Experiences in providing a community educational resource for the All of Us Researcher Workbench.

OBJECTIVE: Educational offerings to fill the bioinformatics knowledge gap are a key component to enhancing access and use of health data from the All of Us Research Program. We developed a Train the Trainer-based, innovative training series including project-based learning, modular on-demand demonstrations, and unstructured tutorial time as a model for educational engagement in the All of Us community. MATERIALS AND METHODS: We highlight our training modules and content, with training survey data informing cycles of development in the creation of a 6-module training series with modular demonstrations. RESULTS: We have conducted 2 public iterations of the Train the Trainer (Tx3) Series based on survey feedback while training over 300 registered researchers to access and analyze data on the All of Us Researcher Workbench. DISCUSSION AND CONCLUSION: Future directions of the Tx3 Series include enhanced focus on project-based learning and learner requests for modularity and asynchronous materials access.

Improved high quality sand fly assemblies enabled by ultra low input long read sequencing.

Phlebotomine sand flies are the vectors of leishmaniasis, a neglected tropical disease. High-quality reference genomes are an important tool for understanding the biology and eco-evolutionary dynamics underpinning disease epidemiology. Previous leishmaniasis vector reference sequences were limited by sequencing technologies available at the time and inadequate for high-resolution genomic inquiry. Here, we present updated reference assemblies of two sand flies, Phlebotomus papatasi and Lutzomyia longipalpis. These chromosome-level assemblies were generated using an ultra-low input library protocol, PacBio HiFi long reads, and Hi-C technology. The new P. papatasi reference has a final assembly span of 351.6 Mb and contig and scaffold N50s of 926 kb and 111.8 Mb, respectively. The new Lu. longipalpis reference has a final assembly span of 147.8 Mb and contig and scaffold N50s of 1.09 Mb and 40.6 Mb, respectively. Benchmarking Universal Single-Copy Orthologue (BUSCO) assessments indicated 94.5% and 95.6% complete single copy insecta orthologs for P. papatasi and Lu. longipalpis. These improved assemblies will serve as an invaluable resource for future genomic work on phlebotomine sandflies.

Genomics of Natural Populations: Gene Conversion Events Reveal Selected Genes within the Inversions of Drosophila pseudoobscura.

When adaptive phenotypic variation or QTLs map within an inverted segment of a chromosome, researchers often despair because the suppression of crossing over will prevent the discovery of selective target genes that established the rearrangement. If an inversion polymorphism is old enough, then the accumulation of gene conversion tracts offers the promise that QTLs or selected loci within inversions can be mapped. The inversion polymorphism of Drosophila pseudoobscura is a model system to show that gene conversion analysis is a useful tool for mapping selected loci within inversions. D. pseudoobscura has over 30 different chromosomal arrangements on the third chromosome (Muller C) in natural populations and their frequencies vary with changes in environmental habitats. Statistical tests of five D. pseudoobscura gene arrangements identified outlier genes within inverted regions that had potentially heritable variation, either fixed amino acid differences or differential expression patterns. We use genome sequences of the inverted third chromosome (Muller C) to infer 98,443 gene conversion tracts for a total coverage of 142 Mb or 7.2 x coverage of the 19.7 Mb chromosome. We estimated gene conversion tract coverage in the 2,668 genes on Muller C and tested whether gene conversion coverage was similar among arrangements for outlier versus non-outlier loci. Outlier genes had lower gene conversion tract coverage among arrangements than the non-outlier genes suggesting that selection removes exchanged DNA in the outlier genes. These data support the hypothesis that the third chromosome in D. pseudoobscura captured locally adapted combinations of alleles prior to inversion mutation events.

Decreasing Prejudicial Attitudes of Fear and Avoidance Toward Those Who Live with a Mental Illness-A Quasi-Experimental Controlled Study.

The undergraduate mental health nursing course is an optimal time to address stigma and prejudice, while developing positive student attitudes toward those who live with mental health conditions. A quasi-experimental, pretest-posttest, nonequivalent-group study with a sample of undergraduate nursing students in New York City (N = 126) was conducted to determine the impact of an undergraduate mental health nursing course on attitudes toward people living with a general mental illness, depression, or schizophrenia. The intervention resulted in a significant reduction in total prejudice scores toward those with a general mental illness when compared to the control (p = 0.033, partial η2 = 0.062). The intervention had no significant impact on total prejudice scores regarding those with depression, or schizophrenia. Subscale analysis revealed the intervention significantly reduced attitudes of fear/avoidance regarding general mental illness (p = 0.040, partial η2 = 0.058) and schizophrenia (p < 0.001, partial η2 = 0.164). There was no impact on authoritarian or malevolent attitudes. Though some attitudes were not amenable to change, this study provides evidence that positive attitudes can be cultivated through undergraduate nursing education. Curricular reform is needed to reduce all facets of prejudice and best prepare future nurses to care for those with mental health conditions.

