A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset.

BACKGROUND: Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions of this tool have yet to become widely available and affordable. RESULTS: Here we report an open-source high-performance computing genome variant calling workflow (HPC-GVCW) for GATK that can run on multiple computing platforms from supercomputers to desktop machines. We benchmarked HPC-GVCW on multiple crop species for performance and accuracy with comparable results with previously published reports (using GATK alone). Finally, we used HPC-GVCW in production mode to call SNPs on a "subpopulation aware" 16-genome rice reference panel with ~ 3000 resequenced rice accessions. The entire process took ~ 16 weeks and resulted in the identification of an average of 27.3 M SNPs/genome and the discovery of ~ 2.3 million novel SNPs that were not present in the flagship reference genome for rice (i.e., IRGSP RefSeq). CONCLUSIONS: This study developed an open-source pipeline (HPC-GVCW) to run GATK on HPC platforms, which significantly improved the speed at which SNPs can be called. The workflow is widely applicable as demonstrated successfully for four major crop species with genomes ranging in size from 400 Mb to 2.4 Gb. Using HPC-GVCW in production mode to call SNPs on a 25 multi-crop-reference genome data set produced over 1.1 billion SNPs that were publicly released for functional and breeding studies. For rice, many novel SNPs were identified and were found to reside within genes and open chromatin regions that are predicted to have functional consequences. Combined, our results demonstrate the usefulness of combining a high-performance SNP calling architecture solution with a subpopulation-aware reference genome panel for rapid SNP discovery and public deployment.

Slideflow: deep learning for digital histopathology with real-time whole-slide visualization.

Deep learning methods have emerged as powerful tools for analyzing histopathological images, but current methods are often specialized for specific domains and software environments, and few open-source options exist for deploying models in an interactive interface. Experimenting with different deep learning approaches typically requires switching software libraries and reprocessing data, reducing the feasibility and practicality of experimenting with new architectures. We developed a flexible deep learning library for histopathology called Slideflow, a package which supports a broad array of deep learning methods for digital pathology and includes a fast whole-slide interface for deploying trained models. Slideflow includes unique tools for whole-slide image data processing, efficient stain normalization and augmentation, weakly-supervised whole-slide classification, uncertainty quantification, feature generation, feature space analysis, and explainability. Whole-slide image processing is highly optimized, enabling whole-slide tile extraction at 40x magnification in 2.5 s per slide. The framework-agnostic data processing pipeline enables rapid experimentation with new methods built with either Tensorflow or PyTorch, and the graphical user interface supports real-time visualization of slides, predictions, heatmaps, and feature space characteristics on a variety of hardware devices, including ARM-based devices such as the Raspberry Pi.

A modular toolkit for environmental Rhodococcus, Gordonia, and Nocardia enables complex metabolic manipulation.

Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as Escherichia coli or Pseudomonas putida, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate Rhodococcus ruber C208, and demonstrate conserved functionality in 11 additional environmental isolates of Rhodococcus, Nocardia, and Gordonia. This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in Rhodococcus erythropolis N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens. Rhodococcus, Gordonia, and Nocardia are three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these, Rhodococcus ruber C208 was shown to degrade polyethylene; Gordonia paraffinivorans can assimilate carbon from solid hydrocarbons; and Nocardia neocaledoniensis (and many other Nocardia spp.) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.

Optimising the implementation of evidence-based osteoarthritis guidelines in primary care: Development of a Knowledge Mobilisation Toolkit.

OBJECTIVE: Implementing clinical guidelines for osteoarthritis (OA) in primary care is complex. Whilst international guidelines detail what best practice for OA looks like, little is known about how this is best implemented. Limited resources are available to guideline developers, practitioners, researchers, or the public to facilitate implementation. Set in the context of a larger research project which sought to understand the factors that influence knowledge mobilisation (KM) in implementation for OA guidelines, this study reports the development of a toolkit to optimise KM for the implementation of evidence-based OA guidelines in primary care. DESIGN: Triangulation of three qualitative data sets was conducted, followed by a stakeholder consensus exercise. Public contributors were involved in dedicated meetings (n = 3) to inform the content, design, and KM plans for the toolkit. RESULTS: From data triangulation, 53 key findings were identified, which were refined into 30 draft recommendation statements, within six domains: approaches to KM; the knowledge mobiliser role; understanding context; implementation planning; the nature of the intervention; and appealing to a range of priorities. Stakeholder voting (n = 27) demonstrated consensus with the recommendations and informed the wording of the final toolkit. CONCLUSIONS: Factors that optimise KM for OA guideline implementation in primary care were identified. Empirical data, practice-based evidence, implementation practice, and stakeholder (including patient and public) engagement have informed a toolkit comprising several overarching principles of KM, which are suitable for use in primary care. Consideration of equitable access when implementing evidence-based OA care among diverse populations is recommended when using the toolkit. Further research is needed to evaluate the toolkit's utility and transferability.

