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Abstract Background The introduction of novel CTCF binding sites in gene regulatory regions in the rodent lineage is partly the effect of transposable element expansion, particularly in the murine lineage. The exact mechanism and functional impact of evolutionarily novel CTCF binding sites are not yet fully understood. We investigated the impact of novel subspecies-specific CTCF binding sites in two Mus genus subspecies, Mus musculus domesticus and Mus musculus castaneus, that diverged 0.5 million years ago. Results CTCF binding site evolution is influenced by the action of the B2-B4 family of transposable elements independently in both lineages, leading to the proliferation of novel CTCF binding sites. A subset of evolutionarily young sites may harbour transcriptional functionality as evidenced by the stability of their binding across multiple tissues in M. musculus domesticus (BL6), while overall the distance of subspecies-specific CTCF binding to the nearest transcription start sites and/or topologically associated domains (TADs) is largely similar to musculus-common CTCF sites. Remarkably, we discovered a recurrent regulatory architecture consisting of a CTCF binding site and an interferon gene that appears to have been tandemly duplicated to create a 15-gene cluster on chromosome 4, thus forming a novel BL6 specific immune locus in which CTCF may play a regulatory role. Conclusions Our results demonstrate that thousands of CTCF binding sites show multiple functional signatures rapidly after incorporation into the genome.

Abstract Background The integrated-Promoting Action on Research Implementation in Health Services (i-PARIHS) framework is an implementation framework that has been developed and refined over the last 20 years. Its underlying philosophy is that implementing research into healthcare practice is complex, unpredictable and non-linear which therefore requires a flexible and responsive approach to implementation. Facilitation is recognized as the central ingredient of this approach, and i-PARIHS now provides a Facilitation Guide with associated tools. This multiple case study of four implementation projects explored how the i-PARIHS framework has been practically operationalized by diverse implementation project teams. Methods A co-design approach was used to elicit the experiences of four implementation project teams who used the i-PARIHS framework to guide their implementation approach. We conducted the established co-design steps of (i) setting up for success, (ii) gathering the experience, and (iii) understanding the experience. In particular we explored teams’ approaches to setting up their projects; why and how they used the i-PARIHS framework and what they learnt from the experience. Results We found both commonalities and differences in the use of i-PARIHS across the four implementation projects: (i) all the projects used the Facilitation Checklist that accompanies i-PARIHS as a starting point, (ii) the projects differed in how facilitation was carried out, (iii) existing tools were adapted for distinct phases: pre-implementation, during implementation, and post-implementation stages; and (iv) project-specific tools were often developed for monitoring implementation activities and fidelity. Conclusions We have provided a detailed overview of how current users of i-PARIHS are operationalising the framework, which existing tools they are using or adapting to use, and where they have needed to develop new tools to best utilise the framework. Importantly, this study highlights the value of existing tools from the published i-PARIHS Facilitation Guide and provides a starting point to further refine and add to these tools within a future Mobilising Implementation of i-PARIHS (or “Mi-PARIHS”) suite of resources. Specifically, Mi-PARIHS might include more explicit guidance and/or tools for developing a structured implementation plan and monitoring fidelity to the implementation plan, including recording how strategies are tailored to an evolving context.

Abstract Background POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria for most animal cells. Mutations in POLG are the most common single-gene cause of diseases of mitochondria and have been mapped over the coding region of the POLG ORF. Results Using PhyloCSF to survey alternative reading frames, we found a conserved coding signature in an alternative frame in exons 2 and 3 of POLG, herein referred to as ORF-Y that arose de novo in placental mammals. Using the synplot2 program, synonymous site conservation was found among mammals in the region of the POLG ORF that is overlapped by ORF-Y. Ribosome profiling data revealed that ORF-Y is translated and that initiation likely occurs at a CUG codon. Inspection of an alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-conserved predicted RNA stem-loop begins 14 nucleotides downstream. Such features are associated with enhanced initiation at near-cognate non-AUG codons. Reanalysis of the Kim et al. (2014) draft human proteome dataset yielded two unique peptides that map unambiguously to ORF-Y. An additional conserved uORF, herein referred to as ORF-Z, was also found in exon 2 of POLG. Lastly, we surveyed Clinvar variants that are synonymous with respect to the POLG ORF and found that most of these variants cause amino acid changes in ORF-Y or ORF-Z. Conclusions We provide evidence for a novel coding sequence, ORF-Y, that overlaps the POLG ORF. Ribosome profiling and mass spectrometry data show that ORF-Y is expressed. PhyloCSF and synplot2 analysis show that ORF-Y is subject to strong purifying selection. An abundance of disease-correlated mutations that map to exons 2 and 3 of POLG but also affect ORF-Y provides potential clinical significance to this finding.

