Pain is a prevalent issue in nursing home residents. Despite the importance of non-pharmacological interventions, they are underused compared to pharmacological treatments, and the respective evidence-based guidelines have hardly been implemented in daily practice. This study was carried out to collaboratively develop a practical, user-friendly toolkit with evidence-based non-pharmacological pain management interventions for improving care for nursing home residents in pain. The toolkit was developed following a systematic approach and including nursing staff from the onset. The aim was to (1) identify relevant interventions, and (2) synthesise the current evidence using up-to-date evidence summaries or rapid reviews. A list of 50 non-pharmacological interventions was compiled, and the 17 interventions receiving the highest ratings from nursing staff were further investigated and included in the toolkit. Evidence summaries were available for 14 interventions, and rapid reviews were conducted for five interventions. For example, empathetic support slightly reduced pain, while results for aromatherapy were inconsistent. Neck and back pain were alleviated by positioning special pillows for residents. The toolkit developed offers practical and comprehensive non-pharmacological pain management interventions to be used in nursing homes. By combining existing evidence and conducting rapid reviews, 17 key interventions could be evaluated. Although the quality of evidence for these interventions varies, the toolkit can be used to enhance individualised, patient-centred care, supporting a holistic approach to pain management along with pharmacological treatments. This article outlines the collaborative creation of an evidence-based toolkit designed for non-pharmacological pain management in nursing homes. The toolkit can assist nursing staff with selecting and implementing appropriate non-pharmacological interventions, complementing pharmacological treatments and tailoring interventions to the specific type of pain and individual residents' preferences.
Charles Bonnet Syndrome (CBS) is a condition characterized by visual hallucinations in individuals with visual impairments. Among military veterans, CBS can cause considerable distress, leading to health-related anxiety and delays in seeking help. Despite its prevalence, awareness of CBS remains limited across healthcare services, resulting in underdiagnosis and inadequate support. There is a need to better understand experiences of managing CBS and accessing healthcare services, from both healthcare and service user perspectives. Additionally, tailored resources are needed to address these gaps. This study explored these experiences and co-produced a toolkit to support military veterans, their families, and healthcare professionals in managing CBS and improving access to appropriate care. A two-phase, qualitative, co-production design was employed. In Phase 1, military veterans with CBS (n = 7) and specialist healthcare professionals working in the visual impairment and veteran sector (n = 13) participated in a workshop that explored the current management of CBS, the accessibility of healthcare services, and support needs. Thematic analysis identified key themes that guided the initial development of the toolkit. In Phase 2, a second focus group with military veterans (n = 4) and specialist healthcare professionals working in the visual impairment and veteran sector (n = 5) gathered feedback on the toolkit and areas for improvement. Thematic analysis was used to identify areas of refinement. A psychoeducational toolkit was developed in the form of podcasts and a video animation, as preferred by users. One podcast focused on raising awareness of CBS among healthcare professionals and providers, two podcasts focused explicitly on military veterans and their families/carers, and finally, an animated whiteboard video targeted toward all audiences. All the podcasts and video animations included a practical strategy for managing visual hallucinations. The multiple toolkits developed address key barriers to healthcare, promote early recognition of CBS, and provide accessible self-management strategies for veterans, their families, and healthcare professionals.
The paper describes the development of a Body Mapping Toolkit for Long Covid Patients, co-created in collaboration with the patient-led organisation Long Covid Support. We discuss how the use of body mapping, a participatory and arts-based research method, can support a more holistic and embodied understanding of Long Covid attentive to the way illness experiences are shaped by patients' social, cultural, and economic contexts. We further demonstrate how, through collaboration with patient organisations, body mapping might be extended beyond this research application to create spaces for peer support within the Long Covid community. Toolkit redevelopment was informed by three online body mapping workshops with a total of 13 participants, two follow-up feedback workshops and a feedback survey, all conducted in 2024. Our findings demonstrate that online body mapping workshops provide a safe space and opportunity to process experiences through creativity and storytelling and an accessible and flexible way for people with particularly challenging symptoms and restrictions to discuss their experiences with others. We also reflect on some of the limitations and challenges we encountered, and how we sought to mitigate these. The article thereby: (i) contributes to current approaches in medical humanities, medical anthropology and health geography concerned with centering patient narratives of illness experience; (ii) illustrates the value co-producing knowledge and resources with patients; and (iii) offers an example of how creative methods can be drawn on as a resource for both research and peer support.
