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The biomedical research community addresses reproducibility challenges in animal studies through standardized nomenclature, improved experimental design, transparent reporting, data sharing, and centralized repositories. The ARRIVE guidelines outline documentation standards for laboratory animals in experiments, but genetic information is often incomplete. To remedy this, we propose the Laboratory Animal Genetic Reporting (LAG-R) framework. LAG-R aims to document animals genetic makeup in scientific publications, providing essential details for replication and appropriate model use. While verifying complete genetic compositions may be impractical, better reporting and validation efforts enhance reliability of research. LAG-R standardization will bolster reproducibility, peer review, and overall scientific rigor.

Genome editing with CRISPR-associated (Cas) proteins holds exceptional promise for "correcting" variants causing genetic disease. To realize this promise, off-target genomic changes cannot occur during the editing process. Here, we use whole genome sequencing to compare the genomes of 50 Cas9-edited founder mice to 28 untreated control mice to assess the occurrence of S. pyogenes Cas9-induced off-target mutagenesis. Computational analysis of whole-genome sequencing data detects 26 unique sequence variants at 23 predicted off-target sites for 18/163 guides used. While computationally detected variants are identified in 30% (15/50) of Cas9 gene-edited founder animals, only 38% (10/26) of the variants in 8/15 founders validate by Sanger sequencing. In vitro assays for Cas9 off-target activity identify only two unpredicted off-target sites present in genome sequencing data. In total, only 4.9% (8/163) of guides tested have detectable off-target activity, a rate of 0.2 Cas9 off-target mutations per founder analyzed. In comparison, we observe ~1,100 unique variants in each mouse regardless of genome exposure to Cas9 indicating off-target variants comprise a small fraction of genetic heterogeneity in Cas9-edited mice. These findings will inform future design and use of Cas9-edited animal models as well as provide context for evaluating off-target potential in genetically diverse patient populations.

PURPOSE To learn how the highest-performing primary care practices manage change when implementing improvements to diabetes care delivery. METHODS We ranked a total of 330 primary care practices submitting practice management assessments and diabetes reports to the Understanding Infrastructure Transformation Effects on Diabetes study in 2017 and 2019 by Optimal Diabetes Care performance. We ranked practices from the top quartile by greatest annual improvement to capture dynamic change. Starting with the top performers, we interviewed practice leaders to identify their most effective strategies for managing change. Interview transcripts were qualitatively analyzed to identify change management strategies. Saturation occurred when no new strategies were identified over 2 consecutive interviews. RESULTS Ten of the top 13 practices agreed to interviews. We identified 199 key comments representing 48 key care management concepts. We also categorized concepts into 6 care management themes and 37 strategic approaches. We categorized strategic approaches into 13 distinct change management strategies. The most common strategies identified were (1) standardizing the care process, (2) performance awareness, (3) enhancing care teams, (4) health care organization participation, (5) improving reporting systems, (6) engaging staff and clinicians, (7) accountability for tasks, (8) engaging leadership, and (9) tracking change. Care management themes identified by most practices included proactive care, improving patient relationships, and previsit planning. CONCLUSIONS Top-performing primary care practices identify a similar group of strategies as important for managing change during quality improvement activities. Practices involved in diabetes improvement activities, and perhaps other chronic conditions, should consider adopting these change management strategies. Key words: quality of health care; quality of health care; diabetes mellitus, type 2; delivery of health care; primary health care; organizational culture, INTRODUCTION Although the need to improve diabetes outcomes in primary care is evident, exactly how a practice successfully manages change in care delivery in l the midst of a busy [...]

PURPOSE To learn whether the COVID-19 pandemic's disruptions and associated reduced health outcomes for people with chronic conditions might have been caused by a decrease in care management processes (CMPs) in primary care clinics METHODS Longitudinal cohort design with repeated survey-based measures of CMPs from 2017, 2019, and 2021 in 269 primary care clinics in Minnesota. RESULTS There were only small differences in organizational characteristics and no differences in overall CMPs between the 269 clinics analyzed and the 287 that only completed surveys in 1 or 2 years. Overall CMP scores rose by similar amounts (1.6% and 2.1%) from 2017 to 2019 and from 2019 to 2021. In 2021, CMP scores were lower in small medical groups than in large medical groups in 2017 (66.1% vs 78.5%, P CONCLUSIONS Although quite disrupted by the pandemic, care management processes for chronic disease care in these resilient primary care clinics actually increased from 2019 to 2021, at least in clinics that were part of large organizations. However, that was not true for clinics from smaller groups and perhaps for other areas of care. Key words: COVID-19; patient care management; primary health care; quality of health care, INTRODUCTION Over the past 2 years (2020, 2021), the COVID-19 pandemic has disrupted nearly every sector of the United States and world economy and everyone's lives. It has been particularly [...]

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery.

Testis-expressed X-linked genes typically evolve rapidly. Here, we report on a testis-expressed X-linked microRNA (miRNA) cluster that despite rapid alterations in sequence has retained its position in the Fragile-X region of the X chromosome in placental mammals. Surprisingly, the miRNAs encoded by this cluster (Fx-mir) have a predilection for targeting the immediately adjacent gene, Fmr1, an unexpected finding given that miRNAs usually act in trans, not in cis Robust repression of Fmr1 is conferred by combinations of Fx-mir miRNAs induced in Sertoli cells (SCs) during postnatal development when they terminate proliferation. Physiological significance is suggested by the finding that FMRP, the protein product of Fmr1, is downregulated when Fx-mir miRNAs are induced, and that FMRP loss causes SC hyperproliferation and spermatogenic defects. Fx-mir miRNAs not only regulate the expression of FMRP, but also regulate the expression of eIF4E and CYFIP1, which together with FMRP form a translational regulatory complex. Our results support a model in which Fx-mir family members act cooperatively to regulate the translation of batteries of mRNAs in a developmentally regulated manner in SCs.

