Open Research Europe

Computational bioacoustics has seen significant advances in recent decades. However, the rate of insights from automated analysis of bioacoustic audio lags behind our rate of collecting the data - due to key capacity constraints in data annotation and bioacoustic algorithm development. Gaps in analysis methodology persist: not because they are intractable, but because of resource limitations in the bioacoustics community. To bridge these gaps, we advocate the open science method of data challenges, structured as public contests. We conducted a bioacoustics data challenge named BioDCASE, within the format of an existing event (DCASE). In this work we report on the procedures needed to select and then conduct useful bioacoustics data challenges. We consider aspects of task design such as dataset curation, annotation, and evaluation metrics. We report the three tasks included in BioDCASE 2025 and the resulting progress made. Based on this we make recommendations for open community initiatives in computational bioacoustics.

The use of domestic pigs in clinical training and biomedical research is expanding rapidly, increasing the need for reliable, noninvasive indicators of health and welfare. Vocal analysis offers a non-invasive promising tool, yet the acoustic repertoire of adult domestic pigs remains poorly defined. However, the vocalization repertoire of adult domestic pigs has yet to be characterized. This study characterizes the vocal repertoire of adult pigs housed in a biomedical research laboratory. Twelve mixed-breed pigs (2-3 months old; 5 males, 7 females) were recorded during routine husbandry and experimental procedures. Vocal classification was conducted using perceptual and objective clustering techniques. First, aural- visual (AV) inspection of spectrograms was used to construct a hierarchical repertoire. Second, a two-step cluster analysis based on six acoustic parameters (5% frequency, first quartile frequency, center frequency, 90% bandwidth, interquartile range bandwidth, and 90% duration) provided an objective classification. Agreement between methods was evaluated using Cramers V. A total of 1,136 vocalizations from 69 recordings were analyzed. AV classification revealed five major vocal classes-- grunt, squeal, complex, scream, and bark--subdividing into 16 distinct call types. Standardized definitions integrating descriptive and quantitative criteria are provided. The two-step cluster analysis identified two clusters as the optimal statistical solution, with moderate agreement between methods (Cramers V = 0.67, p < 0.0001). Most AV-defined call types aligned with previously reported repertoires, although whines, yelps, and stable screams were unique to this study. While two-cluster solutions are commonly reported, our findings indicate that richer acoustic structure exists and that high gradation among pig calls may limit the resolution of statistical clustering. These results establish a detailed acoustic framework for adult pig vocalizations and provide essential groundwork for developing predictive models to enhance welfare assessment and support comparative research in laboratory-housed pigs.

Introduction. Climate change is increasing the frequency and intensity of heatwaves, creating critical challenges for social care settings where both staff and residents face heightened heat related vulnerability. This study examined the impact of heatwaves on UK care homes using a national survey of staff experiences, challenges, and adaptation strategies. Methods. Care home staff (N = 225) in managerial (N = 88) and caregiving roles (N = 137) completed an online survey investigating staff perceptions of heatwaves impact on thermal comfort, health and vulnerability of themselves and residents, alongside current heat resilience strategies and the barriers to their implementation. Results. Two thirds (66%) of the surveyed staff complained of being too hot three or more times per day resulting in a perceived impact on their ability to perform tasks (90%) and on residents' comfort and health (92%). Staff demonstrated strong awareness of older adults' heightened heat vulnerability (95%) and signs of heat illness (87%). Thematic analysis identified five key barriers to providing effective cooling: funding limitations, inadequate equipment, building constraints, staffing pressures, and individual resident needs; and four priority improvement areas: increased access to cooling equipment, improved temperature control, strengthened strategy and policy, and support for staff needs. Conclusions. Heatwaves place considerable strain on care homes, challenging staff capacity to maintain comfortable thermal conditions, despite good knowledge of heat risks. Financial, infrastructural, and staffing constraints limit effective heat resilience practices. Evaluating and implementing affordable, accessible, and context appropriate cooling strategies will be essential to protect both residents and staff as extreme heat events become more frequent.

