Chemical proteomics approaches often yield low peptide recovery because they aim to enrich low-abundance proteins. Poor sample handling further reduces recovery through peptide adsorption to plastic surfaces and losses due to vacuum evaporation. We systematically mapped these losses across buffers, volumes, plastics and pH, then developed an Evotip-compatible handling protocol that minimizes adsorption and removes the need for vacuum evaporation. Losses to plastic adsorption and vacuum evaporation were most apparent at low inputs (< 200 ng) and with larger volumes (> 20 µL) but were also dependent on acidification as well as the buffer and plastic used. The optimized workflow: direct acidification of peptides, frozen storage if needed, and direct loading onto Evotips, resulted in up to ∼90-fold gains versus workflows incorporating vacuum concentration steps, a common practice in proteomics sample preparation, when peptide input was limited to 10 ng. This optimized sample handling method enables high-throughput chemical proteomics by reducing manual handling steps and enables the characterization of low abundance proteins previously lost during sample preparation.
Senescent cells accumulate in chronically diseased liver tissues and are known to actively contribute to disease pathology. To date, these studies have predominantly focussed on senescence in epithelial cells, such as hepatocytes and biliary epithelial cells, and senescence in liver endothelial cells remains largely understudied. Here, we utilise publicly available single-cell RNA-sequencing data, immunohistochemical and immunofluorescent staining to detect senescent endothelial cells within chronically diseased human liver tissues. Next, we develop a novel protocol for the induction of paracrine senescence in primary human liver endothelial cells and explore their functionality. We demonstrate that senescent liver endothelial cells exhibit a reduced scavenging capacity but are still able to support lymphocyte recruitment under physiological flow conditions in vitro. Mechanistically, we determine that inducible T cell costimulator ligand (ICOSL) is an important factor in the specific recruitment of CD4+ T cells, but antibody blockade, genetic knockdown and genetic overexpression of ICOSL in endothelial cells has no effect on CD8+ T cell recruitment. Finally, we show that ICOSL gene expression is upregulated in chronically diseased tissues, present in scar-associated endothelial cells and correlates to CD4+ T cell infiltration. This is the first study to demonstrate that senescent human liver endothelial cells can potentially shape the liver immune microenvironment in chronic liver disease. Targeting senescent endothelial cells could present new therapeutic opportunities to treat chronic liver diseases.
Antimicrobial resistant healthcare-associated infections present an increasing threat to public safety and the sustainability of healthcare systems around the world. Mobile phones have been highlighted as a fomite that negates hand hygiene and contributes to the dissemination of pathogenic microorganisms in healthcare settings. The objective of the current stidy was to investigate the presence of bacteria, antimicrobial resistance and virulence genes associated with high morbidity on 95 mobile phones within healthcare settings. Next-Generation Metagenomic Sequencing was undertaken and FastQ files were subsequently analyzed within COSMOSid to enable taxonomic identification. Antibiotic resistant genes, virulence genes and bacteriophages were co-located with bacteria associated with the highest global mortality. Antibiotic resistant genes were manually annotated and cross referenced with the Comprehensive Antibiotic Resistance Database (CARD) to identify gene-drug interactions. On average, mobile phones were identified to be contaminated with 3.62 of the top 10 highest mortality-causing bacteria and 2.49 ESKAPE pathogens. A total of 262 unique ARGs, 448 unique VFGs, and 314 bacteriophages were identified. Mobile phones within healthcare settings harbor pathogens alongside genes associated with increased virulence and antimicrobial resistance. Additionally, mobile phones, known to be infrequently sanitized, may increase antimicrobial resistance by providing a contaminated platform which facilitates continued horizontal genetic transfer.
