Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects.

The fitness effects of new mutations determine key properties of evolutionary processes. Beneficial mutations drive evolution, yet selection is also shaped by the frequency of small-effect deleterious mutations, whose combined effect can burden otherwise adaptive lineages and alter evolutionary trajectories and outcomes in clonally evolving organisms such as viruses, microbes, and tumors. The small effect sizes of these important mutations have made accurate measurements of their rates difficult. In microbes, assessing the effect of mutations on growth can be especially instructive, as this complex phenotype is closely linked to fitness in clonally evolving organisms. Here, we perform high-throughput time-lapse microscopy on cells from mutation-accumulation strains to precisely infer the distribution of mutational effects on growth rate in the budding yeast, Saccharomyces cerevisiae. We show that mutational effects on growth rate are overwhelmingly negative, highly skewed towards very small effect sizes, and frequent enough to suggest that deleterious hitchhikers may impose a significant burden on evolving lineages. By using lines that accumulated mutations in either wild-type or slippage repair-defective backgrounds, we further disentangle the effects of 2 common types of mutations, single-nucleotide substitutions and simple sequence repeat indels, and show that they have distinct effects on yeast growth rate. Although the average effect of a simple sequence repeat mutation is very small (approximately 0.3%), many do alter growth rate, implying that this class of frequent mutations has an important evolutionary impact.

Designing a Workplace-Based Learning Environment for Learning Health Promotion: A Design-Based Research.

Introduction: The healthcare landscape has a growing emphasis on health promotion (HP), which makes HP important in the training of future physicians. This study employed design-based research to develop a clerkship focused on HP and to outline design principles for shaping workplace learning environments to promote HP learning. Methods: We evaluated a nursing-home clerkship designed at Radboud University Medical Center in the Netherlands, and refined it over three rounds. Data collection involved individual and group interviews with students and supervisors, as well as observations during clerkship-related meetings and activities. These interactions also facilitated the exchange of perspectives between participants and generation of new design ideas, fostering co-creation of the clerkship design. Data were analyzed through iterative thematic inquiry to inform new design choices and develop design principles. Results: Evolved clerkship designs included an app for capturing practice experiences to discuss in relation to students' professional roles, loosening the strict assessment structure, and collaborative creation of a practice assignment about 'Positive Health'. We constructed four design principles, including: to question and discuss students' professional identity, provide concrete and meaningful assignments, aim for a peer-learner role for supervisors, and foster co-creation of the workplace learning environment. Discussion: Our design principles support the design of workplace-based learning for HP, a subject that is novel within healthcare practice. We find that co-creation of workplace-based learning, which requires embracing uncertainty, is pivotal in this context, for students, practitioners, and educational institutions.

Extensive folding variability between homologous chromosomes in mammalian cells.

Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.

Popeye domain containing proteins modulate the voltage-gated cardiac sodium channel Nav1.5.

Popeye domain containing (POPDC) proteins are predominantly expressed in the heart and skeletal muscle, modulating the K2P potassium channel TREK-1 in a cAMP-dependent manner. POPDC1 and POPDC2 variants cause cardiac conduction disorders with or without muscular dystrophy. Searching for POPDC2-modulated ion channels using a functional co-expression screen in Xenopus oocytes, we found POPDC proteins to modulate the cardiac sodium channel Nav1.5. POPDC proteins downregulate Nav1.5 currents in a cAMP-dependent manner by reducing the surface expression of the channel. POPDC2 and Nav1.5 are both expressed in different regions of the murine heart and consistently POPDC2 co-immunoprecipitates with Nav1.5 from native cardiac tissue. Strikingly, the knock-down of popdc2 in embryonic zebrafish caused an increased upstroke velocity and overshoot of cardiac action potentials. The POPDC modulation of Nav1.5 provides a new mechanism to regulate cardiac sodium channel densities under sympathetic stimulation, which is likely to have a functional impact on cardiac physiology and inherited arrhythmias.

Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs.

