Journeying towards best practice data management in biodiversity genomics.

Advances in sequencing technologies and declining costs are increasing the accessibility of large-scale biodiversity genomic datasets. To maximize the impact of these data, a careful, considered approach to data management is essential. However, challenges associated with the management of such datasets remain, exacerbated by uncertainty among the research community as to what constitutes best practices. As an interdisciplinary team with diverse data management experience, we recognize the growing need for guidance on comprehensive data management practices that minimize the risks of data loss, maximize efficiency for stand-alone projects, enhance opportunities for data reuse, facilitate Indigenous data sovereignty and uphold the FAIR and CARE Guiding Principles. Here, we describe four fictional personas reflecting differing user experiences with data management to identify data management challenges across the biodiversity genomics research ecosystem. We then use these personas to demonstrate realistic considerations, compromises and actions for biodiversity genomic data management. We also launch the Biodiversity Genomics Data Management Hub (https://genomicsaotearoa.github.io/data-management-resources/), containing tips, tricks and resources to support biodiversity genomics researchers, especially those new to data management, in their journey towards best practice. The Hub also provides an opportunity for those biodiversity researchers whose expertise lies beyond genomics and are keen to advance their data management journey. We aim to support the biodiversity genomics community in embedding data management throughout the research lifecycle to maximize research impact and outcomes.

Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads.

Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen Neisseria meningitidis. Overall, pangenome graphs offer a promising approach for comparative genomics and comprehensive genetic variation analysis in infectious disease. Moreover, this innovative pipeline, leveraging pangenome graphs, can bridge variant analysis, genome assembly, population genetics, and evolutionary biology, expanding the reach of genomic understanding and applications.

Species-wide genomics of kakapo provides tools to accelerate recovery.

The kakapo is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values and, hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kakapo, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of the small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.

The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot.

There is growing interest in the role of structural variants (SVs) as drivers of local adaptation and speciation. From a biodiversity genomics perspective, the characterization of genome-wide SVs provides an exciting opportunity to complement single nucleotide polymorphisms (SNPs). However, little is known about the impacts of SV discovery and genotyping strategies on the characterization of genome-wide SV diversity within and among populations. Here, we explore a near whole-species resequence data set, and long-read sequence data for a subset of highly represented individuals in the critically endangered kakapo (Strigops habroptilus). We demonstrate that even when using a highly contiguous reference genome, different discovery and genotyping strategies can significantly impact the type, size and location of SVs characterized genome-wide. Further, we found that the mean number of SVs in each of two kakapo lineages differed both within and across generations. These combined results suggest that genome-wide characterization of SVs remains challenging at the population-scale. We are optimistic that increased accessibility to long-read sequencing and advancements in bioinformatic approaches including multireference approaches like genome graphs will alleviate at least some of the challenges associated with resolving SV characteristics below the species level. In the meantime, we address caveats, highlight considerations, and provide recommendations for the characterization of genome-wide SVs in biodiversity genomic research.

Leveraging an existing whole-genome resequencing population data set to characterize toll-like receptor gene diversity in a threatened bird.

Species recovery programs are increasingly using genomic data to measure neutral genetic diversity and calculate metrics like relatedness. While these measures can inform conservation management, determining the mechanisms underlying inbreeding depression requires information about functional genes associated with adaptive or maladaptive traits. Toll-like receptors (TLRs) are one family of functional genes, which play a crucial role in recognition of pathogens and activation of the immune system. Previously, these genes have been analysed using species-specific primers and PCR. Here, we leverage an existing short-read reference genome, whole-genome resequencing population data set, and bioinformatic tools to characterize TLR gene diversity in captive and wild tchuriwat'/tuturuatu/shore plover (Thinornis novaeseelandiae), a threatened bird endemic to Aotearoa New Zealand. Our results show that TLR gene diversity in tchuriwat'/tuturuatu is low, and forms two distinct captive and wild genetic clusters. The bioinformatic approach presented here has broad applicability to other threatened species with existing genomic resources in Aotearoa New Zealand and beyond.

The relevance of pedigrees in the conservation genomics era.

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long-standing tools available to manage genetics-the pedigree-has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome-wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well-informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.

Acute Treatment of Ischemic Stroke.

Ischemic stroke affects 2.5% of the population of the United States and is the leading cause of disability. This article outlines the evidence to support intravenous thrombolysis with alteplase and tenecteplase, thrombolysis in the setting of DWI/flair mismatch, endovascular treatment in the 6-hour and 6- to 24-hour window, and the use of telemedicine in acute stroke. Current controversies and ongoing trials within endovascular treatment are also detailed. Case presentations are included to provide clinical context and the application of data to practice.

Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern.

Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.

Neurohospitalist Practice, Perspectives, and Burnout.