The International Society of Blood Transfusion (ISBT) Public Health Research Toolkit: A report from the Surveillance, Risk Assessment and Policy Sub-group of the ISBT Transfusion Transmitted Infectious Diseases Working Party.

BACKGROUND AND OBJECTIVES: Data provided from blood donors have contributed to the understanding of public health epidemiology and policy decisions. A recent example was during the severe acute respiratory syndrome-related coronavirus (SARS-CoV-2) pandemic when blood services monitored the seroprevalence in blood donors. Based on this experience, blood services have the opportunity to expand their role and participate in public health surveillance and research. The aim of this report is to share available resources to assist blood services in this area. MATERIALS AND METHODS: The Surveillance, Risk Assessment and Policy (SRAP) Sub-group of the International Society of Blood Transfusion (ISBT) Transfusion Transmitted Infectious Diseases (TTID) Working Party developed a Public Health Research Toolkit to assist blood services and researchers interested in expanding their role in public health research. RESULTS: The ISBT Public Health Research Toolkit provides resources for what blood services can offer to public health, examples of donor research studies, the utility of donor data and website links to public health agencies. The toolkit includes a customizable template for those interested in establishing and managing a biobank. CONCLUSION: The ISBT Public Health Research Toolkit includes resources to increase the recognition of the role blood donors can play in public health and to help blood services gain commitment and funding from various agencies for new research and surveillance.

Life cycle strategies in free-living unicellular eukaryotes: Diversity, evolution, and current molecular tools to unravel the private life of microorganisms.

An astonishing range of morphologies and life strategies has arisen across the vast diversity of protists, allowing them to thrive in most environments. In model protists, like Tetrahymena, Dictyostelium, or Trypanosoma, life cycles involving multiple life stages with different morphologies have been well characterized. In contrast, knowledge of the life cycles of free-living protists, which primarily consist of uncultivated environmental lineages, remains largely fragmentary. Various life stages and lineage-specific cellular innovations have been observed in the field for uncultivated protists, but such innovations generally lack functional characterization and have unknown physiological and ecological roles. In the actual state of knowledge, evidence of sexual processes is confirmed for 20% of free-living protist lineages. Nevertheless, at the onset of eukaryotic diversification, common molecular trends emerged to promote genetic recombination, establishing sex as an inherent feature of protists. Here, we review protist life cycles from the viewpoint of life cycle transitions and genetics across major eukaryotic lineages. We focus on the scarcely observed sexual cycle of free-living protists, summarizing evidence for its existence and describing key genes governing its progression, as well as, current methods for studying the genetics of sexual cycles in both cultivable and uncultivated protist groups.

Implementation of the Dementia Isolation Toolkit in long-term care improves awareness but does not reduce moral distress amongst healthcare providers.

BACKGROUND: Healthcare providers may experience moral distress when they are unable to take the ethically or morally appropriate action due to real or perceived constraints in delivering care, and this psychological stressor can negatively impact their mental health, leading to burnout and compassion fatigue. This study describes healthcare providers experiences of moral distress working in long-term care settings during the COVID-19 pandemic and measures self-reported levels of moral distress pre- and post-implementation of the Dementia Isolation Toolkit (DIT), a person-centred care intervention designed for use by healthcare providers to alleviate moral distress. METHODS: Subjective levels of moral distress amongst providers (e.g., managerial, administrative, and front-line employees) working in three long-term care homes was measured pre- and post-implementation of the DIT using the Moral Distress in Dementia Care Survey and semi-structured interviews. Interviews explored participants' experiences of moral distress in the workplace and the perceived impact of the intervention on moral distress. RESULTS: A total of 23 providers between the three long-term care homes participated. Following implementation of the DIT, subjective levels of moral distress measured by the survey did not change. When interviewed, participants reported frequent experiences of moral distress from implementing public health directives, staff shortages, and professional burnout that remained unchanged following implementation. However, in the post-implementation interviews, participants who used the DIT reported improved self-awareness of moral distress and reductions in the experience of moral distress. Participants related this to feeling that the quality of resident care was improved by integrating principals of person-centered care and information gathered from the DIT. CONCLUSIONS: This study highlights the prevalence and exacerbation of moral distress amongst providers during the pandemic and the myriad of systemic factors that contribute to experiences of moral distress in long-term care settings. We report divergent findings with no quantitative improvement in moral distress post-intervention, but evidence from interviews that the DIT may ease some sources of moral distress and improve the perceived quality of care delivered. This study demonstrates that an intervention to support person-centred isolation care in this setting had limited impact on overall moral distress during the COVID-19 pandemic.