Xylem is essential for water and nutrient transport, mechanical support, and carbohydrate storage. Identification and quantification of vascular cell types remain manual, time-consuming, and prone to observer bias, limiting throughput and reproducibility. Automated, integrated tools are critical for scaling wood anatomical studies and enabling comparative analyses across taxa. We assembled a poplar xylem dataset of 1,790 microscopy images with 173,434 annotated instances. Using this dataset, we evaluated seven semantic segmentation models and five YOLOv8 detection models across section types for xylem cell recognition and morphometric attribute extraction and adopted a "Segmentation-then-Detection" pipeline to reduce misidentifications in complex backgrounds. Mask2Former achieved the best segmentation performance, covering transverse sections (whole xylem, vessels, fibers, rays) and tangential sections (rays and four ray cell image types). YOLOv8x and YOLOv8m performed consistently for object detection and morphometrics, and the PLXY-AI toolkit was accordingly developed based on YOLOv8 architecture. The combined pipeline markedly improved fiber identification in challenging images. In a generalization test, 34 of 42 woody angiosperms (81.0%) met > 90% accuracy for identifying all cell types. The workflow and PLXY-AI toolkit enable automated identification and quantification of vessels, fibers, and rays, extracting size and area while substantially reducing manual workload and observer bias. Per-image processing time averages < 1 s. Designed for batch analysis, the pipeline minimizes operational complexity and integrates easily into existing laboratory and computational environments. With a user-friendly graphical interface, this framework supports high-throughput analysis of vascular tissue structure and function across multiple tree species.
Striatal medium spiny neurons expressing D1 dopamine receptors (D1-MSNs) are a key component in the direct pathway of the basal ganglia and exhibit chronically suppressed activity in Parkinson's disease. To enable selective anatomical and functional interrogation of D1-MSNs, we developed an adeno-associated virus (AAV) toolkit that achieved robust and selective transgene expression in D1-MSNs through retrograde transduction of their substantia nigra axons. We first screened an AAV9 capsid insertion library and identified variants with markedly enhanced retrograde access to D1-MSNs. Next, we engineered a series of enhancers and demonstrate that they drive strong and specific gene expression in D1-MSNs after retrograde transduction in both mice and a macaque. Importantly, we demonstrate that our toolkit enables targeted modulation of the direct pathway, eliciting pathway-specific behaviors and rescuing motor deficits in a murine model of Parkinson's disease. These findings highlight the utility of our D1-MSN-targeting tools for basic and translational research.
To evaluate a multipronged toolkit (Connect, Pause and Reflect Toolkit [CPRT]) codesigned to support clinicians' professional fulfilment, meaning, and multidisciplinary connection when caring for children with severe neurological impairment. This study used convergent mixed-methods design. Participants reviewed CPRT and completed an online mixed-methods questionnaire, including a combination of validated, purpose-designed, and qualitative questions. We assessed CPRT engagement, acceptability, and utility, including barriers and enablers to implementation and intrapersonal and interpersonal impacts on clinicians. We adopted a convergent approach, integrating quantitative and qualitative data to critically examine and enrich understanding of participants' responses. Participants (n = 100) rated CPRT as highly acceptable, and valuable in supporting clinicians coping with cognitive and emotional challenges of clinical practice. Self-reported data suggest engaging with CPRT stimulated deep reflection, and multidisciplinary connection, reducing clinicians' isolation. Quantitative and qualitative data converged to suggest CPRT normalized and validated clinicians' struggle and positively reinforced a sense of meaning and professional purpose. This exploratory descriptive study suggests CPRT is acceptable and effective in supporting multidisciplinary clinicians facing immense challenges caring for children with severe neurological impairment. CPRT provides a novel and freely accessible multipronged suite of interventions, to support clinicians' resilience, reflection, and multidisciplinary connection.