BACKGROUND AND PURPOSE: Neurohospitalist neurology is a fast-growing subspecialty with a variety of practice settings featuring neurohospitalist models of care. Since inception, the subspecialty has responded to new challenges in resident training, hospital reimbursement, practice, and burnout. METHODS: To characterize neurohospitalists' current practice and perspectives, we surveyed the neurohospitalists and trainees affiliated with the Neurohospitalist Society using an electronic survey distributed through the society listserv. RESULTS: Of 501 individuals surveyed by e-mail, 119 began the survey (23.8% response rate), with 88.2% self-identifying as neurohospitalists. Most neurohospitalists (63%) are 10 years or less out of training, devoting 70% of their professional time to inpatient clinical activities while also performing administrative or teaching activities. Only 38% are employed by an academic department. Call schedules are common, with 75% of neurohospitalists participating in a hospital or emergency call schedule, while 55% provide telemedicine services. The majority (97%) of neurohospitalists primarily care for adults, most commonly treating patients with cerebrovascular disease, seizures, and delirium/encephalopathy. The majority (87%) are overall pleased with their work, but 36% report having experienced burnout. CONCLUSIONS: Neurohospitalists are a diverse group of neurologists primarily practicing in the inpatient setting while performing a variety of additional activities. They provide a wide array of clinical expertise for acute neurological diseases and neurological emergencies that require hospitalization, including stroke, seizure, and encephalopathy. Neurohospitalists in general are very pleased with their work, while burnout, as in neurology and other areas of medicine, remains a concern.

2017 Program Director Survey: Feedback from your adult neurology residency leadership.

OBJECTIVE: To survey adult neurology program directors (PDs) and inform the future development of neurology training programs. METHODS: All US adult neurology PDs were invited to complete the survey. The goals were to determine the demographic makeup of residency programs, characterize curricula, understand PD and program needs, and compare results to those of a similar survey in 2007. RESULTS: The response rate was 70.6%. PD demographics for age, faculty track status, and academic rank remain unchanged over the last decade. The proportion of female PDs and assistant PDs has increased significantly. The mean number of residents per training program has also increased significantly. Female PDs are more likely to have a junior academic rank than their male colleagues. Disparities remain between the PDs' time spent on teaching/program administration and salary support. Most PDs support moving fellowship applications later in the training cycle. The majority of PDs find the Clinical Competency Committee process useful in assessing resident competence. A minority of PDs feel that the Accreditation Council for Graduate Medical Education Milestones meet their intended purpose. Half of programs include a curriculum to supplement the clinical experience on child neurology rotations. A third of programs include a supplemental curriculum for psychiatry rotations. The majority of programs offer a general fund for residents to use to support their education. CONCLUSION: Deficiencies exist in compensation for PDs' teaching and administrative time and for academic promotion for female PDs. These results serve as a benchmark for comparison across programs and the basis to advocate for further improvements and support for neurology residency training.

Increased blood pressure variability after endovascular thrombectomy for acute stroke is associated with worse clinical outcome.

BACKGROUND AND PURPOSE: Blood pressure variability has been found to contribute to worse outcomes after intravenous tissue plasminogen activator, but the association has not been established after intra-arterial therapies. METHODS: We retrospectively reviewed patients with an ischemic stroke treated with intra-arterial therapies from 2005 to 2015. Blood pressure variability was measured as standard deviation (SD), coefficient of variation (CV), and successive variation (SV). Ordinal logistic regression models were fitted to the outcome of the modified Rankin Scale (mRS) with univariable predictors of systolic blood pressure variability. Multivariable ordinal logistic regression models were fitted to the outcome of mRS with covariates that showed independent predictive ability (P<0.1). RESULTS: There were 182 patients of mean age 63.2 years and 51.7% were female. The median admission National Institutes of Health Stroke Scalescore was 16 and 47.3% were treated with intravenous tissue plasminogen activator. In a univariable ordinal logistic regression analysis, systolic SD, CV, and SV were all significantly associated with a 1-point increase in the follow-up mRS (OR 2.30-4.38, all P<0.002). After adjusting for potential confounders, systolic SV was the best predictor of a 1-point increase in mRS at follow-up (OR 2.63-3.23, all P<0.007). CONCLUSIONS: Increased blood pressure variability as measured by the SD, CV, and SV consistently predict worse neurologic outcomes as measured by follow-up mRS in patients with ischemic stroke treated with intra-arterial therapies. The SV is the strongest and most consistent predictor of worse outcomes at all time intervals.

Increased Blood Pressure Variability Is Associated with Worse Neurologic Outcome in Acute Anterior Circulation Ischemic Stroke.