FAIR Header Reference genome: a TRUSTworthy standard.

The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability and Technology. The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.

A Missed Opportunity to Cultivate Positive Attitudes about Mental Health Recovery among Undergraduate Nursing Students - A Quasi-Experimental Controlled Study.

INTRODUCTION: Mental health recovery is a critical concept that needs to be thoroughly understood and supported by nurses. Undergraduate nurse educators have the opportunity to clarify misconceptions and cultivate positive recovery attitudes. AIM: To assess the impact of an undergraduate nursing course on attitudes toward mental health recovery and the relationship between recovery attitudes and prejudice toward those who experience a mental illness. METHODS: A quasi-experimental pretest-posttest, nonequivalent-control group study was conducted using a sample of undergraduate nursing students in New York City (N = 126). The intervention group was assigned to an undergraduate mental health nursing course and the control group to a pediatric/maternal health nursing course. Attitudes toward mental health recovery and prejudice were measured at the beginning and end of the semester. Two-way mixed analyses of variance were used to determine the differences in students' attitudes. Pearson product-moment correlation analyses were used to assess the relationship between prejudice toward people who experience a mental illness and attitudes toward recovery. RESULTS: The mental health nursing course had no measurable impact on students' recovery attitudes. However, there was a moderate-to-strong inverse relationship between recovery attitudes and prejudice toward those who experience a general mental illness (r = -0.54), depression (r = -0.60), or schizophrenia (r = -0.43). CONCLUSIONS: Curriculum reform is needed to optimize the impact of undergraduate education on students' attitudes. Possible changes include a more holistic approach to mental health that does not over accentuate the biomedical model, the use of nontraditional clinical sites that provide students an opportunity to interact with those further along in their recovery, and the inclusion of those in recovery in curriculum development. As there was a moderate-to-strong inverse relationship between recovery attitudes and prejudice, educational interventions that positively impact one may also impact the other. Further research is needed to investigate if the relationship is causal.

DATA RESOURCES AND ANALYSES FAIR Header Reference genome: A TRUSTworthy standard.

The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability, and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability, and Technology (TRUST). The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility, and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.

Two new species of green treefrogs (Pelodryadidae: Litoria) from the northern slopes of Papua New Guinea's Central Cordillera.

We describe two new species of moderate-sized (male body length 26.5-29.8 mm and 41.0 mm), predominantly green treefrogs in the genus Litoria from hill forest on the northern slopes of Papua New Guinea's Central Cordillera. Phylogenetic analysis of mitochondrial ND4 nucleotide sequences shows that the first species is related to Litoria iris (Tyler) and its allies. It is morphologically most similar to Litoria mystax, a small green treefrog known only from the holotype that was described more than 100 years ago from the north coast of western New Guinea but differs from that species in having longer legs and a broader head. The second species is closest to Litoria gasconi, a species known only from the foothills of the Foja Mountains in Papua Province, Indonesian New Guinea, and the Prince Alexander Mountains in northern Papua New Guinea. It has a net average sequence divergence of 10% from L. gasconi and can be distinguished morphologically from it and from other pelodryadids by the presence of a striking pattern of spots and blotches on the ventral surfaces and on the hidden surfaces of the limbs. These descriptions add to the rapidly increasing known diversity of frogs in hill and lower montane forest, habitats that support the most diverse frog communities on mainland New Guinea.

Acknowledging Stigma: Levels of Prejudice among Undergraduate Nursing Students toward People Living with a Mental Illness-A Quasi-Experimental Single-Group Study.

INTRODUCTION: The undergraduate mental health nursing course may be an optimal time to cultivate students' positive attitudes toward people living with a mental illness. AIM: To determine the impact of an undergraduate mental health nursing course on students' attitudes toward people living with a mental illness, depression, and schizophrenia. METHOD: A quasi-experimental single-group pretest posttest study was conducted using a sample of undergraduate nursing students in New York City (N = 44). Self-reported measures of prejudice toward those living with a mental illness were collected at the beginning of a mental health nursing course and again at its conclusion. RESULTS: A statistically significant decrease in prejudice scores was found concerning mental illness (p = .03, d = 0.23), depression (p = .01, d = 0.31), and schizophrenia (p = .013, d = 0.34). Subscale analysis revealed significant decreases in the fear/avoidance and unpredictability subscales. Yet no significant change was found in the subscales of authoritarianism and malevolence for any of the three conditions. DISCUSSION: A mental health course led to a modest decrease in prejudice. However, certain facets of prejudice remain unchanged. IMPLICATIONS FOR PRACTICE: Major curricular reform is needed to optimize the impact of undergraduate nursing education.