Military aviation training noise remains understudied despite its widespread impacts across urban, rural, and wilderness areas. The predominance of low-frequency noise and repetitive training can create pervasive noise pollution, yet past research often fails to capture the full range of health and quality-of-life effects. This study analyzed two complaint datasets related to Whidbey Island Naval Air Station noise: U.S. Navy records (2017-2020) and Quiet Skies Over San Juan County data (2021-2023). We analyzed and mapped sentiment intensity from noise complaints relative to modeled annual noise exposure, developed a typology to classify impacts, and modeled the environmental and operational factors influencing complaints. Findings revealed widespread negative sentiment and anger, often beyond the bounds of estimated noise contours, suggesting that annual cumulative noise models inadequately estimate community impacts. Complaints consistently highlighted sleep disturbance, hearing and health concerns, and compromised home environments due to shaking, vibration, and disruption of daily life. Residents also reported significant social, recreational, and work disruptions, along with feelings of fear, helplessness, and concern for children's well-being. The number of complaints were strongly associated with training schedules, with late-night sessions being the strongest predictor. A delayed response pattern suggests residents reach a frustration threshold before filing complaints. Overall, our findings demonstrate persistent negative sentiment and diverse impacts from military aviation noise. Results highlight the need for improved noise metrics, modeling and operational adjustments to mitigate the most disruptive effects.

In mammals, loud, high-pitched, and harsh-sounding calls typically accompany heightened emotional arousal, particularly during distress such as separation. However, whether subtle arousal reductions can be detected through acoustic analysis within a single negative context remains unclear. We investigated whether source-related acoustic parameters of puppy whines reflect arousal modulations induced by calming interventions during maternal separation. Thirty-five eight-week-old Beagle puppies were recorded under four conditions combining synthetic appeasing pheromone and a pressure harness. Vocal behavior, activity, whine duration, and intensity, did not significantly differ across treatments, suggesting interventions did not suppress separation-related vocal responses. Nevertheless, calming products selectively altered acoustic parameters known to index arousal in dog vocalizations. Puppies receiving combined treatments produced whines with lower fundamental frequency (fo) and reduced fo variability, while pheromone exposure increased call tonality, reflected by reduced jitter and shimmer and elevated harmonics-to-noise ratios. Spectral entropy remained unchanged, possibly because the proportion of whines containing nonlinear phenomena did not vary across conditions. Reductions in fo, fo variability, and acoustic roughness are consistent with established correlates of lower arousal in mammals, suggesting source-related vocal parameters sensitively capture subtle arousal shifts even when overt vocal behavior remains stable, supporting their use as bioacoustic indicators for evaluating welfare interventions.

Sickle cell disease (SCD) is the most common inherited hemoglobinopathy worldwide. Improving the quality of life of people with SCD requires prenatal and neonatal screening. Our primary objective was to demonstrate that prenatal diagnosis of SCD is possible even in situations of poverty. Secondarily, we described the socioeconomic profile of couples seeking molecular diagnosis of SCD in Kinshasa, Democratic Republic of Congo. Methods This was a cross-sectional study conducted in Kinshasa between January 2020 and December 2025. During this study period, 107 couples underwent prenatal diagnosis. Prenatal diagnosis was performed using amniocentesis with FTA Elute technology. This diagnosis was confirmed at birth using cord blood DNA extracted via the conventional salting-out technique. Results The mean age of the pregnant women was 28 {+/-} 4 years. Eighty-one couples (75.7%) were Christian, nine couples (8.4%) were Muslim, and seventeen couples (15.8%) were animist. Eighty-two couples (76.6%) were known heterozygous AS couples, eleven (10.2%) were heterozygous couples, and fourteen (13.0%) were couples composed of one homozygous SS and one heterozygous AS partner. All pregnancies were singleton. Socioeconomic status was upper middle class (39.2%). The AS genotype was found in 79% of the fetuses. One intrauterine fetal death was observed after amniocentesis. In terms of handling, the FTA Elute technology reduces DNA extraction time to 30 minutes. It is easy to use. Results are available in less than 24 hours. Conclusion The FTA Elute technology is a reliable, less expensive, and easy-to-use prenatal screening technique for sickle cell disease. Sample transport and storage conditions are better suited to resource-limited settings.