Abstract Background Following a neurological event, people’s long-term health and well-being is hampered by a system that struggles to deliver person-centred communication and coordinated care and fails to harness individual and family capability to live well with the condition. We aimed to implement and evaluate a toolkit package to support these processes for people with long-term neurological conditions. Methods This is a multi-phased study drawing on the principles of participatory research. In this pilot phase, the toolkit package was introduced to clinicians, who introduced it to clients in four neurorehabilitation settings (inpatient and community-based). Individual and focus group interviews were carried out with clients (n = 10) and clinicians (n = 9). Data were categorised by the four components of Normalisation Process Theory (NPT), and data within each component was then coded inductively. This analysis was used to inform revisions to the toolkit package and wider implementation processes. Results There was widespread support for the principles underpinning the toolkit package from clients and clinicians. However, it was less clear how the client toolkit could support these principles in clinical practice which impacted buy-in. The flexibility of use of the client toolkit, which we encouraged, made it difficult for clinicians and clients to be clear about its purpose and for clinicians to operationalise in practice. Clinicians and clients identified a number of barriers that limited the time, energy and work users were able or prepared to invest, to the extent that uptake of the toolkit package was modest. Use of the toolkit package appeared more likely when clinicians perceived it to augment existing processes (e.g. goal setting) rather than detract from ‘doing’ therapy. This analysis was used to inform revisions to the toolkit package, including simplification of the client toolkit, development of videos with examples of use and a modular and reflective training package for clinical services. The refinements were intended to improve sense-making and minimise the cognitive barriers associated with implementation of a new intervention. Conclusion Understanding how supporting the client toolkit could add value to the therapeutic encounter was necessary for clinicians to invest time and perceive the worth of the toolkit package. Trial registration ANZCTR: ACTRN12614000537651. Registered 21 May, 2014.

Disease, storms, ocean warming, and pollution have caused the mass mortality of reef-building corals across the Caribbean over the last four decades. Subsequently, stony corals have been replaced by macroalgae, bacterial mats, and invertebrates including soft corals and sponges, causing changes to the functioning of Caribbean reef ecosystems. Here we describe changes in the absolute cover of benthic reef taxa, including corals, gorgonians, sponges, and algae, at 15 fore-reef sites (12-15m depth) across the Belizean Barrier Reef (BBR) from 1997 to 2016. We also tested whether Marine Protected Areas (MPAs), in which fishing was prohibited but likely still occurred, mitigated these changes. Additionally, we determined whether ocean-temperature anomalies (measured via satellite) or local human impacts (estimated using the Human Influence Index, HII) were related to changes in benthic community structure. We observed a reduction in the cover of reef-building corals, including the long-lived, massive corals Orbicella spp. (from 13 to 2%), and an increase in fleshy and corticated macroalgae across most sites. These and other changes to the benthic communities were unaffected by local protection. The covers of hard-coral taxa, including Acropora spp., Montastraea cavernosa, Orbicella spp., and Porites spp., were negatively related to the frequency of ocean-temperature anomalies. Only gorgonian cover was related, negatively, to our metric of the magnitude of local impacts (HII). Our results suggest that benthic communities along the BBR have experienced disturbances that are beyond the capacity of the current management structure to mitigate. We recommend that managers devote greater resources and capacity to enforcing and expanding existing marine protected areas and to mitigating local stressors, and most importantly, that government, industry, and the public act immediately to reduce global carbon emissions.