In pursuit of a gene transfer agent with efficient pulmonary transduction, the UK Respiratory Gene Therapy Consortium has developed a lentiviral vector pseudotyped with the envelope proteins, F and HN from Sendai virus (rSIV.F/HN). In contrast to other viral vectors, pulmonary rSIV.F/HN delivery achieves sustained gene expression ( ~ 2 years in mice) in the lungs and systemic circulation following a single dose. Here, we investigate the application of the rSIV.F/HN vector-platform for wider indications, including systemic disorders that require serum expression of therapeutic proteins. To assess the potential for rSIV.F/HN to produce systemic proteins, intravenous vector delivery was characterised and compared against intrapulmonary administration, achieved via 'nasal sniffing'. Both delivery routes achieved sustained (at least 1 year) systemic expression of the secreted reporter protein Gaussia luciferase. Systemic rSIV.F/HN delivery resulted in widespread protein expression across multiple organs, accompanied by the generation of significant anti-vector neutralising antibodies limiting vector readministration. Conversely, localised airway transduction was observed following pulmonary administration, which we have previously shown is not an impediment to efficient vector readministration. These data support intrapulmonary rSIV.F/HN delivery for systemic protein production, with sustained high-level transgene expression and feasible readministration.
Although progress towards implementation of international agreements since publication of the UCL-Lancet Commission on Migration and Health in December, 2018, has been slow, global trends in migration and forced displacement have continued to rise. However, the COVID-19 pandemic showed that reaching refugees and migrants with health interventions is feasible with political will. The benefits of refugee-inclusive and migrant-inclusive health-care systems during emergencies (eg, COVID-19 and the war in Ukraine) are apparent, with numerous examples of inclusive policy making being rapidly introduced and innovative models developed to support health-care access, including preventive measures such as vaccination. Lessons from these successes should be learned and incorporated into future policy and practice. However, global political and financial uncertainty and disruption-combined with multiple conflicts and natural disasters-have increased individuals' need to move, which will continue to be exacerbated by the climate crisis. Although new conflicts and exacerbations of existing ones have led to a rise in forced displacement within and across national borders, labour migration has also risen dramatically, with the pandemic highlighting the health and social needs of these groups globally. The need for strong leadership and accountability, engagement of policy makers in the highest-level fora, and improved access to quality health services for refugees and migrants has never been greater. In this Review, nearly 8 years after the UCL-Lancet Commission on Migration and Health was published, we renew our call for action to: (1) improve health-care access and optimise outcomes for refugees and migrants by emphasising health in all migration and forced displacement policies; (2) establish data systems to monitor progress, together with appropriate use of new technologies to improve access, prevent harm, and safeguard privacy; (3) support research on adaptation to and mitigation of the health consequences of climate change on refugees and migrants; and (4) renew focus on the political determinants of health outcomes for people on the move. At this pivotal moment, with geopolitical, sociodemographic, and environmental turmoil, political leaders and societies can shape a better future by leveraging the human capital of migrants and upholding the human rights and dignity of all.
Reproducibility challenges in bioimage analysis are common. The proliferation of tools and workflows creates a complex ecosystem that is difficult to reproduce without deliberate, explicit reporting and support. We assess the reproducibility of Gehrels et al.(2023) as a representative bioimage analysis workflow. We do not evaluate the biological claims; instead, we examine the reproducibility of the bioimage analysis methods used and the implications for current peer-review practices in the field. Although some data were deposited in the BioImage Archive and code was available on GitHub, the materials were insufficient to completely reproduce the analysis. Moreover, the repository lacked the configuration to enable straightforward replication of the workflow or results. This case study highlighted how incomplete reporting can significantly hinder the reproduction of bioimage analysis workflows. Because scientific progress relies on verifiable replications, insufficiently reproducible results can erode confidence in the scientific record.
The Tau Global Conference 2025, hosted by the Alzheimer's Association, CurePSP, and the Rainwater Charitable Foundation, convened international experts from academia, industry, government, and philanthropy to explore advances and challenges in tauopathy research. The meeting highlighted progress across tau biology, including emerging models of tau regulation, degradation, and propagation; advances in biomarker development for the diagnosis and staging of tauopathies; and evolving therapeutic strategies targeting diverse aspects of tau pathophysiology. Discussions also emphasized the importance of cross-sector collaboration, and global initiatives to address disparities in tau research. This report synthesizes key insights from the conference and underscores the critical role of interdisciplinary, biomarker-driven, and globally inclusive approaches in accelerating the translation of tau research into effective clinical applications.
