-cohort that had survived a given length (x) of time after transplantation. Cox regression models were built to identify risk factors associated with mortality beyond 2 years after transplantation. The standardized relative mortality risk (SMR) or the ratio of observed to expected number of deaths, was used to quantify all-cause mortality risk after transplantation and compared to age, race and sex-matched general population. Person-years at risk were calculated from an anchor date (i.e., 2-, 5- and 7-years) after transplantation until date of death or last date known alive. The expected number of deaths was calculated using age, race and sex-specific US mortality rates. The median follow up was 5 years (range 2-20) and 300 (32%) patients were observed for more than 7 years. Among those who lived for at least 7 years after transplantation the 12-year probability of survival was 97% (95% CI, 92%-99%). Compared to an age-, race- and sex-matched US population, the risk for late death after transplantation was higher as late as 7 years after transplantation (hazard ratio (HR) 3.2; P= .020) but the risk receded over time. Risk factors for late death included age at transplant and donor type. For every 10-year increment in patient age, an older patient was 1.75 times more likely to die than a younger patient (P= .0004). Compared to HLA-matched siblings the use of other donors was associated with higher risk for late death (HR 3.49; P= .003). Graft failure (beyond 2-years after transplantation) was 7% (95% CI, 5%-9%) and graft failure was higher after transplantation of grafts from donors who were not HLA-matched siblings (HR 2.59, P< .0001). Long-term survival after transplantation is excellent and support this treatment as a cure for sickle cell disease. The expected risk for death recedes over time but the risk for late death is not negligible.

CRISPR-Cas9-mediated knockout of CYP79D1 and CYP79D2 in cassava attenuates toxic cyanogen production.

Cassava (Manihot esculenta) is a starchy root crop that supports over a billion people in tropical and subtropical regions of the world. This staple, however, produces the neurotoxin cyanide and requires processing for safe consumption. Excessive consumption of insufficiently processed cassava, in combination with protein-poor diets, can have neurodegenerative impacts. This problem is further exacerbated by drought conditions which increase this toxin in the plant. To reduce cyanide levels in cassava, we used CRISPR-mediated mutagenesis to disrupt the cytochrome P450 genes CYP79D1 and CYP79D2 whose protein products catalyze the first step in cyanogenic glucoside biosynthesis. Knockout of both genes eliminated cyanide in leaves and storage roots of cassava accession 60444; the West African, farmer-preferred cultivar TME 419; and the improved variety TMS 91/02324. Although knockout of CYP79D2 alone resulted in significant reduction of cyanide, mutagenesis of CYP79D1 did not, indicating these paralogs have diverged in their function. The congruence of results across accessions indicates that our approach could readily be extended to other preferred or improved cultivars. This work demonstrates cassava genome editing for enhanced food safety and reduced processing burden, against the backdrop of a changing climate.

Current status and impending progress for cassava structural genomics.

KEY MESSAGE: We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.

Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade.

The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological data to construct a detailed phylogeny of this group, understand their biogeographic patterns and establish the systematic diversity of this genus. Our molecular genetic data support two major clades, corresponding to L. albertisii and L. fredparkeri, but offer no support for the other four species. Our morphological data also only support two species. We therefore recognize L. albertisii and L. fredparkeri as valid species and place L. biakensis, L. meridionalis, L. huonensis and L. montanus into synonymy. We found that L. albertisii and L. fredparkeri are sympatric in western New Guinea; an atypical pattern compared to other Papuan species complexes in which the distributions of sister taxa are partitioned to the north and south of the island's central mountain range. For the purpose of conservation management, overestimation of species diversity within Leiopython has resulted in the unnecessary allocation of resources that could have been expended elsewhere. We strongly caution against revising the taxonomy of geographically widespread species groups when little or no molecular genetic data and only small morphological samples are available.

The Dioscorea Genus (Yam)-An Appraisal of Nutritional and Therapeutic Potentials.

The quest for a food secure and safe world has led to continuous effort toward improvements of global food and health systems. While the developed countries seem to have these systems stabilized, some parts of the world still face enormous challenges. Yam (Dioscorea species) is an orphan crop, widely distributed globally; and has contributed enormously to food security especially in sub-Saharan Africa because of its role in providing nutritional benefits and income. Additionally, yam has non-nutritional components called bioactive compounds, which offer numerous health benefits ranging from prevention to treatment of degenerative diseases. Pharmaceutical application of diosgenin and dioscorin, among other compounds isolated from yam, has shown more prospects recently. Despite the benefits embedded in yam, reports on the nutritional and therapeutic potentials of yam have been fragmented and the diversity within the genus has led to much confusion. An overview of the nutritional and health importance of yam will harness the crop to meet its potential towards combating hunger and malnutrition, while improving global health. This review makes a conscious attempt to provide an overview regarding the nutritional, bioactive compositions and therapeutic potentials of yam diversity. Insights on how to increase its utilization for a greater impact are elucidated.

Genetic analysis and QTL mapping for multiple biotic stress resistance in cassava.