Background: Hospital canteens provide an effective setting for improving the dietary habits of users. The study evaluates the food choices of users after an educational and environmental intervention, considering nutritional composition and environmental impact, and to compare the results with pre-intervention choices. Methods: A cross-sectional study was conducted in three hospital canteens (C1, C2, C3) in northeastern Italy, during two index weeks in September 2022 (T0) and 2023 (T1). An intervention was introduced between T0 and T1, consisting of posters on healthy eating, descriptive norm messages, and environmental changes regarding fruit and vegetables. Photos of lunch trays were collected, and choices were analyzed for nutritional composition and sustainability. Results: 2,851 trays were analyzed: 1,227 at T0 (798 in C1, 228 in C2 and 201 in C3) and 1,624 at T1 (1,005 in C1, 348 in C2, 271 in C3). In C1 and C3, there was an increase in median energy (+30 kcal; +135 kcal) compared to pre-intervention meals, while in C2 there was a decrease (-118 kcal). Despite a slight improvement in macronutrient composition, at T1 meals in all canteens were still high in lipids (30%E; 39%E; 35%E) and low in carbohydrates (44%E; 39%E; 41%E). The fibre value fell within the recommended range only in C1 and C3. The median carbon (CF) and water (WF) footprints of meals in all canteens remained high: at T1 CF ranged from 966 gCO2eq. to 1,227 gCO2eq. and WF from 1,025 L H2O to 1,207 L H2O. Conclusion: The intervention has led to partial improvements in food choices. To achieve more significant results, it may be necessary to implement a parallel intervention on food offer.

The increasing use of accelerometers as digital health technologies in clinical trials and clinical care is driving the need for data processing to meet medical standards. The aim of this study was to create and test a modular pipeline for the pre-processing of high-resolution accelerometry that assures the quality, transparency and traceability of digital measures from sensor-level data. The objective is for the pipeline to be a foundational layer in the development, implementation and comparison of measures. The study developed the open GENEAcore package to meet the requirements of regulators, verifying the engineering implementation and analytically validating outputs against reference datasets. Early stages included the optimisation of calibration and non-wear detection. Data-driven detection of behavioural transitions was then validated to give direct bout outputs without the need to identify rules for epoch aggregation and interruptions. The utility for measure development was shown by comparing two algorithms for the characterisation of activity intensity in both the epoch and bout paradigms. Non-wear was detected with a balanced accuracy of 92.3% and the commonly used 13mg acceleration standard deviation threshold was empirically validated for the first time. The detection of transitions proved reliable with 99% detected, on average, within 2 seconds of their occurrence to give a mean expected event duration of 68.6s from a log-normal distribution. The different activity intensity algorithms were more than 99% concordant during movement but their outputs diverged in low movement conditions. Importantly, variable duration bouts created 31% higher daily activity durations compared to 1-second epochs. This evaluation of pre-processing steps has confirmed the attention to detail required to create robust and reproducible results for later clinical validation where small changes in an algorithm or its implementation may have clinically meaningful consequences.

Background: Digital phenotyping using wearable devices and ecological momentary assessment (EMA) enables continuous, real-world monitoring of physiological and emotional states, but identifying high-risk stress states in real time remains challenging. We examined day-level associations between emotional distress and heart rate variability (HRV), and assessed whether daily physical activity modifies this relationship using longitudinal wearable and EMA data. Methods: The Smart Momentary Interactive Longitudinal Evaluation Study (SMILES) was a prospective cohort study conducted among STEM graduate students in the U.S. in 2025. Participants wore an Oura Ring Generation 3 continuously for five months and completed daily EMA surveys assessing emotional distress. The primary outcome was nightly HRV measured as the root mean square of successive differences and log-transformed for analysis. Quantile regression within a quadratic inference function framework was used to estimate associations at the 25th, 50th, and 75th percentiles of HRV, accounting for within-participant correlation and time-varying covariates. Findings: Thirty-one participants contributed 1,724 person-days of observation. High emotional distress was associated with lower HRV across the HRV distribution, with the strongest association observed at the lower HRV quantile ({beta} = -0.094, 95\% CI: [-0.111, -0.078]). A significant interaction between daily step count and emotional distress was observed across quantiles, such that higher physical activity was associated with higher HRV on high emotional distress days but not on low-to-moderate distress days. Interpretation: Integration of wearable-derived physiological data with EMA enables real-time identification of high-risk stress states in naturalistic settings. The observed buffering effect of physical activity during periods of elevated emotional distress suggests that wearable-guided, personalized just-in-time adaptive interventions, such as physical activity prompts, could be deployed to improve autonomic regulation and mental health.