Family-Focused Universal Substance Use Prevention in Primary Care: Advancing a Pragmatic National Healthcare Agenda.

This article advances ideas presented at a National Academies of Sciences, Engineering, and Medicine workshop in 2022 that highlighted clinical practice and policy recommendations for delivering universal, family-focused substance use preventive interventions in pediatric primary care. Pediatric primary care is a natural setting in which to offer families universal anticipatory guidance and links to systematic prevention programming; also, several studies have shown that offering effective parenting programs in primary care is feasible. The article describes a blueprint for designing a pragmatic national agenda for universal substance use prevention in primary care that builds on prior work. Blueprint practice schematics leverage efficacious family-focused prevention programs, identify key program implementation challenges and resources, and emphasize adopting a core element approach and utilizing digital interventions. Blueprint policy schematics specify avenues for improving cross-sector policy and resource alignment and collaboration; expanding, diversifying, and strengthening the prevention workforce; and enhancing financing for family-focused prevention approaches. The article then draws from these schematics to assemble a candidate universal prevention toolkit tailored for adolescent patients that contains four interlocking components: education in positive parenting practices, parent and youth education in substance use risks, a parent-youth structured interaction task, and parent and youth linkage to in-person and web-based prevention resources.

Improving patient-centred care in the emergency department: Implementation of a Sensory Toolkit for children with autism.

Emergency department (ED) visits for children with autism can present challenges due to the unique sensory needs of this population. This Quality Improvement (QI) project executed two Plan-Do-Study-Act (PDSA) cycles to create and implement a Sensory Toolkit in the ED for children with autism. Most caregivers (94%; n = 31/33) and healthcare providers (HCPs; 86%; n = 37/44) identified the need for sensory items in the ED. In PDSA Cycle 1, 100% of caregivers (n = 21) and HCPs (n = 3) agreed/strongly agreed that the ED Sensory Toolkit was helpful. In PDSA Cycle 2, 92% of caregivers (n = 12/13) and 100% of HCPs (n = 3) agreed/strongly agreed that they were helpful. The Sensory Toolkit was positively evaluated by caregivers of children with autism and HCPs during the child's visit to the ED. There is an opportunity to adapt the Sensory Toolkit for other EDs and areas of the hospital.

A study to depict challenges and opportunities building industry professionals face when designing inclusive and accessible buildings.

Inclusive Design has been widely promoted in the fields of product, engineering, and user experience design. Despite the educational efforts made by scientists, practitioners, and institutions to raise awareness about accessibility and inclusion, Inclusive Design has not been widely embraced in architectural design practice, where it is often associated with design for disability. This multidisciplinary study, spanning behavioural science, ergonomics, and the social sciences of architecture, explores the challenges architectural design practitioners face when designing inclusively, and identifies opportunities to promote the adoption of Inclusive Design. The results of a questionnaire completed by 114 architectural design practitioners underscore the lack of client awareness of the benefits of inclusive design, highlight the important role practitioners can play in advocating for Inclusive Design, and emphasize the need to develop practices and tools that enhance the design and post-design phases of buildings to ensure inclusion, diversity, equity, and accessibility.

Identifying research practices toward achieving health equity principles within the Cancer Prevention and Control Research Network.