Although the oleaginous yeast Yarrowia lipolytica is a promising microbial cell factory, its application remains constrained by inefficient homology-directed repair (HDR) and a lack of precise genomic integration tools. To address these limitations, we developed a comprehensive genetic toolkit featuring three synergistic advancements. First, we systematically identified 55 neutral integration sites with tunable expression profiles, enabling stable, position-independent gene integration with predictable transcriptional output across a 12.88-fold dynamic range. Second, we established a dual-readout high-throughput screening platform combining colony morphology analysis with hrGFP fluorescence. This approach accurately measures locus-specific homologous recombination (HR) efficiency while eliminating false positives by dominant non-homologous end joining (NHEJ). Third, we engineered a transient HR enhancement system by fusing the Sae2 exonuclease to Cas9 via a flexible (GGGGS)3 linker. This fusion significantly boosts HR efficiency and surpasses the cleavage activity of unmodified Cas9 without introducing permanent genomic modifications or compromising cellular fitness. Finally, HR efficiency for single-gene integration was increased from 46.5% to 77.5% while the dual-locus editing efficiency reached 64.1% when using 500-bp homology arms, and the engineered strains demonstrated improved genetic stability compared to those with constitutive HR enhancement.
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Representations that encode the genome-wide regulatory behavior of transcription regulators provide a foundation for flexible transcription modeling and in silico regulatory analysis. Existing regulator representations are commonly derived from gene co-expression, motif annotations, or static protein features, which capture useful but limited aspects of regulator identity but do not directly model how regulators participate in region-specific regulatory programs across the genome. ChromBERT addresses this gap by learning context-aware regulatory representations from large-scale ChIP-seq data. However, routine bioinformatics applications require lightweight, accessible, and modular tools for generating, adapting, and interpreting these representations in user-defined biological contexts. Here, we present ChromBERT-tools, a user-oriented toolkit built upon ChromBERT that converts its regulatory representation framework into practical workflows for customizable analysis across cellular contexts. ChromBERT-tools provides command-line interfaces and Python APIs organized into three functional layers: representation generation, predictive modeling, and regulatory interpretation. The representation generation layer produces representations of genomic regions and transcription regulators. The predictive modeling layer fine-tunes ChromBERT for genome-wide regulatory activity prediction through classification or regression tasks, with optimized implementation to reduce running time and computational resource requirements. The regulatory interpretation layer supports inference of the context-specific roles of cis-regulatory elements and transcription regulators. These modules can be used independently or integrated into end-to-end workflows, enabling flexible analyses across diverse datasets. ChromBERT-tools lowers the barrier to applying context-specific regulatory representations in routine genomic analyses. ChromBERT-tools is freely available at https://github.com/TongjiZhanglab/ChromBERT-tools, with documentation at https://chrombert-tools.readthedocs.io/en/latest/. A frozen archival snapshot is available on Zenodo under DOI: 10.5281/zenodo.20094206. Supplementary data are available at Bioinformatics online.
Xylanases are central to lignocellulosic biomass degradation, yet current methods lack the specificity to resolve how enzymes distinguish complex xylan structures decorated with arabinofuranose (Araf) and 4-O-methyl-glucuronic acid (MeGlcA). Here, we report a suite of chemically-defined activity-based probes (ABPs) that enable the selective detection of arabinoxylan- and glucuronoxylan-specific xylanases (AXXs and GXXs). These cyclophellitol-derived ABPs covalently label retaining xylanases at their active sites, allowing precise mapping of substrate specificity across diverse glycoside hydrolase families. Crystallographic and mass spectrometric analyses reveal the molecular basis of probe selectivity, while in-gel and pull-down assays demonstrate their effectiveness in profiling xylanase activities in complex bacterial and fungal proteomes, including cellulosomes. By integrating activity-based protein profiling (ABPP) with sequence similarity networks (SSNs), we further show that xylanase specificity can be predicted from sequence alone, enabling rapid functional annotation of uncharacterized xylanases. This chemoproteomic strategy provides a powerful platform for discovering and engineering substrate-specific enzymes for biomass valorisation, microbial ecology, and biotechnological applications.
In a timely advance for antimycobacterial biotechnology, Abouhmad et al. engineered modular 'mycolysins' that combine mycobacteriophage lysis functions with membrane-active peptides to efficiently breach the mycobacterial envelope and achieve pathogen intracellular killing. Their work opens a route that may accelerate the development of biologics against tuberculosis and nontuberculous mycobacterial diseases.