Plant DNA metabarcoding enables the identification of plant taxa in mixed samples, with the trnL (UAA) intron and its P6 loop mini-barcode region performing as well as or better than other commonly used markers. Reliable metabarcoding requires high-quality reference databases, yet a regularly maintained trnL resource is currently lacking. Consequently, most studies use uncurated sequences downloaded directly from public repositories without essential validation. We address these gaps by providing guidance through a systematic comparison of three database curation tools - OBITools3/ecoPCR, RESCRIPt, and MetaCurator - to generate three trnL reference sequence databases and evaluate their classification performance across commonly sequenced trnL regions (CD, CH, and GH). Reference trnL sequences and taxonomy files were retrieved from public sequence repositories and curated using standardized filtering steps to reduce taxonomic errors, sequence ambiguity, and redundancy. Four simulated query datasets--two base sets and their mutated counterparts--were constructed to assess classification performance of the databases using the Naive Bayesian Classifier implemented in DADA2.- The evaluation showed that performance differed by trnL region: MetaCurator and RESCRIPt yielded higher and similar metrics for trnL CD; OBITools3/ecoPCR and RESCRIPt were comparable for trnL CH; and MetaCurator attained the highest performance for trnL GH region. All reference databases, taxonomy, and evaluation files are available at Zenodo (https://doi.org/10.5281/zenodo.17969450). The complete computational workflow and scripts are available on GitHub (https://github.com/oskuddar/trnL_DB). Although evaluation was focused on plant taxa in the United States, the resulting databases are suitable for use as global trnL reference databases.

The end-of-career stage of the police lifecycle represents a profound shift in identity and psychological stability, yet it remains historically neglected in research. This mixed-methods study investigated perspectives of UK police leavers and those approaching retirement (N = 325) regarding desired improvements to organisational support. Content analysis identified four themes: Holistic support and long-term welfare, Institutional culture and professional worth, Navigating the structural transition, and Individual and systemic perspectives. Findings suggest that the psychological contract between the officer and the organisation is often breached at the exit point, shifting from a relational bond to a transactional disposal. Middle-ranking officers and early leavers report the highest levels of institutional abandonment. To address these gaps, this paper makes recommendations for developing effective transitions. By implementing post-service welfare, and adopting structured resettlement models, police organisations can fulfil their duty of care and mend the psychological contract for those who have served.

BackgroundChronic Kidney Disease of unknown etiology is a growing health concern in low-and middle-income countries. While occupational heat stress is recognized as a potential contributor to kidney dysfunction among agricultural workers, the causal relationship between heat stress, core body temperature (Tc), and kidney function remains unclear. MethodsWe conducted an observational study over two harvest seasons in Guatemala, following 148 male sugarcane workers across six months. Heat stress was measured using heat index (HI) and Tc with ingestible telemetric temperature pills. Particulate matter (PM) exposure was measured using personal breathing zone samplers worn during the work shift. We evaluated changes in kidney function using pre-and post-shift estimated glomerular filtration rate (eGFR). We applied G-computation to estimate causal effects and modeled hypothetical policy interventions reducing HI, Tc, and PM exposure, simulating occupational heat reduction strategies. ResultsThe average daily HI was 37.4 {degrees}C (SD: 2.0) with an average Tc increase of 1.16 {degrees}C (SD: 0.48) per shift. Both HI and Tc were associated with declines in eGFR across the work shift. At an HI of 34 {degrees}C, workers experienced an average eGFR decline of about 5 mL/min/1.73 m{superscript 2}, while at 40 {degrees}C the decline exceeded 16 mL/min/1.73 m{superscript 2}. High HI early in the season and elevated Tc later in the season contributed to kidney decline. A simulated intervention reducing HI exposure by 5% improved eGFR change by 1.46 mL/min/1.73 m{superscript 2}. PM exposure did not have a significant impact on eGFR decline. ConclusionReducing workday heat exposure may mitigate acute kidney function decline. These findings support the development of policy interventions aimed at reducing external heat exposure and internal heat strain to protect kidney health. More research is needed to investigate the potential contribution of other environmental factors, including PM exposure.