PURPOSE: Although there is national recognition for health equity-oriented research, there is limited guidance for researchers to engage partnerships that promote health equity in cancer research. The Cancer Prevention and Control Research Network's (CPCRN) Health Equity Work Group developed a toolkit to guide researchers in equitable collaborations. METHODS: The CPCRN's Health Equity Work Group collectively outlined health and racial equity principles guiding research collaborations with partners that include communities, community-based organizations, implementing partners in the clinical setting including providers and health care organizations, and policy makers. Using a network-wide survey to crowdsource information around ongoing practices, we leveraged and integrated the network's experience and collaborations. RESULTS: Data from the survey formed the preliminary basis for the toolkit, with a focus on sharing fiscal resources with partners, training and capacity building, collaborative decision-making, community-driven research agenda setting, and sustainability. The final toolkit provides reflection considerations for researchers and collated exemplary resources, supported by the contemporary research. CONCLUSIONS: The toolkit provides a guide to researchers at all experience levels wanting to engage in equitable research collaborations. Future efforts are underway to evaluate whether and how researchers within and outside CPCRN are able to incorporate these principles in research collaborations.

Pseudoword spelling: insights into sublexical representations and lexical interactions.

ABSTRACTIn this work we introduce a new tool for measuring English spelling-sound consistency, the PG Toolkit, which we use to conduct detailed analyses of pseudoword spellings that provide new insights into the nature of sublexical and lexical representations. There are several key findings: first, sound-spelling consistency measured at two different "grain sizes", phonographeme and onset/rime, each explained unique variance in pseudoword spelling. Second, lexical skill was more related to pseudoword accuracy at the onset/rime level than at the phonographeme level, and individuals who chose more consistent mappings to spell pseudowords tended to have better lexical skill. Finally, no unique contribution of consistency in the reading direction ("feedback") was found after controlling for consistency in the spelling direction. Taken together, the results validate the various measures provided by the PG Toolkit and establish new evidence that supports an interpretation of sublexical processes as operations over hierarchically-structured representations.

Measuring quality of life in care homes when self-report is challenging: the construct validity, structural characteristics and internal consistency of the mixed-methods adult social care outcomes toolkit.

INTRODUCTION: The adult social care outcomes toolkit (ASCOT) measures social care-related quality of life (SCRQoL) using self-completion questionnaires and interviews. Many care home residents find such methods inaccessible, leading to a reliance on proxy-reporting. This study aimed to establish the psychometric properties of the mixed-methods toolkit [ASCOT-Care Homes, 4 outcome (CH4)] for measuring SCRQoL when residents cannot self-report. METHODS: Two cross-sectional, mixed-methods studies were undertaken in care homes for older people in England between 2015 and 2020. We used the ASCOT-CH4 (observation, and interviews with residents and proxies) to collect information about SCRQoL and collected additional data on residents' needs and characteristics, and variables hypothesised to be related to SCRQoL.Hypothesis testing was applied to establish construct validity, Cronbach's alpha for internal consistency and exploratory factor analysis for structural validity. RESULTS: The combined dataset included 475 residents from 54 care homes (34 nursing, 20 residential). Half had a diagnosis of dementia. Less than a third of residents were able to complete an ASCOT interview. Observations and proxy interviews informed researcher ratings, meaning there were no missing ASCOT-CH4 scores. ASCOT-CH4 was found to be a weak unidimensional scale, consistent with other ASCOT measures, with acceptable internal consistency (α = 0.77, 8 items). Construct validity was supported by the findings. CONCLUSIONS: The ASCOT-CH4 is an alternative to conventional proxy-questionnaires for measuring the SCRQoL of care home residents, with good psychometric properties. A limitation is that users need a range of data collection skills. Future research should explore whether findings are replicable when data are collected by other researchers.

Greening Family Medicine clinic operations and clinical care, where do we start? A scoping review of toolkits and aids.

BACKGROUND: There is a pressing need for healthcare to respond to the climate crisis. Family physicians, given their central role in community healthcare provision, are strategically placed to lead, support, and promote sustainable healthcare, yet guidance on how to do this is fragmented. OBJECTIVE: To identify and evaluate toolkits and aids on sustainable healthcare to act as a curated resource for family physicians and their care teams interested in delivering evidence-based sustainable healthcare in their clinical practices. METHODS: A scoping review was completed of the published and grey literature across 4 databases and 2 search engines to identify articles and aids/toolkits from 1990 to present. Toolkits were subsequently evaluated for purpose, evidence-base, implementation process, adaptability to family medicine, and outcome measures. RESULTS: The search identified 17,751 articles. Screening resulted in 20 published articles and 11 toolkits. Most articles presented simple checklists to support greening clinic initiatives, 3 studies focussed on partial carbon footprint analyses, and 4 on educational initiatives. Toolkits ranged in sustainability topics and degree of depth covered, and adaptability and outcome measures. None of the resources identified have been formally evaluated for effectiveness. CONCLUSIONS: A range of aids exist to support greening of clinic operations; however, there is a significant gap in the literature for greening clinical care. Two toolkits were found to be comprehensive, one requiring tracking and reporting of sustainability initiatives. This scoping review provides a starting point for motivated family doctors and community clinics to initiate change and support more sustainable healthcare.