Systematics of the Nososticta salomonis complex (Odonata: Zygoptera: Platycnemididae).

We examined the morphology, colour patterns and genetic relationships of Nososticta populations allied to N. salomonis (Selys) from across Melanesia. Seven species-level taxa are recognised in the N. salomonis 'complex': N. africana (Schmidt), N. boonei sp. nov., N. chrismulleri Theischinger & Richards, N. hedigeri sp. nov., N. salomonis (Selys), N. stueberi sp. nov., and N. tagula sp. nov. All of these species are black damselflies with blue markings, and they differ from all other Nososticta by having: 1) a prominent spike on the male superior appendage, 2) a prominent angular base of the male inferior appendage, and 3) a complex posterior lobe on the female pronotum bearing two pairs of processes in the rough shape of a chair when viewed laterally. A molecular phylogeny based on the DNA barcode fragment of the COI gene plus two nuclear genes indicates that these seven species are closely related, but more extensive sampling of Nososticta species is required to confirm that they form a monophyletic group.

Induction of Type 2 Diabetes in Mice to Understand Vascular Changes That Drive Diabetic Retinopathy.

Diabetic retinopathy is a common complication of type 2 diabetes. Research into this comorbidity is challenging due to the slow progression of pathological changes and the limited transgenic models available to study disease progression and mechanistic changes. Here, we describe a non-transgenic mouse model of accelerated type 2 diabetes using a high-fat diet in combination with streptozotocin delivered via osmotic mini pump. This model, when subjected to fluorescent gelatin vascular casting, can be used to study vascular changes in type 2 diabetic retinopathy.

Five new species of the pelodryadid genus Litoria Tschudi from the southern versant of Papua New Guinea's Central Cordillera, with observations on the diversification of reproductive strategies in Melanesian treefrogs.

New Guinea has the most diverse insular frog fauna in the world, and rates of species discovery and description have increased rapidly in the last two decades. Pelodryadid treefrogs are the second most diverse family of anurans on the island but their taxonomy, relationships, and especially ecology remain poorly documented. Based on differences in morphology, advertisement calls (where available) and phylogenetic analyses of a 787 base pair alignment from the mitochondrial ND4 gene and flanking tRNA, we describe five new species of small treefrogs from hill and lower montane forests in the high rainfall belt that straddles the southern versant of Papua New Guinea's Central Cordillera. Three of these species are known only from forest growing on karst substrates, adding to the growing number of herpetofauna species currently known only from the extensive karst habitats of Papua New Guinea's South-fold Mountains. We also describe the arboreal breeding strategies of two of the new species, and report obligate treehole (phytotelm) breeding in New Guinean frogs for the first time. The new phytotelm-breeding species has juveniles with colour and patterning that closely resemble bird droppings, suggesting defensive mimicry or masquerade. A preliminary phylogeny suggests that arboreal-breeding frogs do not form a monophyletic group and that arboreal breeding has evolved multiple times within the New Guinean pelodryadid radiation. A further striking feature of the phylogeny is poor support for most basal nodes in the most diverse radiation of Melanesian Pelodryadidae, suggesting rapid ecological diversification and speciation, potentially following colonisation from Australia and/or mountain uplift. These new taxa and observations highlight previously unrecognised ecological and reproductive diversity in the Melanesian Pelodryadidae.

Hip hemiarthroplasty for the treatment of femoral neck fractures in dialysis patients.