The International Mouse Phenotyping Consortium (IMPC) systematically produces and phenotypes mouse lines with presumptive null mutations to provide insight into gene function. The IMPC now uses the programmable RNA-guided nuclease Cas9 for its increased capacity and flexibility to efficiently generate null alleles in the C57BL/6N strain. In addition to being a valuable novel and accessible research resource, the production of 3313 knockout mouse lines using comparable protocols provides a rich dataset to analyze experimental and biological variables affecting in vivo gene engineering with Cas9. Mouse line production has two critical steps – generation of founders with the desired allele and germline transmission (GLT) of that allele from founders to offspring. A systematic evaluation of the variables impacting success rates identified gene essentiality as the primary factor influencing successful production of null alleles. Collectively, our findings provide best practice recommendations for using Cas9 to generate alleles in mouse essential genes, many of which are orthologs of genes linked to human disease. [ABSTRACT FROM AUTHOR]

This corrects the article DOI: 10.1038/nature19356.

PURPOSE The aim of this study was to determine what strategies and factors are most important for high performance in the primary care of patients with diabetes. METHODS We performed a mixed-methods, cross-sectional, observational analysis of interviews and characteristics of primary care clinics in Minnesota and bordering areas. We compared strategies, facilitators, and barriers identified by 31 leaders of 17 clinics in high-, middle-, and low-performance quartiles on a standardized composite measure of diabetes outcomes for 416 of 586 primary care clinics. Semistructured interview data were combined with quantitative data regarding clinic performance and a survey of the presence of care management processes. RESULTS The interview analysis identified 10 themes providing unique insights into the factors and strategies characterizing the 3 performance groups. The main difference was the degree to which top-performing clinics used patient data to guide proactive and outreach methods to intensify treatment and monitor effect. Top clinics also appeared to view visit-based care management processes as necessary but insufficient, whereas all respondents regarded being part of a large system as mostly helpful. CONCLUSIONS Top-performing clinic approaches to diabetes care differ from lower-performing clinics primarily by emphasizing data-driven proactive outreach to patients to intensify treatment. Although confirmatory studies are needed, clinical leaders should consider the value of this paradigm shift in approach to care. Key words: quality of health care; diabetes mellitus; delivery of health care; primary health care; organizational culture, INTRODUCTION In a recent study of US National Health and Nutrition Examination Survey data, Kazemian et al reported that measures of diabetes care outcomes did not improve from 2005 to [...]

Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.

Gene duplication is a major evolutionary force driving adaptation and speciation, as it allows for the acquisition of new functions and can augment or diversify existing functions. Here, we report a gene duplication event that yielded another outcome--the generation of antagonistic functions. One product of this duplication event--UPF3B--is critical for the nonsense-mediated RNA decay (NMD) pathway, while its autosomal counterpart--UPF3A--encodes an enigmatic protein previously shown to have trace NMD activity. Using loss-of-function approaches in vitro and in vivo, we discovered that UPF3A acts primarily as a potent NMD inhibitor that stabilizes hundreds of transcripts. Evidence suggests that UPF3A acquired repressor activity through simple impairment of a critical domain, a rapid mechanism that may have been widely used in evolution. Mice conditionally lacking UPF3A exhibit "hyper" NMD and display defects in embryogenesis and gametogenesis. Our results support a model in which UPF3A serves as a molecular rheostat that directs developmental events.

PURPOSE The purpose of this study was to assess whether primary care practices certified as medical homes differ in having the practice systems required for that designation and in attaining favorable outcomes for their patients with diabetes, and whether those systems are associated with better diabetes outcomes. METHODS We undertook a cross-sectional observational study, Understanding Infrastructure Transformation Effects on Diabetes (UNITED), of 586 Minnesota adult primary care practices, comparing those that were certified vs uncertified as medical homes in 2017, with analyses supplemented by previously published studies of these practices. We collected survey information about the presence of medical home practice systems for diabetes care and obtained 6 standardized measures of diabetes care collected yearly from all Minnesota practices. RESULTS Of 416 practices completing questionnaires (71% of all practices, 92% of participating practices), 394 had data on diabetes care measures. Uncertified practices (39%) were more likely than certified practices to be rural, but their patient populations were similar. Certified practices had more medical home practice systems (79.2% vs 74.9%, P =.01) and were more likely to meet a composite measure of optimal diabetes care (46.8% vs 43.2%, P CONCLUSIONS Practices certified as medical homes have more practice systems and higher performance on diabetes care than uncertified practices, but there is extensive overlap, and any differences may reflect self-selection for certification. Key words: diabetes mellitus; organizational innovation; patient-centered care; primary health care; quality assurance, health care; practice-based research, INTRODUCTION In the last 10 years, the concept of a medical home for patients, a patient-centered medical home (PCMH), has resurfaced from its origins in pediatrics in 1967. (1,2) The [...]