Glioblastoma multiforme (GBM) encompasses brain malignancies marked by phenotypic and transcriptional heterogeneity thought to render these tumors aggressive, resistant to therapy, and inevitably recurrent. However, little is known about how the spatial organization of GBM genomes underlies this heterogeneity and its effects. Here, we compile a cohort of 28 patient-derived glioblastoma stem cell-like lines (GSCs) known to reflect the properties of their tumor-of-origin; six of these were primary-relapse tumor pairs from the same patient. We generate and analyze 5 kbp-resolution chromosome conformation capture (Hi-C) data from all GSCs to systematically map thousands of standalone and complex structural variants (SVs) and the multitude of neoloops arising as a result. By combining Hi-C, histone modification, and gene expression data with chromatin folding simulations, we explain how the pervasive, uneven, and idiosyncratic occurrence of neoloops sustains tumor-specific transcriptional programs via the formation of new enhancer-promoter contacts. We also show how even moderately recurrent neoloops can relate to patient-specific vulnerabilities. Together, our data provide a resource for dissecting GBM biology and heterogeneity, as well as for informing therapeutic approaches.

Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk.

BACKGROUND: Lung cancer is the leading cause of cancer-related death in the world. In contrast to many other cancers, a direct connection to modifiable lifestyle risk in the form of tobacco smoke has long been established. More than 50% of all smoking-related lung cancers occur in former smokers, 40% of which occur more than 15 years after smoking cessation. Despite extensive research, the molecular processes for persistent lung cancer risk remain unclear. We thus set out to examine whether risk stratification in the clinic and in the general population can be improved upon by the addition of genetic data and to explore the mechanisms of the persisting risk in former smokers. METHODS: We analysed transcriptomic data from accessible airway tissues of 487 subjects, including healthy volunteers and clinic patients of different smoking statuses. We developed a computational model to assess smoking-associated gene expression changes and their reversibility after smoking is stopped, comparing healthy subjects to clinic patients with and without lung cancer. RESULTS: We find persistent smoking-associated immune alterations to be a hallmark of the clinic patients. Integrating previous GWAS data using a transcriptional network approach, we demonstrate that the same immune- and interferon-related pathways are strongly enriched for genes linked to known genetic risk factors, demonstrating a causal relationship between immune alteration and lung cancer risk. Finally, we used accessible airway transcriptomic data to derive a non-invasive lung cancer risk classifier. CONCLUSIONS: Our results provide initial evidence for germline-mediated personalized smoke injury response and risk in the general population, with potential implications for managing long-term lung cancer incidence and mortality.

Multimodal in-vehicle lighting system increases daytime light exposure and alertness in truck drivers under Arctic winter conditions.

Drowsiness while driving negatively impacts road safety, especially in truck drivers. The present study investigated the feasibility and alerting effects of a daylight-supplementing in-truck lighting system (DS) providing short-wavelength enriched light before, during, and after driving. In a within-participants design, eight truck drivers drove a fully-loaded truck under wintry Scandinavian conditions (low daylight levels) with a DS or placebo system for five days. Subjective and objective measures of alertness were recorded several times daily, and evening melatonin levels were recorded three times per study condition. DS significantly increased daytime light exposure without causing negative side effects while driving. In addition, no negative carry-over effects were observed on evening melatonin and sleepiness levels or on nighttime sleep quality. Moreover, objective alertness (i.e., psychomotor vigilance) before and after driving was significantly improved by bright light exposure. This effect was accompanied by improved subjective alertness in the morning. This field study demonstrated that DS was able to increase daytime light exposure in low-daylight conditions and to improve alertness in truck drivers before and after driving (e.g., during driving rest periods). Further studies are warranted to investigate the effects of daylight-supplementing in-cabin lighting on driving performance and road safety measures.

Phase 1, first-in-human study of TYRP1-TCB (RO7293583), a novel TYRP1-targeting CD3 T-cell engager, in metastatic melanoma: active drug monitoring to assess the impact of immune response on drug exposure.