BackgroundPhotobiomodulation (PBM) therapy has demonstrated therapeutic potential in promoting cellular repair, modulating inflammation, and enhancing mitochondrial function. Platelet-rich plasma (PRP) is widely used in regenerative medicine due to its concentration of growth factors and cytokines. Very small embryonic-like stem cells (VSELs), a rare population of pluripotent stem cells present in adult tissues, have emerged as a potential contributor to tissue regeneration. While PBM and PRP are used in combination, how VSELs or Multi-lineage stress enduring (MUSE) cells are at play, and the biological mechanisms underlying their synergistic effects remain incompletely characterized. ObjectiveThis exploratory pilot study aimed to evaluate whether application of the MD Biophysics laser to autologous PRP is associated with measurable changes in VSEL-related antibody marker expression, and to identify directional trends to inform future controlled studies. MethodsPRP samples were collected from participants across seven test dates (July 2024 to February 2025), yielding 18 participant-session datasets. Samples were analyzed before (Pre) and after (Post) laser application using flow cytometry conducted at a UCLA Flow Cytometry Laboratory. Four VSEL-associated antibody markers were assessed: CD45-CD34+, CXCR4+, CD133+, and SSEA-4+. Analyses were descriptive and focused on paired differences and directional trends due to the exploratory design and absence of a control group. ResultsThree of four VSEL-associated markers (CXCR4+, CD133+, and SSEA-4+) demonstrated a group-level increase in median paired differences following laser application. Directional increases were observed in 12/18 sessions for CXCR4+, 10/18 for CD133+, and 9/18 for SSEA-4+. CD45-CD34+ showed a near-equal distribution of increases and decreases. Ki-67 positivity indicated the presence of viable, proliferative cells. While no findings reached statistical significance due to limited sample size, consistent directional trends were observed across multiple markers. ConclusionApplication of PBM to autologous PRP was associated with directional increases in multiple VSEL-associated antibody markers, suggesting a potential role for stem cell activation or mobilization in the mechanism of action. Although preliminary and not statistically powered, these findings provide hypothesis-generating evidence supporting further investigation. The observed trends informed iterative protocol refinement and establish a foundation for future controlled, adequately powered studies to evaluate clinical efficacy and underlying biological mechanisms.

Objectives: Accurate classification of menopausal stage is fundamental to midlife health research. Although the Stages of Reproductive Ageing Workshop (STRAW+10) criteria provide gold-standard criteria, their application in research settings is inconsistent. Classification challenges are compounded in individuals without observable menstrual cycles due to surgical or contraceptive-induced amenorrhoea. The Reproductive Ageing in Women (RAW) Questionnaire and accompanying classification Framework was developed and validated to improve consistency and inclusivity when classifying menopausal stage. Study design: A multi-phase study was conducted between May 2022 and July 2025. Phase one involved questionnaire development based on STRAW+10 and the Menopause-Specific Quality of Life Questionnaire. Phase two assessed content validity via expert review (n=3). Phase three evaluated face validity using think-aloud interviews and focus groups (n=14). Phase four validated RAW within a cross-sectional cohort study (n=156), and assessed construct validity (n=30), test-retest reliability (6-21 days; n=128; Kendall's Tau-b and Cohen's kappa), and biological validity using follicle stimulating hormone (FSH). Results: Feedback supported clarity, relevance and usability, with refinements improving inclusivity for surgical and contraceptive-induced amenorrhoea. Construct validity demonstrated consistent application of classification criteria. Questionnaire classification showed 93% concordance with self-identified menopausal status in the construct sample and 87.8% agreement within the cohort sample. Test-retest reliability was excellent ({tau}, p=0.940, p<0.001). Follicle stimulating hormone levels differed across RAW-classified stages (p<0.001), with 96.1% concordance between RAW pre and postmenopausal classifications and FSH thresholds. Conclusions: Prioritising menstrual characteristics while incorporating age and symptom criteria improves methodological consistency and inclusivity in menopausal stage classification. Longitudinal validation is warranted to assess temporal sensitivity across the menopausal transition.