Patient and Public Involvement (PPI) is a continually growing component of health and social care research in the UK and internationally, ensuring that research is conducted with and by the public rather than simply about them. Doctoral research represents a critical opportunity to embed meaningful PPI early in researchers' careers, yet practical recommendations tailored to this context remain limited. Existing studies often focus on individual case reflections or programme-level evaluations, with few capturing the collective experiences of doctoral researchers, PPI contributors, and coordinators. This paper aims to co-produce practical recommendations to support meaningful patient and public involvement in doctoral health and social care research. This paper presents co-produced reflections and recommendations to support PPI in doctoral research. The writing process was approached collaboratively, with a team incorporating public contributors, doctoral researchers, and a public involvement coordinator working together through iterative discussion and revision. The approach aligns with the principles of authentic co-production, creating both "space to talk" through open, respectful dialogue and "space to change" through mutual adaptation. The team's experiences highlighted both shared benefits and challenges within the process. PPI enriched doctoral research by refining study design, questions, enhancing recruitment, and improving accessibility of outputs, while also offering PPI contributors opportunities for learning and impact. Challenges included managing emotional topics, balancing timelines, and recognising that not all suggestions could be implemented. The coordinator's role proved vital in bridging between researchers and public contributors, supporting communication, reimbursement processes, and continuity of relationships. Doctoral researchers emphasised the importance of building trust, using accessible language, and developing distinct relational skills alongside academic expertise. From these collective insights, the team developed practical recommendations for three key audiences: doctoral students, PPI contributors, and PPI coordinators. PPI in doctoral research offers mutual benefits for contributors and early-career researchers, strengthening both research quality and personal and professional development. Genuine co-production requires time, respect, and institutional support, but can foster strong partnerships and more relevant, impactful research. The recommendations presented here aim to help doctoral researchers, PPI contributors, and coordinators embed authentic, equitable, and sustainable involvement across health and social care research. Patient and Public Involvement (PPI) means that research is carried out with and by members of the public, rather than to or about them. It helps research to be more relevant, inclusive, and useful for the people it aims to benefit. This paper describes and examines the experience of involving patients and the public in doctoral (PhD) research. Doctoral projects often have limited funding and time, but they also offer opportunities for close, long-term collaboration between students and public contributors. The aims and content of the paper was developed collaboratively by doctoral researchers, public contributors, and a PPI coordinator who reflected together on what worked well and what could be improved. The process showed the importance of building trust, communicating clearly, and recognising that both researchers and public contributors bring valuable skills and knowledge. Having a PPI coordinator to support students and contributors, provide training, and manage practical arrangements such as payments was also found to be helpful. From these shared experiences, practical recommendations were developed for doctoral students, public contributors, and PPI coordinators. These focus on getting started, building relationships, communicating effectively, and ending involvement respectfully. Meaningful PPI during doctoral research was found to improve study quality and impact for patients, families, and the wider public, while helping new researchers to develop collaborative and inclusive ways of working that keep the focus on what matters to patients and the public.
Left bundle branch block (LBBB) describes a specific cardiac conduction abnormality which may be a cause, consequence, or exacerbator of cardiovascular dysfunction and events. Electrocardiogram-derived definitions, which depend heavily on QRS duration (QRSd), are imperfect and continue to evolve, with limited data on predicting LBBB development. This study aimed to determine whether changes in electrical axis identify patients at risk of future development of LBBB. Retrospective data from 35,749 UK Biobank participants were analyzed, excluding those with overt cardiovascular disease. The primary endpoint was LBBB development. Associations with axis metrics (computed from baseline cardiac magnetic resonance imaging and 12-lead electrocardiogram) were investigated using Kaplan-Meier analysis and Cox proportional hazards models adjusted for age, sex, hypertension, left ventricular ejection fraction and QRSd. The cohort (age 63.4 ± 7.6 years, 45% male, QRSd: 87.4 ± 12.8 ms) was followed for a median of 6 years. Compared with the event-free population (N = 35,688), those who developed LBBB (N = 41) were older (69.2 vs 64.0 years; P < 0.001), more likely to have hypertension (31.7% vs 11.6%; P < 0.001), and had a significantly lower (more posterior) electrical axis (φElectrical: 69.1° vs 80.3°; P = 0.01). In multivariable analysis, lower φElectrical (HR: 0.73; 95% CI: 0.56-0.94; P = 0.014) was significantly associated with incident LBBB. Individuals with both high QRSd and low φElectrical had a four-fold increased risk (HR: 4.09; 95% CI: 1.84-8.99; P < 0.001). Posterior deviation of the transverse electrical axis complements QRSd in identifying individuals at risk of developing LBBB. These findings suggest that the electrical axis is capturing early conduction disease and may contribute to risk stratification of future development of LBBB.