Developing the Driving and Dementia Roadmap: a knowledge-to-action process.

OBJECTIVES: Despite three decades of research, gaps remain in meeting the needs of people with dementia and their family/friend carers as they navigate the often-tumultuous process of driving cessation. This paper describes the process of using a knowledge-to-action (KTA) approach to develop an educational web-based resource (i.e. toolkit), called the Driving and Dementia Roadmap (DDR), aimed at addressing some of these gaps. DESIGN: Aligned with the KTA framework, knowledge creation and action cycle activities informed the development of the DDR. These activities included systematic reviews; meta-synthesis of qualitative studies; interviews and focus groups with key stakeholders; development of a Driving and Dementia Intervention Framework (DD-IF); and a review and curation of publicly available resources and tools. An Advisory Group comprised of people with dementia and family carers provided ongoing feedback on the DDR's content and design. RESULTS: The DDR is a multi-component online toolkit that contains separate portals for current and former drivers with dementia and their family/friend carers. Based on the DD-IF, various topics of driving cessation are presented to accommodate users' diverse stages and needs in their experiences of decision-making and transitioning to non-driving. CONCLUSION: Guided by the KTA framework that involved a systematic and iterative process of knowledge creation and translation, the resulting person-centered, individualized and flexible DDR can bring much-needed support to help people with dementia and their families maintain their mobility, community access, and social and emotional wellbeing during and post-driving cessation.

You & Me: Test and Treat study protocol for promoting COVID-19 test and treatment access to underserved populations.

BACKGROUND: Infections and deaths from the COVID-19 pandemic have disproportionately affected underserved populations. A community-engaged approach that supports decision making around safe COVID-19 practices is needed to promote equitable access to testing and treatment. You & Me: Test and Treat (YMTT) will evaluate a systematic and scalable community-engaged protocol that provides rapid access to COVID-19 at-home tests, education, guidance on next steps, and information on local resources to facilitate treatment in underserved populations. METHODS: This direct-to-participant observational study will distribute at-home, self-administered, COVID-19 testing kits to people in designated communities. YMTT features a Public Health 3.0 framework and Toolkit prescribing a tiered approach to community engagement. We will partner with two large community organizations, Merced County United Way (Merced County, CA) and Pitt County Health Department (Pitt County, NC), who will coordinate up to 20 local partners to distribute 40,000 COVID tests and support enrollment, consenting, and data collection over a 15-month period. Participants will complete baseline questions about their demographics, experience with COVID-19 infection, and satisfaction with the distribution event. Community partners will also complete engagement surveys. In addition, participants will receive guidance on COVID-19 mitigation and health-promoting resources, and accessible and affordable therapeutics if they test positive for COVID-19. Data collection will be completed using a web-based platform that enables creation and management of electronic data capture forms. Implementation measures include evaluating 1) the Toolkit as a method to form community-academic partnerships for COVID-19 test access, 2) testing results, and 3) the efficacy of a YMTT protocol coupled with local resourcing to provide information on testing, guidance, treatment, and links to resources. Findings will be used to inform innovative methods to address community needs in public health research that foster cultural relevance, improve research quality, and promote health equity. DISCUSSION: This work will promote access to COVID-19 testing and treatment for underserved populations by leveraging a community-engaged research toolkit. Future dissemination of the toolkit can support effective community-academic partnerships for health interventions in underserved settings. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT05455190 . Registered 13 July 2022.

A participatory ergonomics intervention to re-design work and improve the musculoskeletal health of paramedics: protocol for a cluster randomised controlled trial.