Introduction: Although checkpoint inhibitors (CPIs) have improved outcomes for patients with metastatic melanoma, those progressing on CPIs have limited therapeutic options. To address this unmet need and overcome CPI resistance mechanisms, novel immunotherapies, such as T-cell engaging agents, are being developed. The use of these agents has sometimes been limited by the immune response mounted against them in the form of anti-drug antibodies (ADAs), which is challenging to predict preclinically and can lead to neutralization of the drug and loss of efficacy. Methods: TYRP1-TCB (RO7293583; RG6232) is a T-cell engaging bispecific (TCB) antibody that targets tyrosinase-related protein 1 (TYRP1), which is expressed in many melanomas, thereby directing T cells to kill TYRP1-expressing tumor cells. Preclinical studies show TYRP1-TCB to have potent anti-tumor activity. This first-in-human (FIH) phase 1 dose-escalation study characterized the safety, tolerability, maximum tolerated dose/optimal biological dose, and pharmacokinetics (PK) of TYRP1-TCB in patients with metastatic melanoma (NCT04551352). Results: Twenty participants with cutaneous, uveal, or mucosal TYRP1-positive melanoma received TYRP1-TCB in escalating doses (0.045 to 0.4 mg). All participants experienced ≥1 treatment-related adverse event (TRAE); two participants experienced grade 3 TRAEs. The most common toxicities were grade 1-2 cytokine release syndrome (CRS) and rash. Fractionated dosing mitigated CRS and was associated with lower levels of interleukin-6 and tumor necrosis factor-alpha. Measurement of active drug (dual TYPR1- and CD3-binding) PK rapidly identified loss of active drug exposure in all participants treated with 0.4 mg in a flat dosing schedule for ≥3 cycles. Loss of exposure was associated with development of ADAs towards both the TYRP1 and CD3 domains. A total drug PK assay, measuring free and ADA-bound forms, demonstrated that TYRP1-TCB-ADA immune complexes were present in participant samples, but showed no drug activity in vitro. Discussion: This study provides important insights into how the use of active drug PK assays, coupled with mechanistic follow-up, can inform and enable ongoing benefit/risk assessment for individuals participating in FIH dose-escalation trials. Translational studies that lead to a better understanding of the underlying biology of cognate T- and B-cell interactions, ultimately resulting in ADA development to novel biotherapeutics, are needed.

Biodistribution of Drug/ADA Complexes: The Impact of Immune Complex Formation on Antibody Distribution.

The clinical use of therapeutic monoclonal antibodies (mAbs) for the treatment of cancer, inflammation, and other indications has been successfully established. A critical aspect of drug-antibody pharmacokinetics is immunogenicity, which triggers an immune response via an anti-drug antibody (ADA) and forms drug/ADA immune complexes (ICs). As a consequence, there may be a reduced efficacy upon neutralization by ADA or an accelerated drug clearance. It is therefore important to understand immunogenicity in biological therapies. A drug-like immunoglobulin G (IgG) was radiolabeled with tritium, and ICs were formed using polyclonal ADA, directed against the complementary-determining region of the drug-IgG, to investigate in vivo biodistribution in rodents. It was demonstrated that 65% of the radioactive IC dose was excreted within the first 24 h, compared with only 6% in the control group who received non-complexed 3H-drug. Autoradiographic imaging at the early time point indicated a deposition of immune complexes in the liver, lung, and spleen indicated by an increased radioactivity signal. A biodistribution study confirmed the results and revealed further insights regarding excretion and plasma profiles. It is assumed that the immune complexes are readily taken up by the reticuloendothelial system. The ICs are degraded proteolytically, and the released radioactively labeled amino acids are redistributed throughout the body. These are mainly renally excreted as indicated by urine measurements or incorporated into protein synthesis. These biodistribution studies using tritium-labeled immune complexes described in this article underline the importance of understanding the immunogenicity induced by therapeutic proteins and the resulting influence on biological behavior.

Exploring workplace-based learning in distributed healthcare settings: a qualitative study.

BACKGROUND: Distributed healthcare settings such as district hospitals, primary care, and public health facilities are becoming the real-life settings for workplace-based learning required to educate the future healthcare workforce. Therefore, a major focus should be on designing and developing workplace-based learning in these learning environments. Healthcare professionals and educational policymakers play a significant role in these settings as role models in workplace-based learning, and as leaders in integrating learning into their work environments. It is relevant to explore their beliefs, attitudes, and behaviors towards workplace-based learning in their own settings, in order to provide context-relevant recommendations that can assist in shaping workplace-based learning environments. METHODS: We used individual interviews to understand professionals' experiences with workplace-based learning in distributed healthcare settings. We - three clinicians, an educationalist, and a philosopher - thematically analyzed transcripts of 13 interviews with healthcare professionals and educational policymakers from different healthcare settings who were involved in the clinical phase of undergraduate medical education. RESULTS: Clustering and categorizing of the data led to the construction of five overarching themes: Identification with and attitude towards medical education, Sense of ownership, Perceived time and space, Mutual preconceptions and relations, and Curriculum for a changing profession. CONCLUSIONS: These themes accentuate aspects relevant to the development of workplace-based learning in distributed healthcare settings on the individual, team, or organizational level. We highlight the significance of individual professionals in the development of workplace-based learning and emphasize the need for recognition and support for those occupying the 'broker' role at the intersection of education and practice. For future research and educational practice, we recommend prioritizing initiatives that build on good-practices in workplace-based learning and involve dedicated individuals in distributed healthcare settings.