Background. Although research suggests that blood pressure variability (BPV) is detrimental in the weeks to months after acute ischemic stroke, it has not been adequately studied in the acute setting. Methods. We reviewed acute ischemic stroke patients from 2007 to 2014 with anterior circulation stroke. Mean blood pressure and three BPV indices (standard deviation, coefficient of variation, and successive variation) for the intervals 0-24, 0-72, and 0-120 hours after admission were correlated with follow-up modified Rankin Scale (mRS) in ordinal logistic regression models. The correlation between BPV and mRS was further analyzed by terciles of clinically informative stratifications. Results. Two hundred and fifteen patients met inclusion criteria. At all time intervals, increased systolic BPV was associated with higher mRS, but the relationship was not significant for diastolic BPV or mean blood pressure. This association was strongest in patients with proximal stroke parent artery vessel occlusion and lower mean blood pressure. Conclusion. Increased early systolic BPV is associated with worse neurologic outcome after ischemic stroke. This association is strongest in patients with lower mean blood pressure and proximal vessel occlusion, often despite endovascular or thrombolytic therapy. This hypothesis-generating dataset suggests potential benefit for interventions aimed at reducing BPV in this patient population.

Tissue Plasminogen Activator Prescription and Administration Errors within a Regional Stroke System.

BACKGROUND: Intravenous (IV) tissue plasminogen activator (tPA) utilization in acute ischemic stroke (AIS) requires weight-based dosing and a standardized infusion rate. In our regional network, we have tried to minimize tPA dosing errors. We describe the frequency and types of tPA administration errors made in our comprehensive stroke center (CSC) and at community hospitals (CHs) prior to transfer. METHODS: Using our stroke quality database, we extracted clinical and pharmacy information on all patients who received IV tPA from 2010-11 at the CSC or CH prior to transfer. All records were analyzed for the presence of inclusion/exclusion criteria deviations or tPA errors in prescription, reconstitution, dispensing, or administration, and for association with outcomes. RESULTS: We identified 131 AIS cases treated with IV tPA: 51% female; mean age 68; 32% treated at the CSC, and 68% at CHs (including 26% by telestroke) from 22 CHs. tPA prescription and administration errors were present in 64% of all patients (41% CSC, 75% CH, P < .001), the most common being incorrect dosage for body weight (19% CSC, 55% CH, P < .001). Of the 27 overdoses, there were 3 deaths due to systemic hemorrhage or ICH. Nonetheless, outcomes (parenchymal hematoma, mortality, modified Rankin Scale score) did not differ between CSC and CH patients nor between those with and without errors. CONCLUSION: Despite focus on minimization of tPA administration errors in AIS patients, such errors were very common in our regional stroke system. Although an association between tPA errors and stroke outcomes was not demonstrated, quality assurance mechanisms are still necessary to reduce potentially dangerous, avoidable errors.

A pilot study of audiovisual family meetings in the intensive care unit.

PURPOSE: We hypothesized that virtual family meetings in the intensive care unit with conference calling or Skype videoconferencing would result in increased family member satisfaction and more efficient decision making. METHODS: This is a prospective, nonblinded, nonrandomized pilot study. A 6-question survey was completed by family members after family meetings, some of which used conference calling or Skype by choice. Overall, 29 (33%) of the completed surveys came from audiovisual family meetings vs 59 (67%) from control meetings. RESULTS: The survey data were analyzed using hierarchical linear modeling, which did not find any significant group differences between satisfaction with the audiovisual meetings vs controls. There was no association between the audiovisual intervention and withdrawal of care (P = .682) or overall hospital length of stay (z = 0.885, P = .376). CONCLUSIONS: Although we do not report benefit from an audiovisual intervention, these results are preliminary and heavily influenced by notable limitations to the study. Given that the intervention was feasible in this pilot study, audiovisual and social media intervention strategies warrant additional investigation given their unique ability to facilitate communication among family members in the intensive care unit.

Reproducibility of ABC/2 method to determine infarct volume and mismatch percentage with CT perfusion.

BACKGROUND: Our aim is to implement a simple, rapid, and reliable method using computed tomography perfusion imaging and clinical judgment to target patients for reperfusion therapy in the hyper-acute stroke setting. We introduce a novel formula (1-infarct volume [CBV]/penumbra volume [MTT] × 100%) to quantify mismatch percentage. METHODS: Twenty patients with anterior circulation strokes who underwent CT perfusion and received intravenous tissue plasminogen activator (IV tPA) were analyzed retrospectively. Nine blinded viewers determined volume of infarct and ischemic penumbra using the ABC/2 method and also the mismatch percentage. RESULTS: Interrater reliability using the volumetric formula (ABC/2) was very good (intraclass correlation [ICC] = .9440 and ICC = .8510) for hemodynamic parameters infarct (CBV) and penumbra (MTT). ICC coefficient using the mismatch formula (1-MTT/CBV × 100%) was good (ICC of .635). CONCLUSIONS: The ABC/2 method of volume estimation on CT perfusion is a reliable and efficient approach to determine infarct and penumbra volumes. The 1-CBV/MTT × 100% formula produces a mismatch percentage assisting providers in communicating the proportion of salvageable brain and guides therapy in the setting of patients with unclear time of onset with potentially salvageable tissue who can undergo mechanical retrieval or intraarterial thrombolytics.