Minimally invasive neuromodulation technologies seek to marry the neural selectivity of implantable devices with the low-cost and non-invasive nature of transcutaneous electrical stimulation (TES). The Injectrode® is a needle-delivered electrode that is injected onto neural structures under image guidance. Power is then transcutaneously delivered to the Injectrode using surface electrodes. The Injectrode serves as a low-impedance conduit to guide current to the deep on-target nerve, reducing activation thresholds by an order of magnitude compared to using only surface stimulation electrodes. To minimize off-target recruitment of cutaneous fibers, the energy transfer efficiency from the surface electrodes to the Injectrode must be optimized. TES energy is transferred to the Injectrode through both capacitive and resistive mechanisms. Electrostatic finite element models generally used in TES research consider only the resistive means of energy transfer by defining tissue conductivities. Here, we present an electroquasistatic model, taking into consideration both the conductivity and permittivity of tissue, to understand transcutaneous power delivery to the Injectrode. The model was validated with measurements taken from (n = 4) swine cadavers. We used the validated model to investigate system and anatomic parameters that influence the coupling efficiency of the Injectrode energy delivery system. Our work suggests the relevance of electroquasistatic models to account for capacitive charge transfer mechanisms when studying TES, particularly when high-frequency voltage components are present, such as those used for voltage-controlled pulses and sinusoidal nerve blocks.

The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD).sup.1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the 'proportion expressed across transcripts', which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project.sup.2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies. A novel variant annotation metric that quantifies the level of expression of genetic variants across tissues is validated in the Genome Aggregation Database (gnomAD) and is shown to improve rare variant interpretation., Author(s): Beryl B. Cummings [sup.1] [sup.2] [sup.3] , Konrad J. Karczewski [sup.1] [sup.2] , Jack A. Kosmicki [sup.1] [sup.2] [sup.4] , Eleanor G. Seaby [sup.1] [sup.2] [sup.5] , Nicholas A. [...]

Introduction: Patients diagnosed with coronavirus disease 2019 (COVID-19) require significant healthcare resources. While published research has shown clinical characteristics associated with severe illness from COVID-19, there is limited data focused on the emergency department (ED) discharge population. Methods: We performed a retrospective chart review of all ED-discharged patients from Wake Forest Baptist Health and Wake Forest Baptist Health Davie Medical Center between April 25–August 9, 2020, who tested positive for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) from a nasopharyngeal swab using real-time reverse transcription polymerase chain reaction (rRT-PCR) tests. We compared the clinical characteristics of patients who were discharged and had return visits within 30 days to those patients who did not return to the ED within 30 days. Results: Our study included 235 adult patients who had an ED-performed SARS-CoV-2 rRT-PCR positive test and were subsequently discharged on their first ED visit. Of these patients, 57 (24.3%) had return visits to the ED within 30 days for symptoms related to COVID-19. Of these 57 patients, on return ED visits 27 were admitted to the hospital and 30 were not admitted. Of the 235 adult patients who were discharged, 11.5% (27) eventually required admission for COVID-19-related symptoms. With 24.3% patients having a return ED visit after a positive SARS-CoV-2 test and 11.5% requiring eventual admission, it is important to understand clinical characteristics associated with return ED visits. We performed multivariate logistic regression analysis of the clinical characteristics with independent association resulting in a return ED visit, which demonstrated the following: diabetes (odds ratio [OR] 2.990, 95% confidence interval [CI, 1.21–7.40, P = 0.0179); transaminitis (OR 8.973, 95% CI, 2.65–30.33, P = 0.004); increased pulse at triage (OR 1.04, 95% CI, 1.02–1.07, P = 0.0002); and myalgia (OR 4.43, 95% CI, 2.03–9.66, P = 0.0002). Conclusion: As EDs across the country continue to treat COVID-19 patients, it is important to understand the clinical factors associated with ED return visits related to SARS-CoV-2 infection. We identified key clinical characteristics associated with return ED visits for patients initially diagnosed with SARS-CoV-2 infection: diabetes mellitus; increased pulse at triage; transaminitis; and complaint of myalgias.