BackgroundTeleworking is associated with lifestyle risk factors, such as insufficient physical activity (PA) and increased sedentary time (ST); however, effective interventions tailored to teleworkers are lacking. We aimed to evaluate the effectiveness of a 12-week multicomponent occupational lifestyle intervention on daily step counts among Japanese teleworkers. MethodsThis 12-week, two-arm, parallel-group, cluster randomised controlled trial conducted across 12 clusters in six Japanese companies involved 310 teleworkers (mean age 43.0 years; 72.6% men) randomized to the intervention (6 clusters, n=156) or a waitlist control group (6 clusters, n=154). The multicomponent occupational lifestyle intervention included individual (online lectures, feedback, and email messages), physical (posters and a pop-up), and organizational (encouraging messages from an executive) strategies. The primary outcome was the change in daily step counts, measured using an accelerometer over 14 consecutive days at baseline and at week 12. Analyses were based on the intention-to-treat approach using a generalised estimating equation model. FindingsThe intervention group showed an adjusted mean change in daily step counts of +219 steps (95% confidence interval [CI] -165 to 604), compared with +188 steps (95% CI -183 to 560) in the control group. The adjusted between-group difference was +55 steps (95% CI -550 to 660; p=0.844). No significant effects on the secondary outcomes (ST, light PA, or moderate-to-vigorous PA) were observed. InterpretationThe multicomponent occupational lifestyle intervention did not significantly increase daily step counts among Japanese teleworkers. Therefore, further studies should be done on tailored interventions for teleworkers. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTeleworking has increased globally, particularly following the coronavirus disease pandemic, and has been associated with reduced physical activity and increased sedentary behaviour, both of which are risk factors for cardiovascular disease. Previous studies have also reported that telework environments may contribute to musculoskeletal and other somatic symptoms. Multicomponent interventions in traditional office settings can effectively increase physical activity and reduce sedentary time. These interventions commonly employ strategies at multiple levels of the social-ecological model, including individual approaches (e.g., lectures or incentives), interpersonal approaches (e.g., team-based activities), environmental modifications (e.g., office rearrangements or sit-stand desks), and organisational support (e.g., leadership encouragement). The applicability of such interventions to teleworking populations remains unclear because teleworkers face distinct challenges such as social isolation, blurred work-life boundaries, and heterogeneous home working environments. These contextual differences highlight the need for interventions specifically tailored to teleworkers. Added value of this studyWe evaluated the effectiveness of a multicomponent occupational lifestyle intervention specifically designed for teleworkers, a population whose work environment differs substantially from traditional office settings. Our findings provide novel evidence that can inform the development of more targeted strategies to promote physical activity in evolving work environments. This study also provides objective measurements of physical activity using accelerometers, enabling detailed evaluation of step counts, sedentary time, and different activity intensities among teleworkers. Additionally, we used daily diaries to distinguish activity patterns across workdays, weekends, teleworking days, and commuting days, providing a nuanced understanding of behavioural patterns in remote work contexts. Implications of all the available evidenceOur findings indicate that low-cost, remotely delivered multicomponent interventions may be insufficient to produce meaningful behavioural change among teleworkers. Similar strategies, including individual, physical, and organisational components, have been effective in traditional workplace interventions; however, their implementation in teleworking environments may not adequately address the specific challenges faced by remote workers. In particular, the lack of strong sociocultural support mechanisms, such as team-based step competitions or workplace champions, may limit engagement and reduce the effectiveness of such programmes. Therefore, further investigation is needed to explore more diverse and targeted intervention strategies, identify the specific needs and behavioural patterns of teleworkers, and apply more precise eligibility criteria to better address heterogeneity within teleworking populations.