The optimal timing of a treatment within therapy lines can maximize its benefit while minimizing risks and side effects. Because patients differ in clinical and biological characteristics, personalized treatment planning can support physicians' decision-making. However, multistate disease progression complicates the comparison of treatment strategies, motivating the development of a user-friendly web tool for multistate disease progression simulation and treatment decision support. Microsimulation is a natural approach for comparing prespecified treatment-timing strategies, where it generates disease trajectories for a large number of virtual patients matched to an individual patient's observed data. In our framework, microsimulation is performed using a multistate model to capture state-to-state transition hazards. We develop TxMicroSim, a web-based interface built with R Shiny, to compare treatment-timing strategies by estimating model-projected restricted mean survival times (RMSTs). The application consists of three main steps: defining the multistate structure, building the multistate model, and performing microsimulation. First, the user specifies the multistate structure, with the treatment of interest as one of the states and an absorbing state representing the time-to-event endpoint. The user also identifies transitions that lead into the treatment state, defining the strategy-driven transitions used to compare treatment-timing strategies. Next, to build clock-reset transition-specific flexible parametric proportional hazards models, the user can either upload data for model fitting or manually enter covariate hazard ratios and baseline hazard parameters. Two baseline hazard specifications are supported: a piecewise constant function and a natural cubic spline. Finally, the user enters patient-specific information, including covariates, the initial disease state at diagnosis, and the treatment start time for strategy-driven transitions. Microsimulation is used to compute RMST up to a prespecified time horizon under each strategy. Throughout the app, interactive visualizations are provided for the multistate structure, estimated hazard ratios and baseline hazards, and RMST comparisons across treatment strategies. TxMicroSim is a flexible web tool that compares treatment-timing strategies and quantifies survival impact using interpretable summaries and interactive visualizations.
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The vagina undergoes important changes across the life course that are shaped not only by hormonal transitions but also by shifts in the vaginal microbial environment. Despite growing interest in the vaginal microbiome, research has disproportionately centered reproductive-aged populations, leaving the aging vagina comparatively understudied. This article examines the aging vagina through a life-course lens, with emphasis on microbial and clinical transitions associated with midlife and older adulthood. The article highlights menopause-related changes and approaches for reducing stigma and missed clinical opportunities. Particular attention is given to menopause-related declines in estrogen, reduced glycogen availability, increased vaginal pH, and accompanying changes in microbial balance, as well as their relationship to dryness, irritation, genitourinary symptoms, and susceptibility to adverse outcomes. The article also provides health professionals with a practical educational framework for symptom recognition, patient communication, vaginal health assessment, menopause-related education, stigma reduction, and prevention of missed clinical opportunities. Positioning the aging vagina within life-course and microbial-health frameworks can strengthen prevention, improve symptom recognition, and support more ageinclusive, informed, and responsive care for older women.
Effective implementation of evidence-based programmes in real-world settings requires the capacity to adapt programmes and tailor implementation strategies to local contexts. Many primary cancer prevention (PCP) programmes that are effective in controlled settings struggle in routine practice. Although several frameworks outline principles of adaptation and tailoring, practical guidance on how to operationalise these processes remains limited. The PIECES project aims to help address this gap by developing, implementing, and evaluating structured support for tailored implementation of PCP programmes. Within the PIECES project, a toolkit was co-developed with practitioners and researchers to provide theory- and evidence-informed guidance for adapting, tailoring, implementing, and evaluating PCP programmes. The toolkit aims to strengthen implementation competencies through structured planning, collaborative learning, and evidence-informed decision-making. This paper presents the protocol for the PIECES study which evaluates the toolkit's usability, feasibility, and mechanisms of impact of PCP programmes across diverse healthcare and community settings. The PIECES study uses a multi-site pre-post comparative case study design with a mixed-methods implementation evaluation across 11 sites in Europe and Australia, reflecting variation in organisational structures, resources, and cultural contexts. The primary outcome is change in implementation competencies among toolkit users. Guided by the UK MRC Process Evaluation Framework and Proctor's implementation outcomes, the process evaluation examines toolkit usability, feasibility, user satisfaction, and perceived impact on implementation processes and outcomes. Quantitative and qualitative data, toolkit log data, and structured field notes will be collected at six-month intervals (2025-2027). In parallel, a realist evaluation will explore how, why, and under what conditions the toolkit supports tailored implementation. Together, these approaches provide complementary descriptive and explanatory insights into the mechanisms and contextual factors shaping tailored implementation of PCP programmes. This study is expected to contribute to implementation science by evaluating a structured, evidence-informed tool designed to strengthen capacity for tailored implementation of PCP programmes. Its multi-country design offers a natural field-laboratory to explore how implementation support tools function across varying contexts. By integrating process and realist evaluation approaches, the study is designed to generate practical and theoretical evidence to inform scalable, context-sensitive strategies and enhance the sustainability and impact of evidence-based prevention efforts. ClinicalTrials.gov ID NCT06718322.