OBJECTIVES: This study sought to delineate the postoperative outcomes in dialysis patients undergoing hip hemiarthroplasty (HHA) for the treatment of femoral neck fractures (FNF) in order to better optimise pre- and postoperative management and minimise short-term morbidity and mortality rates. METHODS: 16,955 patients who had undergone HHA for femoral neck fractures from 2005 to 2018 were isolated from a multi-institutional surgical registry, of which 343 (2.0%) were on dialysis and 16,612 (98.0%) were not. The cohorts were identified/analysed for differences in their comorbidities, demographic factors, and 30-day postoperative complications using Fischer's exact tests and Mann-Whitney U-tests. Coarsened exact matching (CEM) was implemented in order to control for baseline difference in demographics and comorbidities. Multivariate logistic regression analyses were used to assess the impact of dialysis as an independent risk factor for various complications, including reoperations, readmissions, and mortality. RESULTS: Upon CEM-matching (L1-statistic <0.001), weighted multivariate logistic regression analyses demonstrated dialysis to be an independent risk factor for minor complications (OR 3.051, p < 0.001), pneumonia (OR 3.943, p < 0.001), urinary tract infections (UTIs) (OR 2.684, p < 0.001), major complications (OR 1.892, p < 0.001), unplanned intubation (OR 2.555, p = 0.047), cardiac arrest (OR 11.897, p < 0.001), deep vein thrombosis (DVT), (OR 2.610, p = 0.049), and mortality (OR 2.960, p < 0.001). CONCLUSIONS: Dialysis independently increased the risk for unplanned intubation, cardiac arrest, blood transfusions, pneumonia, DVT, and mortality. In communicating postoperative expectations, surgeons should aim to clarify the patients' preferences and potential resuscitation designations prior to surgical intervention due to the increased risk of serious complications. A lower threshold of suspicion for DVT in this population is reasonable. Identifying high-risk patient populations that may experience increased rates of complications, with the ensuing financial expenditures, due to medical complexity rather than subpar management may help providers avoid penalties in caring for these patients.

Melanesia holds the world's most diverse and intact insular amphibian fauna.

Identifying hotspots of biological diversity is a key step in conservation prioritisation. Melanesia-centred on the vast island of New Guinea-is increasingly recognised for its exceptionally species-rich and endemic biota. Here we show that Melanesia has the world's most diverse insular amphibian fauna, with over 7% of recognised global frog species in less than 0.7% of the world's land area, and over 97% of species endemic. We further estimate that nearly 200 additional candidate species have been discovered but remain unnamed, pointing to a total fauna in excess of 700 species. Nearly 60% of the Melanesian frog fauna is in a lineage of direct-developing microhylids characterised by smaller distributions than co-occurring frog families, suggesting lineage-specific high beta diversity is a key driver of Melanesian anuran megadiversity. A comprehensive conservation status assessment further highlights geographic concentrations of recently described range-restricted threatened taxa that warrant urgent conservation actions. Nonetheless, by world standards, the Melanesian frog fauna is relatively intact, with 6% of assessed species listed as threatened and no documented extinctions; and thus it provides an unparalleled opportunity to understand and conserve a megadiverse and relatively intact insular biota.

Comparative genomic and biochemical analyses identify a collagen galactosylhydroxylysyl glucosyltransferase from Acanthamoeba polyphaga mimivirus.

Humans and Acanthamoeba polyphaga mimivirus share numerous homologous genes, including collagens and collagen-modifying enzymes. To explore this homology, we performed a genome-wide comparison between human and mimivirus using DELTA-BLAST (Domain Enhanced Lookup Time Accelerated BLAST) and identified 52 new putative mimiviral proteins that are homologous with human proteins. To gain functional insights into mimiviral proteins, their human protein homologs were organized into Gene Ontology (GO) and REACTOME pathways to build a functional network. Collagen and collagen-modifying enzymes form the largest subnetwork with most nodes. Further analysis of this subnetwork identified a putative collagen glycosyltransferase R699. Protein expression test suggested that R699 is highly expressed in Escherichia coli, unlike the human collagen-modifying enzymes. Enzymatic activity assay and mass spectrometric analyses showed that R699 catalyzes the glucosylation of galactosylhydroxylysine to glucosylgalactosylhydroxylysine on collagen using uridine diphosphate glucose (UDP-glucose) but no other UDP-sugars as a sugar donor, suggesting R699 is a mimiviral collagen galactosylhydroxylysyl glucosyltransferase (GGT). To facilitate further analysis of human and mimiviral homologous proteins, we presented an interactive and searchable genome-wide comparison website for quickly browsing human and Acanthamoeba polyphaga mimivirus homologs, which is available at RRID Resource ID: SCR_022140 or https://guolab.shinyapps.io/app-mimivirus-publication/ .

Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia.

Panicum miliaceum L. was domesticated in northern China at least 7000 years ago and was subsequentially adopted in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, where vast quantities archaeobotanical material were well preserved via desiccation. The rich botanical material found at Areni-1 includes P. miliaceum grains that were identified morphologically and14C dated to the medieval period (873 ± 36 CE and 1118 ± 35 CE). To investigate the demographic and evolutionary history of the Areni-1 millet, we used ancient DNA extraction, hybridization capture enrichment, and high throughput sequencing to assemble three chloroplast genomes from the medieval grains and then compared these sequences to 50 modern P. miliaceum chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity with domesticated accessions separated by a maximum of 5 SNPs and little inference on demography could be made. However, in phylogenies the chloroplast genomes separated into two clades, similar to what has been reported for nuclear DNA from P. miliaceum. The chloroplast genomes of two wild (undomesticated) accessions of P. miliaceum contained a relatively large number of variants, 11 SNPs, not found in the domesticated accessions. These results demonstrate that P. miliaceum grains from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.