Continuous Renal Replacement Therapy During Long-term Normothermic Machine Perfusion of Human Donor Livers for up to 7 D.

Background: Normothermic machine perfusion (NMP) is used to preserve and test donor livers before transplantation. During NMP, the liver is metabolically active and produces waste products, which are released into the perfusate. In this study, we describe our simplified and inexpensive setup that integrates continuous renal replacement therapy (CRRT) with NMP for up to 7 d. We also investigated if the ultrafiltrate could be used for monitoring perfusate concentrations of small molecules such as glucose and lactate. Methods: Perfusate composition (urea, osmolarity, sodium, potassium, chloride, calcium, magnesium, phosphate, glucose, and lactate) was analyzed from 56 human NMP procedures without CRRT. Next, in 6 discarded human donor livers, CRRT was performed during NMP by integrating a small dialysis filter (0.2 m2) into the circuit to achieve continuous ultrafiltration combined with continuous fluid substitution for up to 7 d. Results: Within a few hours of NMP without CRRT, a linear increase in osmolarity and concentrations of urea and phosphate to supraphysiological levels was observed. After integration of CRRT into the NMP circuit, the composition of the perfusate was corrected to physiological values within 12 h, and this homeostasis was maintained during NMP for up to 7 d. Glucose and lactate levels, as measured in the CRRT ultrafiltrate, were strongly correlated with perfusate levels (r = 0.997, P < 0.001 and r = 0.999, P < 0.001, respectively). Conclusions: The integration of CRRT into the NMP system corrected the composition of the perfusate to near-physiological values, which could be maintained for up to 7 d. The ultrafiltrate can serve as an alternative to the perfusate to monitor concentrations of small molecules without potentially compromising sterility.

Entirely noninvasive outcome prediction in central nervous system lymphomas using circulating tumor DNA.

ABSTRACT: State-of-the-art response assessment of central nervous system lymphoma (CNSL) by magnetic resonance imaging is challenging and an insufficient predictor of treatment outcomes. Accordingly, the development of novel risk stratification strategies in CNSL is a high unmet medical need. We applied ultrasensitive circulating tumor DNA (ctDNA) sequencing to 146 plasma and cerebrospinal fluid (CSF) samples from 67 patients, aiming to develop an entirely noninvasive dynamic risk model considering clinical and molecular features of CNSL. Our ultrasensitive method allowed for the detection of CNSL-derived mutations in plasma ctDNA with high concordance to CSF and tumor tissue. Undetectable plasma ctDNA at baseline was associated with favorable outcomes. We tracked tumor-specific mutations in plasma-derived ctDNA over time and developed a novel CNSL biomarker based on this information: peripheral residual disease (PRD). Persistence of PRD after treatment was highly predictive of relapse. Integrating established baseline clinical risk factors with assessment of radiographic response and PRD during treatment resulted in the development and independent validation of a novel tool for risk stratification: molecular prognostic index for CNSL (MOP-C). MOP-C proved to be highly predictive of outcomes in patients with CNSL (failure-free survival hazard ratio per risk group of 6.60; 95% confidence interval, 3.12-13.97; P < .0001) and is publicly available at www.mop-c.com. Our results highlight the role of ctDNA sequencing in CNSL. MOP-C has the potential to improve the current standard of clinical risk stratification and radiographic response assessment in patients with CNSL, ultimately paving the way toward individualized treatment.

Intraoperative transit-time flow measurement of caval veins before and after bidirectional cavopulmonary anastomosis.