Allosteric communication between non-contacting sites in proteins plays a fundamental role in biological regulation and drug action. While allosteric gain-of-function variants are known drivers of oncogene activation, the broader importance of allostery in genetic disease and protein evolution is less clear. Here, we introduce a comparative framework that disentangles functional disruption by mutations from protein destabilization. Applying this framework across diverse datasets-ranging from paired experimental measurements of abundance and activity to proteome-wide comparisons of evolutionary fitness and biophysical stability predictions-we provide evidence that allostery is a widespread cause of loss-of-function variant pathogenicity in human genetic diseases. In addition, our analyses reveal a conserved distance-dependent decay of allosteric mutational effects outside of protein active sites. As an important mechanism of pathogenicity, allostery needs to be better mapped, understood, and predicted across the human proteome.
Cell-to-cell communication is essential for maintaining homeostasis and coordinating complex biological processes in multicellular organisms. Classically, cells communicate using secreted peptides and metabolites and through cell contact-dependent signaling. Emerging studies over the past 20 years indicate that many cell types, including innate immune cells such as macrophages, participate in a process called intercellular mitochondria transfer, in which macrophages either donate their own mitochondria to other cells or accept mitochondria originating from another cell type. This raises the intriguing possibility that macrophages use mitochondria transfer as a mechanism of cell-to-cell communication. In this review, we describe the distinct mechanisms and functional roles of mitochondria transfer in macrophages across different organ systems and highlight how this biology contributes to health maintenance and disease pathogenesis.
Origins of DNA replication (Ori) are genomic loci where DNA synthesis begins, essential for bacterial viability, eukaryotic development, and genome integrity. While early computational methods relied on compositional skews and motif heuristics, recent years have seen a shift toward artificial intelligence approaches. This review systematically surveys Ori prediction methods published through August 2025, integrating biological background with curated datasets, benchmarks, and a classification of computational strategies from rule-based models to deep learning. We summarize performance across organisms, cell types, and platforms, and highlight key trends, challenges, and opportunities in benchmarking, interpretability, and cross-species generalization-providing both an accessible entry point for practitioners and a roadmap for future methodological development.
Infectious disease modelling (IDM) is increasingly used to understand disease transmission and inform public health policy. Its growth and influence on policy have not been quantified, partly due to the large volume of literature. Using a large language model (LLM)-assisted review, we quantified the expansion of IDM publications, trends in policy citations, and regional disparities in research contributions and uptake. An LLM-assisted bibliometric review was conducted in Embase, Medline, and Scopus, identifying IDM publications to December 2024 via GPT-4o (OpenAI). Eligible studies employed mathematical, statistical, or mechanistic models for infectious disease outcomes. LLM accuracy was iteratively refined through human review. We extracted publication metadata, geographic scope, and policy citations via Overton, a global database of policy documents. Growth trends were analysed using negative binomial regression; geographic disparities were assessed by World Bank income classifications. We identified 33,255 IDM publications over 44 years, with distinct growth phases. Publication volume rose with the emergence of HIV/AIDS, expanded through successive outbreaks (Ebola, SARS, H1N1, MERS, Zika), surged just before COVID-19, then declined after 2021. Policy citations accounted for 1.7% of IDM publications, mirroring overall growth and peaking during periods of heightened public health attention. Citations largely reflected national research outputs, with some cross-regional adoption of IDM evidence. Strengthening IDM's policy impact may require fostering collaboration pu and improving uptake mechanisms. Post-COVID-19, policy citations declined despite continued IDM growth, suggesting a lag or shift in priorities.