BACKGROUND: In this paper, we present the protocol for a cluster randomised controlled trial to evaluate the effectiveness and implementation of a participative risk management intervention to address work-related musculoskeletal disorders (WMSDs). The aims of the study include to evaluate the implementation process and the impact of the intervention on work related musculoskeletal pain and discomfort and exposure to physical and psychosocial hazards in paramedics over a 12-month period. METHODS: The intervention in this study is to implement A Participative Hazard Identification and Risk Management (APHIRM) toolkit in an ambulance service. Eighteen work groups containing eligible participants (registered paramedics) will be randomised into the intervention or wait-list control arm in one of three rolling recruitment periods. The APHIRM toolkit survey will be offered at baseline and 12 months later, to all current eligible participants in each work group allocated to the trial. The intervention work groups will receive the remainder of the APHIRM toolkit procedures. Identifying data about individual participants will not be collected in the survey, to protect participant privacy and encourage participation. Changes in primary (musculoskeletal pain and discomfort) and secondary (exposure to physical and psychosocial hazards at work) outcomes measured in the survey will be analysed comparing the baseline and follow up response of the cluster. A process evaluation is included to analyse the implementation and associated barriers or facilitators. DISCUSSION: This study is important in providing a comprehensive approach which focusses on both physical and psychosocial hazards using worker participation, to address WMSDs, a well-known and significant problem for ambulance services. The effectiveness of the intervention in work groups will be rigorously evaluated. If significant positive results are observed, the intervention may be adopted in ambulance services, both nationally and internationally. TRIAL REGISTRATION: ISRCTN77150219. Registered 21 November 2021.

PhysioKit: An Open-Source, Low-Cost Physiological Computing Toolkit for Single- and Multi-User Studies.

The proliferation of physiological sensors opens new opportunities to explore interactions, conduct experiments and evaluate the user experience with continuous monitoring of bodily functions. Commercial devices, however, can be costly or limit access to raw waveform data, while low-cost sensors are efforts-intensive to setup. To address these challenges, we introduce PhysioKit, an open-source, low-cost physiological computing toolkit. PhysioKit provides a one-stop pipeline consisting of (i) a sensing and data acquisition layer that can be configured in a modular manner per research needs, and (ii) a software application layer that enables data acquisition, real-time visualization and machine learning (ML)-enabled signal quality assessment. This also supports basic visual biofeedback configurations and synchronized acquisition for co-located or remote multi-user settings. In a validation study with 16 participants, PhysioKit shows strong agreement with research-grade sensors on measuring heart rate and heart rate variability metrics data. Furthermore, we report usability survey results from 10 small-project teams (44 individual members in total) who used PhysioKit for 4-6 weeks, providing insights into its use cases and research benefits. Lastly, we discuss the extensibility and potential impact of the toolkit on the research community.

Local Net Charge State of Collagen Triple Helix Is a Determinant of FKBP22 Binding to Collagen III.

Mutations in the FKBP14 gene encoding the endoplasmic reticulum resident collagen-related proline isomerase FK506 binding protein 22 kDa (FKBP22) result in kyphoscoliotic Ehlers-Danlos Syndrome (EDS), which is characterized by a broad phenotypic outcome. A plausible explanation for this outcome is that FKBP22 participates in the biosynthesis of subsets of collagen types: FKBP22 selectively binds to collagens III, IV, VI, and X, but not to collagens I, II, V, and XI. However, these binding mechanisms have never been explored, and they may underpin EDS subtype heterogeneity. Here, we used collagen Toolkit peptide libraries to investigate binding specificity. We observed that FKBP22 binding was distributed along the collagen helix. Further, it (1) was higher on collagen III than collagen II peptides and it (2) was correlated with a positive peptide charge. These findings begin to elucidate the mechanism by which FKBP22 interacts with collagen.

Building Research for Academic and Community Equity (BRACE): A Toolkit for Community Research Partnerships.

Health and human service community organizations and researchers have important insights and resources to share with each other, yet often have very little information about how to interact in meaningful and equitable ways. Conceptualized by and for community organization professionals wanting to equitably interact with academic researchers, BRACE (Building Research for Academic and Community Equity) is a toolkit easily accessible to community members which explains research information and jargon in clear terms. BRACE uses community-based participatory research (CBPR) principles to guide both community organizations and academics seeking to partner on research. The BRACE toolkit's two main sections focus on identifying ideal aspects of community-academic research partnerships and writing grant proposals. Tools such as BRACE have the potential to increase the impact of community-engaged research by providing concrete guides for building partnerships and potentially sustaining them through grant funding.