BACKGROUND: Haemodynamic changes in caval venous flow distribution occurring during bidirectional cavopulmonary anastomosis operation are still largely unknown. METHODS: Transit time flow measurements were performed in 15 cavopulmonary anastomosis operations. Superior and inferior caval vein flows were measured before and after the cavopulmonary anastomosis. Ratio of superior caval vein to overall caval veins flow was calculated. RESULTS: Mean superior caval vein flow ratio before cavopulmonary anastomosis was higher than previously reported for healthy children. Superior caval vein flow ratio decreased in 14/15 patients after cavopulmonary anastomosis: mean 0.63 ± 0.12 before versus 0.43 ± 0.14 after. No linear correlation between intraoperative superior caval vein pressure and superior caval vein flow after cavopulmonary anastomosis was found. Neither Nakata index nor pulmonary vascular resistance measured at preoperative cardiac catheterisation correlated with intraoperative flows. None of patients died or required a take down. CONCLUSIONS: The higher mean superior caval vein flow ratio before cavopulmonary anastomosis compared to healthy children suggests flow redistribution in univentricular physiology to protect brain and neurodevelopment. The decrease of superior caval vein flow ratio after cavopulmonary anastomosis may reflect the flow redistribution related to trans-pulmonary gradient. The lack of correlation between superior caval vein pressure and superior caval vein flow could be explained by limited sample size and multifactorial determinants of caval veins flow, although pressure remain essential. Larger sample of measurements are needed to find flow range potentially predictive for clinical failure. To authors' knowledge, this is the first intraoperative flow measurement of both caval veins during cavopulmonary operations.

Distribution of Antibiotic Resistance in a Mixed-Use Watershed and the Impact of Wastewater Treatment Plants on Antibiotic Resistance in Surface Water.

The aquatic environment has been recognized as a source of antibiotic resistance (AR) that factors into the One Health approach to combat AR. To provide much needed data on AR in the environment, a comprehensive survey of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic residues was conducted in a mixed-use watershed and wastewater treatment plants (WWTPs) within the watershed to evaluate these contaminants in surface water. A culture-based approach was used to determine prevalence and diversity of ARB in surface water. Low levels of AR Salmonella (9.6%) and Escherichia coli (6.5%) were detected, while all Enterococcus were resistant to at least one tested antibiotic. Fewer than 20% of extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae (17.3%) and carbapenem-resistant Enterobacteriaceae (CRE) (7.7%) were recovered. Six ARGs were detected using qPCR, primarily the erythromycin-resistance gene, ermB. Of the 26 antibiotics measured, almost all water samples (98.7%) had detectable levels of antibiotics. Analysis of wastewater samples from three WWTPs showed that WWTPs did not completely remove AR contaminants. ARGs and antibiotics were detected in all the WWTP effluent discharges, indicating that WWTPs are the source of AR contaminants in receiving water. However, no significant difference in ARGs and antibiotics between the upstream and downstream water suggests that there are other sources of AR contamination. The widespread occurrence and abundance of medically important antibiotics, bacteria resistant to antibiotics used for human and veterinary purposes, and the genes associated with resistance to these antibiotics, may potentially pose risks to the local populations exposed to these water sources.

CRISPR-Cas12a-integrated transgenes in genomic safe harbors retain high expression in human hematopoietic iPSC-derived lineages and primary cells.

Discovery of genomic safe harbor sites (SHSs) is fundamental for multiple transgene integrations, such as reporter genes, chimeric antigen receptors (CARs), and safety switches, which are required for safe cell products for regenerative cell therapies and immunotherapies. Here we identified and characterized potential SHS in human cells. Using the CRISPR-MAD7 system, we integrated transgenes at these sites in induced pluripotent stem cells (iPSCs), primary T and natural killer (NK) cells, and Jurkat cell line, and demonstrated efficient and stable expression at these loci. Subsequently, we validated the differentiation potential of engineered iPSC toward CD34+ hematopoietic stem and progenitor cells (HSPCs), lymphoid progenitor cells (LPCs), and NK cells and showed that transgene expression was perpetuated in these lineages. Finally, we demonstrated that engineered iPSC-derived NK cells retained expression of a non-virally integrated anti-CD19 CAR, suggesting that several of the investigated SHSs can be used to engineer cells for adoptive immunotherapies.