In Sub-Saharan Africa cassava (Manihot esculenta Crantz) is one of the most important food crops where more than 40% of the population relies on it as their staple carbohydrate source. Biotic constraints such as viral diseases, mainly Cassava Mosaic Disease (CMD) and Cassava Brown Streak Disease (CBSD), and arthropod pests, particularly Cassava Green Mite (CGM), are major constraints to the realization of cassava's full production potential in Africa. To address these problems, we aimed to map the quantitative trait loci (QTL) associated with resistance to CBSD foliar and root necrosis symptoms, foliar CMD and CGM symptoms in a full-sib mapping population derived from the genotypes AR40-6 and Albert. A high-density linkage map was constructed with 2,125 SNP markers using a genotyping-by-sequencing approach. For phenotyping, clonal evaluation trials were conducted with 120 F1 individuals for two consecutive field seasons using an alpha-lattice design at Chambezi and Naliendele, Tanzania. Previously identified QTL for resistance to CBSD foliar symptoms were corroborated, and a new putative QTL for CBSD root necrosis identified (qCBSDRNc14AR) from AR40-6. Two QTL were identified within the region of the previously recognized CMD2 locus from this population in which both parents are thought to possess the CMD2 locus. Interestingly, a minor but consistent QTL, qCGM18AR, for CGM resistance at 3 months after planting stage was also detected and co-localized with a previously identified SSR marker, NS346, linked with CGM resistance. Markers underlying these QTL may be used to increase efficiencies in cassava breeding programs.

Scalability and cost-effectiveness analysis of whole genome-wide association studies on Google Cloud Platform and Amazon Web Services.

OBJECTIVE: Advancements in human genomics have generated a surge of available data, fueling the growth and accessibility of databases for more comprehensive, in-depth genetic studies. METHODS: We provide a straightforward and innovative methodology to optimize cloud configuration in order to conduct genome-wide association studies. We utilized Spark clusters on both Google Cloud Platform and Amazon Web Services, as well as Hail (http://doi.org/10.5281/zenodo.2646680) for analysis and exploration of genomic variants dataset. RESULTS: Comparative evaluation of numerous cloud-based cluster configurations demonstrate a successful and unprecedented compromise between speed and cost for performing genome-wide association studies on 4 distinct whole-genome sequencing datasets. Results are consistent across the 2 cloud providers and could be highly useful for accelerating research in genetics. CONCLUSIONS: We present a timely piece for one of the most frequently asked questions when moving to the cloud: what is the trade-off between speed and cost?

Species delimitation and systematics of the green pythons (Morelia viridis complex) of melanesia and Australia.

Molecular data sets and the increasing use of integrative systematics is revealing cryptic diversity in a range of taxa - particularly in remote and poorly sampled landscapes like the island of New Guinea. Green pythons (Morelia viridis complex) are one of the most conspicuous elements of this island's fauna, with large numbers taken from the wild to supply international demand for exotic pets. We test hypotheses about species boundaries in green pythons from across New Guinea and Australia with mitochondrial genomes, 389 nuclear exons, and comprehensive assessment of morphological variation. Strong genetic structuring of green python populations and species delimitation methods confirm the presence of two species, broadly occurring north and south of New Guinea's central mountains. Our data also support three subspecies within the northern species. Subtle but consistent morphological divergence among the putative taxa is concordant with patterns of molecular divergence. Our extensive sampling identifies several zones of hitherto unknown biogeographical significance on the island of New Guinea. We revise the taxonomy of the group, discuss the relevance of our findings in the context of Papuan biogeography and the implications of our systematic changes for the conservation management of these taxa.

A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.

The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages ("synteny") and local gene order. A network analysis of developmental gene expression will aid future studies.

Cane toads beneath bird rookeries: utilization of a natural disturbance by an invasive species.

Many invasive species exploit anthropogenically disturbed habitats, but most of those taxa evolved long before humans. Presumably, then, an ability to use natural (non-anthropogenic) disturbances pre-adapted invaders to a world later degraded by people. Studies on invasive species in naturally disturbed habitats thus can clarify the ancestral niche of invaders. In the Australian tropics, metallic starlings Aplonis metallica nest communally in emergent rainforest trees during the wet-season, and invasive cane toads Rhinella marina join other predators (mammals, birds, reptiles, and other anurans) to exploit the food resources beneath those trees. Compared to conspecifics found along nearby roads through the forest, cane toads beneath bird-nesting trees occur at higher densities, and are smaller in body size. The sex ratio is female-biased, and recapture records suggest that females may be philopatric at these sites (whereas recaptures were rare for both sexes found along the roads). Some toads were found under the same trees in successive wet-seasons. Spooling showed that distances moved per night were similar along the road versus under the trees, but toads under trees showed lower net displacements. Diets also differed (based upon scat analysis), with tree toads feeding more on beetles and less on ants. These nutrient-rich hotspots are exploited primarily by adult females and juvenile toads, whereas adult males congregate at breeding sites. By magnifying pre-existing intraspecific divergences in habitat use, bird rookeries may enhance population viability of cane toads by enabling critical age and sex classes to exploit food-rich patches that are rarely used by adult males.