"Sex" is a compound of many different concepts that contribute to a multiplicity of meanings. As a result, "sex" appears in a wide range of scientific research for different purposes, from describing a process of recombination and cell division to systems of categorising individuals. Identifying the meaning of "sex" in any particular context requires understanding the construction of contributing component concepts and their relationship with one another. We offer the metaphor of a labyrinth to describe the process of interpreting the meaning "sex" and uncovering its context-dependent purpose. In this way, the meanings of "sex" related to "sexual reproduction", "sex types", "sex determination", and/or "sexual systems" can be elucidated by identifying how these concepts relate to suppositions about what properties of "recombination, "meiosis", "syngamy", or "gametes" are present and to which aspects of a trait, individual, or lineage they apply. By denoting "sex" and related terminology within quotation marks, we emphasise the contextualism of language in the theory and practise of research and resultant knowledge about the natural world. The structure of a labyrinth reflects the incredible capacity of "sex" to describe the diversity and disparity of eukaryotic reproductive systems. The analytical framework of the labyrinth highlights that many branching paths lead to distinct destinations and different conceptual versions can arise in the consideration of reproductive trait evolution based on the inclusions and possible connections among concepts. Through a critical evaluation of the concepts that contribute to the labyrinth of "sex" across biology, we gain a more nuanced appreciation for the operation of "sex" within scientific knowledge.
Asthma is an obstructive respiratory disease with greatest morbidity in low- and middle-income countries: 15% of the Filipino population are estimated to have asthma, half of whom have inadequately controlled disease. There are many known genetic associations with asthma, but lack of representation across ancestries means that understudied populations do not yet stand to benefit equally from genomic research. We performed the first genetic association study of asthma in a Filipino population. We performed a candidate-variant association study in 1,678 unrelated mothers (129 with self-reported asthma) of the Cebu Longitudinal Health and Nutrition Survey (CLHNS). Using the largest published multi-ancestry asthma GWAS (Global Biobank Meta-Analysis Initiative, GBMI), we selected sentinel single-nucleotide polymorphisms (SNPs) associated in the multi-ancestry analysis (P < 5 × 10- 8), and in GBMI East Asian (EAS) participants (P < 5 × 10- 6). SNPs (or proxies r2 > 0.8) were tested for association with asthma, adjusting for age and 15 principal components. Variants were then aggregated into a genetic risk score (GRS), weighted by effect sizes reported in the EAS GBMI asthma GWAS. We examined whether the identified top signals from GBMI EAS GWAS were associated in our study. Twenty-seven SNPs were analysed. Only one intronic variant in SMAD3 was associated with asthma at a Bonferroni-corrected threshold (rs17293632, OR 1.80, 95%CI 1.28-2.54, P = 0.0008). SMAD3 is involved in TGF-β signalling, related to airway remodelling in asthma. The GRS was associated with increased odds of asthma (OR per weighted allele increase 1.07 [95%CI 1.01-1.14], P = 0.022). Five of the 37 top signals in the EAS GWAS were associated in our study, although none of these five signals reached a Bonferroni p-value threshold of P = 1.35 × 10- 3. Despite the small sample size, we detected a known SNP-asthma association in CLHNS using a candidate-variant approach, and demonstrated the value of aggregating variants into GRS when power is limited (using confidently ascribed weights from large GWAS). However, we were underpowered to undertake a GWAS, and thus to discover novel associations. Commitment by the genomics field as a whole to cohort development and investment in understudied populations will be key to addressing inequity in asthma genetic research. Not applicable.
Cognitive neuroscience research often relies on convenience sampling of participants, which can result in biased sample demographics and an under-representation of older adults. There is a need to identify more effective routes to widen participation among older adults and to explore age-related differences in the motivators and barriers to research involvement. This mixed methods study combined qualitative data from two focus groups, conducted with N = 11 healthy older adults aged 55-73, and an online questionnaire completed by N = 336 adults aged 18-88. Analysis of the focus group discussions identified 3 main themes that were most important to older adults: a) The importance of receiving transparent information about the aims, procedures and safety of the study, b) Distinguishing between medical and non-medical research, and c) Contributing to the "collective good". The questionnaire echoed that altruism, and the prospect of scientific discovery, are increasingly important motivators with advancing age, whereas financial incentives become less important. Older adults have more free time to participate, are less deterred by the prospect of pain, and express more trust in researchers than younger people. Attitudes towards different imaging methods (MRI, EEG, NIBS and Eye tracking) varied, with fewest negative emotions for eye-tracking and most for non-invasive brain stimulation, but positive attitudes generally increased and negative attitudes reduced with age. These findings can inform age-tailored recruitment strategies to improve diversity in neuroimaging research. Improving communication, addressing practical barriers, and framing studies in a meaningful context may help increase participation among groups who are traditionally underrepresented in neuroimaging research.