RNA-guided nucleases enable DNA editing and offer promise for treating genetic diseases, particularly when used for precise sequence replacement. However, many of the most effective enzymes, such as Streptococcus pyogenes Cas9, are too large for delivery using vectors like adeno-associated virus. This has prompted interest in smaller alternatives from the Cas12f and TnpB families. Yet, these nucleases often show low activity in mammalian cells, limiting their utility. We use directed evolution in human cells to select variants with greatly improved activity. The resulting variants, Cas12f1Super and TnpBSuper, exhibit up to 11-fold increase in editing efficiency without increased off-target effects. When tested as a base editor, Cas12f1Super shows up to tenfold improvement relative to the previously engineered CasMINI, suggesting utility beyond nuclease-related activities. These compact and efficient genome editors expand the current toolkit and hold promise for both research and therapeutic use in mammalian systems.
Climate change is shifting agriculture toward multifactorial abiotic stresses (drought, heat, and salinity). This study aims to characterize emergent, non-additive plant responses to combined stresses and to define the epigenetic and microbial frameworks that govern environmental memory and adaptive plasticity. We conducted a meta-synthesis of molecular and ecological studies, evaluating high-throughput data on DNA methylation, histone modifications, and ncRNA profiles. We further analyzed the plant holobiont to determine how rhizosphere and endosphere microbiota influence host stress imprinting. The analysis revealed that stress combinations trigger distinct transcriptomic and metabolic signatures, which are stabilized by an "epigenetic toolkit" such as RNA-directed DNA methylation and chromatin remodeling. Furthermore, plant-associated microbiota serve as an extrinsic regulatory layer, modulating host epigenetic states to prime plants for compound stress. While translational pathways such as epigenetic editing, CRISPR-mediated epigenome editing, and microbiome engineering show promise, their field-scale stability remains context-dependent. Building climate resilience requires a paradigm shift from traditional single-trait breeding toward multi-scale regulatory approaches. Harnessing the synergy between the plant epigenome and the microbiome enables the development of 'primed' crop varieties-an integrated strategy vital for safeguarding global food security amid intensifying environmental volatility.
This study described the implementation of the Registered Nurses' Association of Ontario® (RNAO) Vascular Access Best Practice Guideline in a hospital in the Basque health system and evaluated its impact on vascular access care by comparing changes in phlebitis rates before and after implementation. A longitudinal pre-post observational study was conducted using routinely collected data on peripheral venous catheters from 2020 to 2023. A retrospective analysis of prospectively collected institutional data was performed. To describe the implementation process, implementation logs were reviewed, including meeting minutes, audit reports, and internal monitoring documents. Data on peripheral venous catheter insertions and phlebitis cases were extracted from the hospital's clinical data system. Annual phlebitis rates were calculated and compared using the χ2 test, with statistical significance set at p-value <0.05. The implementation process followed the RNAO Best Practice Guideline Implementation Toolkit and was structured around three components: knowledge dissemination, professional training, and changes in clinical practice. A total of 3,272 peripheral venous catheter insertions was recorded in 2020 and 1,210 insertions in 2023. The phlebitis rate in 2020 was 6.3% (95% CI: 5.5%-7.2%), and decreased to 3.9% (95% CI: 2.9%-5.2%) in 2023, representing a statistically significant reduction and reaching values below the 5% threshold recommended by the Infusion Nurses' Society. The implementation of the RNAO Vascular Access Guideline was associated with a statistically and clinically significant reduction in phlebitis rates. These findings support the use of structured implementation strategies in improving vascular access care. http://links.lww.com/IJEBH/A612.
A facile and environment-friendly synthetic strategy toward iodo-indoloquinolines with high site-selectivity and atom-efficiency is reported, featuring an oxidative functionalization of 2-aminobenzyl alcohols with indoles in the presence of molecular iodine under an O2 atmosphere. This methodology enables further indoloquinoline-based transformations and broadens the toolkit for constructing structurally diverse indoloquinoline scaffolds.