The vast diversity of B and T cell receptors generated through the recombination of Variable (V), Diversity (D), and Joining (J) gene segments plays a critical role in adaptive immunity. Profiling immune repertoires at the DNA level provides a robust and stable approach to capture the clonal composition of these receptors. immunoPETE is an assay designed to target recombined human T-cell Receptor Beta (TRB), T-cell Receptor Delta (TRD), and Immunoglobulin Heavy (IGH) chain genes directly from genomic DNA. Simultaneous profiling of B and T cell receptor chains in a single reaction provides internally normalized clone counts and facilitates the study of B-T cell interactions. Full-length amplicon consensus sequences representative of original template DNA molecules are accurately reconstructed using Unique Molecular Identifiers (UMIs). An in-house pipeline compiles VDJ rearrangements from the Complementarity-Determining Region 3 (CDR3) of TRB, TRD and IGH chains into comprehensive readouts at cell-level resolution. In this study, we describe the immunoPETE end-to-end workflow, followed by a comprehensive benchmarking of its performance in adaptive immune profiling. Where applicable, we used both natural and contrived samples and characterized the assays accuracy, linearity, and reproducibility across several metrics: retrieving CDR3 sequences, determining B and T cell ratios, total cell count, yield, fraction of functional rearrangements, clonal diversity, composition of dominant clones, pairwise similarity, and V/J gene usage frequencies. Furthermore, we assessed its quantitative limits concerning the total number of lymphocytes and the detection of rare clones. As an example of its applications, we show that adding immune biomarkers extracted from immunoPETE data to clinical factors improves prediction of progression-free survival in a cohort of non-muscle invasive bladder cancer (NMIBC) patients. Finally, we discuss the broad applications of immunoPETE in the study of aging, cancers, infections, and autoimmune disorders with reference to select published studies.

In the search for universals shaping acoustic communication across species, we increasingly look for patterns known from human languages and music in non-human animals. These parallels are often explored separately and with limited ecological context. Here, we take a deep dive into the temporal structure of a complex call used by the little auk (Alle alle), a pelagic seabird with elaborate vocal behaviour and socially complex colonial life. Based on syllable durations, intervals and silences, we examine its conformance to linguistic laws, rhythmic structure and information content. This reveals intricate problems of temporal organisation: while the calls conform not only to linguistic laws of brevity but also to the initial and final lengthening known from human prosody, these effects interact with the internal structure of the call and information carried within it. To our knowledge, this is the first time that conformance to multiple linguistic laws, exceeding simple vocal efficiency, has been described for a non-human, non-vocal learning animal. The calls rhythmic structure shows a progressive rallentando -- a systematic slowing driven by changes in syllable and silence durations and the intervals between syllable onsets. The exact patterns of this rallentando are indicative of the callers sex and individually specific. These results reveal how seabird communication is shaped not only by efficiency universals, but also the specific pressures of colonial life. Our work highlights the temporal structure as an important axis of communication evolution, but also serves as a reminder to consider the species ecological reality and the function, not only presence, of temporal organisation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/713940v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@13de3a8org.highwire.dtl.DTLVardef@2d64adorg.highwire.dtl.DTLVardef@2ca53aorg.highwire.dtl.DTLVardef@113c38d_HPS_FORMAT_FIGEXP M_FIG C_FIG