A multi-institutional study of five Canadian universities was undertaken to examine the impact of living in residence on students' first-year grade point averages (GPAs), retention to the second year, and graduation. While previous studies have linked living in residence to improved academic outcomes, most of the research has been based on American institutions, and many featured small sample sizes. Research within a Canadian context has been limited, signaling a need for meaningful data on the value that the residence experience provides. In this first-of-its-kind study, we explored the quantitative relationship between living in residence and the achievement of outcomes associated with postsecondary success, analyzing data from more than 146,000 university student records across five Canadian institutions. Linear and logistic regression analyses were used to model the impact of demographic variables such as age, gender, program of study, and fee status on academic outcomes. Results showed that living in residence in the first year of university had positive effects on retention to the second year and persistence to graduation, with benefits particularly pronounced for international students. The effect of living in residence on students' GPAs was found to be inconclusive, with a very small positive effect for international students. [Discussion questions developed by Denise Davidson, Courtney Enderline, Paige Friesema, and Amanda McIntyre.]

Objective: To provide a summary of the translational gaps in musculoskeletal research as identified in the Mine the Gap workshop and propose possible solutions. Methods: The Mine the Gap online workshop was hosted on October 14th and 15th, 2020. Five international panels, each comprised of a clinician, clinical researcher and basic scientist, presented gaps and proposed solutions for the themes of biomechanics, pain, biological measurements, phenotypes and imaging. This was followed by an interactive panel discussion with consumer insights. Results: A number of translational gaps and proposed solutions across each of the five themes were identified. A consumer panel provided constructive feedback highlighting the need for improved resources, communication and shared decision making, and treatment individualisation. Conclusion: This brief report provides a greater understanding of the diverse work and gaps relevant to fundamental/discovery scientists, clinical researchers and clinicians working across the musculoskeletal field. The numerous translational gaps highlight the need to improve communication and collaboration across the musculoskeletal field.

Bacteria and phytoplankton form close associations in the ocean that are driven by the exchange of chemical compounds. The bacterial signal 2-heptyl-4-quinolone (HHQ) slows phytoplankton growth; however, the mechanism responsible remains unknown.

The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.

Aim: To gather and understand the experience of hospital mealtimes from the perspectives of those receiving and delivering mealtime care (older inpatients, caregivers and staff) using photovoice methods to identify touchpoints and themes to inform the co‐design of new mealtime interventions. Methods: This study was undertaken on acute care wards within a single metropolitan hospital in Brisbane, Australia in 2019. Photovoice methods involved a researcher accompanying 21 participants (10 older patients, 5 caregivers, 4 nurses and 2 food service officers) during a mealtime and documenting meaningful elements using photographs and field notes. Photo‐elicitation interviews were then undertaken with participants to gain insight into their experience. Data were analysed using inductive thematic analysis, involving a multidisciplinary research team including a consumer. Results: Themes were identified across the three touchpoints: (1) preparing for the meal (the juggle, the anticipation), (2) delivering/receiving the meal (the rush, the clutter and the wait) and (3) experiencing the meal (the ideal, pulled away and acceptance). Despite a shared understanding of the importance of meals and shared vision of 'the ideal' mealtime, generally this was a time of tension, missed cares and dissatisfaction for staff, patients and caregivers. There was stark contrast in some aspects of mealtime experience, with simultaneous experiences of 'the rush' (staff) and 'the wait' (patients and caregivers). There was an overwhelming sense of acceptance and lack of control over change from all. Conclusions: This study identified themes during hospital mealtimes which have largely gone unaddressed in the design of mealtime interventions to date. This research may provide a framework to inform the future co‐design of mealtime interventions involving patients, caregivers and multidisciplinary staff, centred around these key touchpoints. Practice Implications: Mealtimes are experienced differently by patients, caregivers, nurses and food service officers across three key touchpoints: preparing for, delivering/receiving and experiencing the meal. Improving mealtime experiences therefore necessitates a collaborative approach, with co‐designed mealtime improvement programs that include specific interventions focusing each touchpoint. Our data suggest that improvements could focus on reducing clutter, clarifying mealtime roles and workflows and supporting caregiver involvement. Impact: What problem did the study address?: Mealtimes are the central mechanism to meet patients' nutritional needs in hospital; however, research consistently shows that many patients do not eat enough to meet their nutritional requirements and that they often do not receive the mealtime assistance they require.Interventions to improve hospital mealtimes have, at best, shown only modest improvements in nutritional intake and mealtime care practices. Gaining deeper insight into the mealtime experience from multiple perspectives may identify new opportunities for improvement. What were the main findings?: Patients, caregivers and staff have shared ideals of comfort, autonomy and conviviality at mealtimes, but challenges of complex teamwork and re‐prioritisation of mealtimes in the face of prevailing power hierarchies make it difficult to achieve this ideal.There are three discrete touchpoints (preparing for, delivering/receiving and experiencing the meal) that require different approaches to improvement.Our data suggests a need to focus improvement on reducing clutter, clarifying mealtime roles and workflows and supporting caregivers. Where and on whom will the research have an impact?: The research provides a framework for multidisciplinary teams to begin co‐designing improvements to mealtime care to benefit patients, caregivers and staff, while also providing a method for researchers to understand other complex care situations in hospital. Reporting Method: This manuscript is written in adherence with the Standards for Reporting Qualitative Research. Patient or Public Contribution: Patients and caregivers were involved in the conception and design of the study through their membership of the hospital mealtime reference group. A consumer researcher (GP) was involved in the team to advise on study conduct (i.e. recruitment methods and information), data analysis (i.e. coding transcripts), data interpretation (i.e. review and refinement of themes) and manuscript writing (i.e. review and approval of final manuscript). [ABSTRACT FROM AUTHOR]