The female reproductive tract (FRT) is susceptible to sexually transmitted infections (STIs), including human immunodeficiency virus (HIV), which negatively impact and threaten the lives of women worldwide. While the hormonal regulation of innate and adaptive immunity in the FRT during the menstrual cycle is well-studied, changes in mucosal immune protection throughout the FRT that occur with aging after menopause remain largely unknown. This review summarizes hormonal and age-related immune changes throughout the FRT, focusing on their effects on the function of epithelial cells and immune cells in the uterus, cervix and vagina, highlighting implications for HIV infection. After menopause, as reproductive function ceases, two interconnected processes, menopause and immunosenescence, drive alterations in immune protection. As women age following menopause, significant aspects of innate and adaptive immunity in the FRT are compromised in a site-specific manner. At some FRT sites, as cell numbers decline, immunological compensation characterized by increased immunological activity is observed. Overall, these changes in mucosal immune protection contribute to a heightened risk of STIs and HIV acquisition. Further research is essential to establish a basis for developing new therapeutic interventions to restore immune protection and mitigate conditions that endanger the health and lives of aging women.
Digital surgery technologies, including robotic systems, artificial intelligence (AI) algorithms, augmented reality platforms, and advanced data analytics, are rapidly transforming surgical practice. While these technologies hold tremendous potential to improve patient outcomes, they introduce unique regulatory challenges that current frameworks are not fully equipped to address. This white paper from the SAGES Surgical Data Science Committee characterizes the regulatory challenges specific to digital surgery technologies and proposes general regulatory principles designed to balance patient safety with efficient delivery of beneficial innovations. We identify key regulatory gaps across three categories of digital surgery technologies, including enhanced instrumentation and robotics, advanced visualization systems, and AI data analytics and capture. Unlike diagnostic tools, these technologies guide real-time, irreversible actions where errors can cause immediate and permanent patient harm. Critical challenges include the lack of clinically meaningful performance metrics, ambiguous liability across hardware and software stakeholders, performance drift in adaptive algorithms, algorithmic bias, data governance concerns, and insufficient cybersecurity standards for intraoperative systems. To address these gaps, we propose a three-tier risk-stratified classification framework aligned with existing FDA pathways, guidance on predetermined change control plans for adaptive technologies, recommendations for performance metrics that balance technical and clinical evaluation, established evaluation frameworks such as IDEAL and stage-specific reporting guidelines to structure development and assessment, a defined role for professional societies and collaborative communities in shaping clinically relevant standards, and evidence requirements reflecting the procedural context of these tools. Regulation of digital surgery must balance innovation with safety, recognizing that both excessive and insufficient oversight can harm patients. Traditional metrics and trial designs are insufficient, as evaluation must be anchored in clinically meaningful outcomes, ongoing surveillance, and real-world validation. The framework presented provides a foundation for achieving this balance through risk-proportionate, evidence-based regulatory approaches.
Assembly of the gut microbiota in infancy is an important health determinant, yet the viral component, the virome, remains poorly described. Here, we conduct a meta-analysis of 12 infant cohorts across 8 countries to model gut virome development over the first three years of life. Our results revealed distinct diversity patterns, where viral richness increased significantly over the first eight months of life alongside a loss of community evenness. We define virome developmental velocity, the rate of change between sequential samples, which significantly decreased over time. This was mirrored by community-wide convergence, as infant viromes became more similar with age. Functionally, the transition to a stable state involved a significant decrease in extracellular temperate phages and shifts in phage-encoded auxiliary metabolic genes, which can modulate host metabolism. Our work provides a baseline characterization of gut virome development, marked by a conserved successional trajectory, providing a framework to identify disease-associated perturbations.