Accurate quantification of rodent licking behavior is essential for studies of fluid intake, including investigations of alcohol use disorder and obesity. Existing lickometry systems vary widely in sensing modality, cost, scalability, and data resolution, and many available systems either require specialized housing or store only binary lick/no lick data based on thresholding. Here we present CLiQR (Capacitive Lick Quantification in Rodents), an open-source capacitive lickometry system designed for high-throughput recording of licking behavior in home-cage environments while preserving the full capacitance time series. The system uses MPR121 capacitive sensors connected to custom metal-tipped serological pipette sippers and a centralized desktop computer to record data from up to 24 animals concurrently, with capacity for two-bottle choice experiments. Validation experiments demonstrated that the capacitive signals reliably distinguish licking from non-licking interactions. Total lick counts showed a strong positive correlation with measured fluid consumption (r = 0.827, p < 0.0001), confirming that detected events provide a meaningful proxy for intake. All information necessary to reproduce the system is shared openly in this manuscript and online. By combining scalability, full-trace data acquisition, and low cost, CLiQR provides a flexible and extensible platform for high-throughput behavioral neuroscience experiments and enables retrospective improvement of lick-detection algorithms. Significance StatementUnderstanding ingestive behavior requires measuring both total consumption and consumption pattern. Licking microstructure provides information about motivation, palatability, and behavioral strategies (i.e., binge-like front-loading); yet many existing lickometry systems are limited by high cost, low scalability, specialized housing requirements, or loss of information due to event-only data storage. We introduce CLiQR, an open-source capacitive lickometry system that enables high-throughput, home-cage recording from dozens of animals while preserving the full time series of capacitance data. By retaining raw data, CLiQR allows post hoc validation and reanalysis of licking behavior, addressing a key limitation of many current systems. This approach increases experimental flexibility, improves data transparency, and lowers barriers to large-scale studies of ingestive behavior.

The common pine sawfly, Diprion pini, is a widespread defoliator of pine forests across Europe and Asia, with outbreaks causing substantial ecological and economic damages. However, genomic resources for this species have been limited, hindering advances in molecular ecology or pest management. Here, we present a near chromosome-level reference genome for D.pini, generated using PacBio HiFi reads, Oxford Nanopore MionION long reads, and 10x Genomics linked reads. The final assembly is organized into mostly chromosome-sized scaffolds. It spans a length of 268 Mb, comprises 81 scaffolds, and has a scaffold N50 of 18.7 Mb. BUSCO analysis (hymenoptera_odb10) indicates a high genome completeness of 97.2%. With 22,7 kb the mitochondrial genome is unusually large due to an extended non-coding control region (6,874 bp). Gene prediction identified 26,335 protein-coding genes, of which 12,769 were functionally annotated. Comparative analyses with other sawflies and Apocrita identified 2,472 proteins unique to D. pini, some of which are putatively associated with the processing of plant secondary metabolites. Notably, our genome assembly highlights that, when a closely related, high-quality reference genome is available, chromosome-scale assemblies can be generated without the need of Hi-C sequencing. The genome provides a valuable foundation for the development of improved monitoring and management strategies for D. pini outbreaks and contributes to advancing fundamental research on Hymenoptera evolution.

Study objectives Consumer sleep technologies (CSTs) enable low-burden longitudinal sleep monitoring, and their output measures are often interpreted as equivalent to polysomnography (PSG) measures. We applied a measurement reliability-aware approach to determine whether CST-derived 'sleep' measures (1) are interchangeable or device-specific, (2) can reliably assess trait-like sleep characteristics of an individual, (3) can be reduced to latent principal components of sleep, and (4) can be used for classification and biomarker discovery. Methods Data from 74 older adults (20 people living with dementia [PLWD]) were collected at-home (upto 14 nights; Total=752nights) using four tools simultaneously: research-grade actigraphy (Axivity), a wearable (Withings Watch), a nearable (Withings Sleep Analyzer) and Sleep Diary, followed by one in-lab PSG assessment. We used repeated-measures correlation analyses, intraclass correlation coefficients (ICC), principal component analysis (PCA) and binary classification models to address our objectives. Results Single-night between-device correlations and correlations with PSG were moderate (0.3[&le;]r<0.7) for some duration- and timing-related measures, but other associations were weak (r<0.3). Seventy-one percent of sleep measures reached acceptable reliability (ICC[&ge;]0.7) within seven nights of aggregation, but the required aggregation window varied across measures, tools and between PLWD and Controls. Reliability-filtered PCA yielded stable and interpretable principal components, but Duration was the only component showing moderate between-device association. Principal components were successfully used to classify PLWD vs Controls but feature importance varied across devices. Conclusions Aggregation of CST derived measures across 7-14 nights, yielded reliable measures, most of which were device-specific, with duration being the only essential aspect transferable between devices.