Aim: To identify, describe and synthesise what is known about family carers' experiences and perspectives of engagement in delirium prevention and care for adults in hospital. Design: Systematic review and synthesis of qualitative evidence. Data Sources: Comprehensive literature search within PubMed, CINAHL, EMBASE, Scopus, Cochrane Central and PsycInfo databases to August 2022. Peer reviewed original qualitative research published in English. Methods: Data were extracted using Covidence systematic review software. Methodological quality was reviewed against the Critical Appraisal Skills Program (CASP) Qualitative Checklist. Thematic synthesis was used to develop analytical themes. Confidence in the Evidence from Reviews of Qualitative Research (GRADE‐CERQual) framework was applied to findings. Results: Of 3429 records identified, 29 met criteria for final inclusion. Studies included a range of settings (intensive care, medical and surgical wards) and family carer types (spouse, daughter, parent and friend). Three primary themes Shared Caregiving, Partnership and Support, Communication for Shared Understanding and three cross‐cutting contextual themes Care Transitions, Family Carer Context and Hospital Context were identified. Family carers have mixed experiences of involvement in delirium care and prevention. Family carer engagement in care impacted perceptions of care quality and their own self‐efficacy. Where person‐centred care expectations were not met, some family carers adopted compensatory or care contingency strategies. Information sharing and timely support from hospital staff who understood the carer context supported carer involvement. Supportive physical environments and addressing power imbalances allowed greater engagement. Conclusion: Family carers often wish to be involved in delirium prevention and care, but need to be recognised as individuals, listened to, informed and supported to optimise their contribution. Impact: The review findings can guide health professional and decision makers to optimise family carer involvement in delirium care programs. Protocol Registration: PROSPERO [CRD42020221854]. Reporting: ENTREQ. No Patient or Public Contribution. [ABSTRACT FROM AUTHOR]

Cobalamin, vitamin B12, is an important micronutrient that has been investigated for decades in the marine context because it is required for phytoplankton growth. The biologically active forms (Me‐B12, Ado‐B12) and the synthetic form (CN‐B12) quickly convert to OH‐B12 after light exposure in various aqueous solutions, but puzzlingly have been frequently reported to dominate dissolved cobalamin pools in the sunlit ocean. Here, we document photodegradation timescales for these cobalamin forms in natural seawater using targeted mass spectrometry, providing quantitative evidence that OH‐B12 is expected to be the dominant dissolved form in irradiated seawater. Then, through high‐resolution mass spectrometry, we identify four photodegradation products of OH‐B12 which represent potential building blocks microbes could salvage and remodel to satisfy cellular cobalamin requirements. Taken together, these results clarify the impact of light on marine cobalamin dynamics, laying a foundation for a more quantitative understanding of the role of cobalamin in microbial communities and biogeochemical cycles. [ABSTRACT FROM AUTHOR]