Workplace-based learning about health promotion in individual patient care: a scoping review.

OBJECTIVE: To outline current knowledge regarding workplace-based learning about health promotion in individual patient care. DESIGN: Scoping review. DATA SOURCES: PubMed, ERIC, CINAHL and Web of Science from January 2000 to August 2023. ELIGIBILITY CRITERIA: We included articles about learning (activities) for healthcare professionals (in training), about health promotion in individual patient care and in the context of workplace-based learning. DATA EXTRACTION AND SYNTHESIS: The studies were evaluated using a charting template and were analysed thematically using a template based on Designable Elements of Learning Environments model. RESULTS: From 7159 studies, we included 31 that described evaluations of workplace-based learning about health promotion, around a variety of health promotion topics, for different health professions. In the articles, health promotion was operationalised as knowledge, skills or attitudes related to specific lifestyle factors or more broadly, with concepts such as health literacy, advocacy and social determinants of health. We assembled an overview of spatial and instrumental, social, epistemic and temporal elements of learning environments in which health promotion is learnt. CONCLUSIONS: The studies included in our analysis varied greatly in their approach to health promotion topics and the evaluation of learning outcomes. Our findings suggest the importance of providing opportunities for health profession learners to engage in authentic practice situations and address potential challenges they may experience translating related theory into practice. Additionally, our results highlight the need for conscious and articulated integration of health promotion in curricula and assessment structures. We recommend the exploration of opportunities for health profession students, professionals and patients to learn about health promotion together. Additionally, we see potential in using participatory research methods to study future health promotion learning. STUDY REGISTRATION: Open Science Framework, https://doi.org/10.17605/OSF.IO/6QPTV.

Mutational topography reflects clinical neuroblastoma heterogeneity.

Neuroblastoma is a pediatric solid tumor characterized by strong clinical heterogeneity. Although clinical risk-defining genomic alterations exist in neuroblastomas, the mutational processes involved in their generation remain largely unclear. By examining the topography and mutational signatures derived from all variant classes, we identified co-occurring mutational footprints, which we termed mutational scenarios. We demonstrate that clinical neuroblastoma heterogeneity is associated with differences in the mutational processes driving these scenarios, linking risk-defining pathognomonic variants to distinct molecular processes. Whereas high-risk MYCN-amplified neuroblastomas were characterized by signs of replication slippage and stress, homologous recombination-associated signatures defined high-risk non-MYCN-amplified patients. Non-high-risk neuroblastomas were marked by footprints of chromosome mis-segregation and TOP1 mutational activity. Furthermore, analysis of subclonal mutations uncovered differential activity of these processes through neuroblastoma evolution. Thus, clinical heterogeneity of neuroblastoma patients can be linked to differences in the mutational processes that are active in their tumors.

Incidence rate of injury and injury sites in European and Swiss karate competitions: a prospective epidemiological study of 2404 fights.

Objectives: To compare the rates and injury sites among competitors in European and Swiss karate tournaments and to identify differences in these incidence rates by sex and age. Methods: This prospective cohort study collected data from two European and four national tournaments in Switzerland between 2011 and 2019. The on-site medical staff completed an anonymised report sheet with demographic data and injury characteristics in all injuries requiring medical treatment. The incidence rates per 1000 exposed athletes (AoE) and 1000 min of exposition (MoE) were analysed. Furthermore, the relative risk of injury related to sex and age was calculated and compared. Results: In total, 228 injuries were observed in 2404 fights, for an incidence rate of 47.4 per 1000 AoE (95% CI 41.5 to 54.0) or 22.5 injuries per 1000 MoE (95% CI 19.7 to 25.6), respectively. The oldest age group (senior) of both sexes had a 3.6-fold (95% CI 2.7 to 4.8) significantly higher relative risk of injury than younger participants. Furthermore, there was a 2.9-fold (95% CI 1.6 to 5.6) statistically higher risk of injury for males in the senior age group compared with senior females. The most injured body part was the head, followed by the lower extremity, trunk and upper extremity. Conclusion: Senior athletes, especially senior males, had significantly more injuries compared with younger and female senior competitors. Medical staff should be aware of the increased propensity for injury among this age and sex group to facilitate injury prevention and intervention.

Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.

Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient's disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase's ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.