Immunophenotypic assessment of PNH clones in major and minor cell lineages in the peripheral blood of patients with paroxysmal nocturnal hemoglobinuria.

BACKGROUND: Flow cytometric immunophenotyping is essential for the diagnosis of paroxysmal nocturnal hemoglobinuria (PNH). Most cases have easy to interpret flow cytometry profiles with red cells, neutrophils and monocytes showing complete deficiency of glycophosphatidylinositol (GPI) linked antigen expression. Some cases are more challenging to interpret due to the presence of multiple populations of PNH cells and variable levels of GPI antigen expression. METHODS: We studied 46 known PNH patients, many with complex immunophenotypic profiles using a novel, single tube, multi-parameter 7-color immunophenotyping assay that allowed simultaneous detection and assessment of PNH clones within multiple lineages of peripheral blood leucocytes. Red cell PNH clones were also assessed in total and immature (CD71+) components by CD59 expression. RESULTS: For individual patients, total PNH clones in each cell lineage were highly correlated. Monocytes, eosinophils and basophils showed the highest proportions of PNH cells. Red cell PNH clones were typically smaller than monocyte and neutrophil PNH clones. In most cases, PNH clones were detectable in minor leucocyte populations where multiple populations of PNH cells were present, variability in the proportions of type II and type III cells was seen across different cell lineages, even though total PNH clones remained similar. CONCLUSIONS: This study shows that PNH patients with multiple PNH clones do not always display the same abnormality across all cell lineages routinely tested. There is no simple explanation for this but is likely due to a combination of complex molecular, genetic and biochemical dysfunction in different blood cell types.

Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens.

Plant DNA preserved in ancient specimens has recently gained importance as a tool in comparative genomics, allowing the investigation of evolutionary processes in plant genomes through time. However, recovering the genomic information contained in such specimens is challenging owing to the presence of secondary substances that limit DNA retrieval. In this chapter, we provide a DNA extraction protocol optimized for the recovery of DNA from degraded plant materials. The protocol is based on a commercially available DNA extraction kit that does not require handling of hazardous reagents.

Impaired postprandial adipose tissue microvascular blood flow responses to a mixed-nutrient meal in first-degree relatives of adults with type 2 diabetes.

Adipose tissue microvascular blood flow (MBF) is stimulated postprandially to augment delivery of nutrients and hormones to adipocytes. Adipose tissue MBF is impaired in type 2 diabetes (T2D). Whether healthy individuals at-risk of T2D show similar impairments is unknown. We aimed to determine whether adipose tissue MBF is impaired in apparently healthy individuals with a family history of T2D. Overnight-fasted individuals with no family history of T2D for two generations (FH-, n = 13), with at least one parent with T2D (FH+, n = 14) and clinically diagnosed T2D (n = 11) underwent a mixed meal challenge (MMC). Metabolic responses [blood glucose, plasma insulin, plasma nonesterified fatty acids (NEFAs), and fat oxidation] were measured before and during the MMC. MBF in truncal subcutaneous adipose tissue was assessed by contrast ultrasound while fasting and 60 min post-MMC. FH+ had normal blood glucoses, increased adiposity, and impaired post-MMC adipose tissue MBF (Δ0.70 ± 0.22 vs. 2.45 ± 0.60 acoustic intensity/s, P = 0.007) and post-MMC adipose tissue insulin resistance (Adipo-IR index; Δ45.5 ± 13.9 vs. 7.8 ± 5.1 mmol/L × pmol/L, P = 0.007) compared with FH-. FH+ and T2D had an impaired ability to suppress fat oxidation post-MMC. Fat oxidation incremental area under the curve (iAUC) (35-55 min post-MMC, iAUC) was higher in FH+ and T2D than in FH- (P = 0.005 and 0.009, respectively). Postprandial MBF was negatively associated with postprandial fat oxidation iAUC (P = 0.01). We conclude that apparently healthy FH+ individuals display blunted postprandial adipose tissue MBF that occurs in parallel with adipose tissue insulin resistance and impaired suppression of fat oxidation, which may help explain their heightened risk for developing T2D.NEW & NOTEWORTHY Adipose tissue blood flow plays a key role in postprandial nutrient storage. People at-risk of type 2 diabetes have impaired postmeal adipose tissue blood flow. Impaired adipose tissue blood flow is associated with altered fat oxidation. Risk of type 2 diabetes may be elevated by poor adipose tissue blood flow.