Additional file 1 of Diffusion of medications for opioid use disorder treatment in jail settings: a convergent mixed methods study of jail staff perspectives

Additional file 1. Directed acyclic graph (DAG). Description: DAG model of mixed effect regression model indicating minimum sufficient adjustment set to estimate the effect of MOUD-specific training on MOUD diffusion and staff attitudes towards MOUD. Produced using DAGitty software [32]

Racial Segregation Across U.S. Nursing Homes: A Systematic Review of Measurement and Outcomes

BACKGROUND AND OBJECTIVES: Nursing homes remain subjected to institutional racial segregation in the United States. However, a standardized approach to measure segregation in nursing homes does not appear to be established. A systematic review was conducted to identify all formal measurement approaches to evaluate racial segregation among nursing home facilities, and to then identify the association between segregation and quality of care in this context. RESEARCH DESIGN AND METHODS: PubMed, Scopus, and Web of Science databases were searched (January 2018) for publications relating to nursing home segregation. Following the PRISMA guidelines, studies were included that formally measured racial segregation of nursing homes residents across facilities with regional-level data. RESULTS: Eight studies met the inclusion criteria. Formal segregation measures included the Dissimilarity Index, Disparities Quality Index, Modified Thiel\u27s Entropy Index, Gini coefficient, and adapted models. The most common data sources were the Minimum Data Set (MDS; resident-level), the Certification and Survey Provider Enhanced Reporting data (CASPER; facility-level), and the Area Resource File/ U.S. Census Data (regional-level). Most studies showed evidence of racial segregation among U.S. nursing home facilities and documented a negative impact of segregation on racial minorities and facility-level quality outcomes. DISCUSSION AND IMPLICATIONS: The measurement of racial segregation among nursing homes is heterogeneous. While there are limitations to each methodology, this review can be used as a reference when trying to determine the best approach to measure racial segregation in future studies. Moreover, racial segregation among nursing homes remains a problem and should be further evaluated

Data from: Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae)

Goodeniaceae is a primarily Australian flowering plant family with a complex taxonomy and evolutionary history. Previous phylogenetic analyses have successfully resolved the backbone topology of the largest clade in the family, Goodenia s.l., but have failed to clarify relationships within the species-rich and enigmatic Goodenia clade C, a prerequisite for taxonomic revision of the group. We used genome skimming to retrieve sequences for chloroplast, mitochondrial, and nuclear markers for 24 taxa representing Goodenia s.l., with a particular focus on Goodenia clade C. We performed extensive hypothesis tests to explore incongruence in clade C and evaluate statistical support for clades within this group, using datasets from all three genomic compartments. The mitochondrial dataset is comparable to the chloroplast dataset in providing resolution within Goodenia clade C, though backbone support values within this clade remain low. The hypothesis tests provided an additional, complementary means of evaluating support for clades. We propose that the major subclades of Goodenia clade C (C1–C3 + Verreauxia) are the result of a rapid radiation, and each represents a distinct lineage

Jabailyetal_COS alignments

Genetic samples taken in the field and vouchered at PERTH.Zip file of alignments of 85 Conserved ortholog sets. Illumina library with paired-end reads. HybPiper pipeline with default settings (Johnson et al., 2016) to assemble reads corresponding to COS loci based on the probe set published by Mandel et al. (2014

Jabailyetal_NRR

Genetic samples taken in the field and vouchered at PERTH. Genomic skimming accomplished on Illumina Hiseq 2500 rapid run with 150 bp paired-end chemistry. Filtered and reference-guided assembled against Verreauxia sequence

Jabailyetal_G3PDH

Genetic samples taken in the field and vouchered at PERTH. Genomic skimming accomplished on Illumina Hiseq 2500 rapid run with 150 bp paired-end chemistry. Filtered and reference-guided assembled against Verreauxia sequence

Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies

Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments’ ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia + Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A + Goodenia B) (Velleia + Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera

NGS resolution of Core Goodeniaceae data files

See "Dryad Description" file inside zip folder

Co-option of the gibbon-specific LAVA retrotransposon in DNA repair pathways [preprint]

Transposable elements (TEs) can shape gene regulation networks by being co-opted as enhancers. However, the contribution of lineage-specific TE insertions to recent adaptations remains poorly understood. Gibbons present a suitable model to study these contributions, as they have evolved many distinct traits, including heavily rearranged genomes and a novel TE called LAVA. The LAVA retrotransposon is still active in the gibbon genome and is thought to have contributed to evolution of gibbon-specific traits. In this study, we characterized fixed and polymorphic LAVA insertions across multiple gibbon genomes and found that 10% of all LAVA elements overlap chromatin states associated with enhancer function. Moreover, LAVA was enriched in multiple transcription factor motifs, was bound by the important lymphoid transcription factor PU.1, and was associated with higher levels of gene expression in cis. Interestingly, despite the highly similar genomic distribution and epigenetic characteristics of fixed and polymorphic LAVA, only fixed LAVA insertions showed strong signatures of positive selection, and were enriched near genes implicated in DNA repair. Altogether, our population genetics, epigenetics, and evolutionary analyses indicate that several LAVA insertions have been co-opted in the gibbon genome as cis-regulatory elements. Specifically, a subset of the fixed LAVA insertions appear to have been co-opted to enhance regulation of DNA repair genes, likely as an adaptive mechanism to improve genome integrity in response to the genomic rearrangements occurring in the gibbon lineage