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.

This paper presents a six-stage methodological framework for Convolutional Neural Net-work (CNN)-based cetacean vocalization detection and classification in Passive Acoustic Monitoring (PAM), implemented as the open-source toolkit ai-pam-pipeline. The frame-work is generalizable across species and fully parameterised through a single configuration file, guaranteeing exact experimental reproducibility. Two experiments are reported. Experiment A examines the effect of FFT window length Nfft [isin] {256, 512, 1024} on binary Bottlenose dolphin (Tursiops truncatus) whistle detection using stratified 10-fold cross-validation on an in-domain dataset (Oltremare, 192 kHz) and a cross-domain benchmark (DCLDE 2022). In-domain performance is uniformly high (macro F1{approx} 0.98; Wilcoxon, all p > 0.05). Cross-domain results diverge substantially: Nfft = 256 is significantly superior (p = 0.006, rank-biserial r = 0.89). The mechanism is an upsampling amplification effect: coarser spectral bins produce wider, higher-contrast FM traces after bilinear resampling to fixed image dimensions. This superiority is threshold-invariant: precision equals 1.000 across all configurations and thresholds{theta} [isin] [0.1, 0.9], confirming that the advantage is not an artifact of threshold choice. These findings demonstrate that preprocessing choices -- often treated as secondary implementation details -- can significantly affect cross-domain generalisation. While Nfft serves here as a controlled case study, the framework is designed to enable systematic, reproducible evaluation of arbitrary preprocessing parameters within a unified experimental protocol. Experiment B demonstrates multiclass capability on five T. truncatus vocalization cate-gories (macro F1 = 0.843); inter-class confusion between click trains and burst-pulse sounds reflects biological signal overlap rather than classifier failure.

Wastewater surveillance is increasingly used for antimicrobial resistance (AMR) monitoring in urban environments, but low-resource settings often lack a piped sewerage system. Instead, coprophagous flies--flies that ingest feces--may serve as composite samplers for monitoring fecal wastes present in terrestrial environments. We evaluated whether the class 1 integron-integrase gene intI1 was associated with genetic markers of AMR and fecal source tracking markers (FST) in coprophagous flies collected from latrine entrances and food preparation areas in low-income urban Maputo, Mozambique. We quantified intI1, an enteric 16S rRNA target (for normalization), three FST markers, and 30 ARG targets using qPCR. We normalized concentrations of intI1 and each target to enteric 16S rRNA. We fit linear mixed models with a random intercept for housing compound to estimate within-fly associations between log10 relative abundance of intI1 and log10 relative abundance of each target with and without adjustment for fly taxonomic group, capture location, and standardized fly mass. We also modeled per-fly unique ARG count (i.e., number of ARG targets detected) using Poisson regression. Of 188 flies assayed, 176 passed internal controls; intI1 and enteric 16S rRNA were detected in 95% and 96% of flies, respectively. Higher relative abundance of intI1 was positively associated with ARG and FST targets, with the strongest associations observed for sulfonamide-(sul1: {beta} = 0.87; 95% CI: 0.81, 0.94; sul2: {beta} = 0.81; 95% CI: 0.73, 0.89), tetracycline- (tetA: {beta} = 0.78; 95% CI: 0.70, 0.85; tetB: {beta} = 0.69; 95% CI: 0.60, 0.79), and trimethoprim-related (dfrA17: {beta} = 0.78; 95% CI: 0.70, 0.86) genes. Associations with FST markers were weaker (i.e., human mtDNA: {beta} = 0.46; 95% CI: 0.37, 0.55; human-associated Bacteroides: {beta} = 0.34; 95% CI: 0.25, 0.43). Higher relative abundance of intI1 was also associated with a greater number of ARGs detected: each 10-fold increase in intI1 was associated with an 8% higher expected unique ARG count (aRR=1.08, 95% CI: 1.04-1.12). These findings support the need for further research across different settings exploring intI1 carried by coprophagous flies as a potential standardized screening target for AMR surveillance in unsewered terrestrial environments.

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.

Pig vocalizations convey information about the emotional states of individuals, varying with arousal and valence. Studies show that different call types reflect distinct emotional contexts and social interactions for the receivers. However, little is known about the brain mechanisms behind the perception of conspecifics vocalizations. This study used BOLD fMRI to explore how pigs brains respond to emotionally varied vocalizations, with the aim to identify activity in regions linked to emotion, reward, and social processing. Eight healthy 2-month-old pigs underwent auditory brainstem response (ABR) testing and BOLD fMRI to assess brain responses to pig vocalizations with different hedonic valence. Sounds were delivered via MRI-compatible earphones, and imaging was performed on a 1.5T scanner. Data were analyzed using voxel-based and ROI-based statistics in SPM12 with small volume correction (SVC). Due to hearing anomalies or MRI artefacts, only 5 pigs were included in the final analysis. Functional MRI revealed that vocalizations activated regions of the auditory pathway and the left amygdala (pFWE at peak < 0.05 after SVC for all), with specific differences between positive and negative sounds. Clusters of activated voxels covering part of hippocampal areas, caudate nuclei and putamen were found with both positive and aversive vocal sounds. Limbic regions, including the amygdala and insula (p<0.05), as well as the right hippocampus after SVC (pFWE = 0.015) were uniquely engaged during the perception of negative conspecific vocalizations, indicating distinct processing based on emotional valence. This study shows for the first time that piglets brain can process and differentiate emotional vocalizations from other pigs, even under general anesthesia. Positive and negative vocal sound playbacks activated distinct brain regions related to hearing, emotion and reward. These findings highlight pigs cognitive and emotional processing of vocal cues. This study is part of a wider research program aimed at developing the fMRI protocol with acoustic stimulation in juvenile pigs.

Dog (Canis lupus familiaris) vocal communication occurs across a wide range of social contexts, including dog-human social play, a common and dynamic interaction in which diverse vocal signals are expressed, particularly in young dogs. However, most available open datasets of dog vocalizations focus primarily on barks, leaving other sound types underrepresented. Here we present a bioacoustic dataset of dog-human social play sessions recorded under standardized laboratory conditions, comprising 30 play sessions involving 17 young dogs (6-24 months old) of different breeds playing with familiar humans. Raw audio recordings are accompanied by two layers of annotations covering the dog sounds produced during sessions. Video recordings of the sessions are provided for contextual reference, along with metadata describing each dog and the experimental sessions. Additionally, permutation-based classification analysis showed that annotated sound categories exhibit above-chance and generalizable acoustic differences across individuals. The dataset may support research on dog vocal communication and expand the range of sounds documented during positive dog-human social interactions.

Clinical metagenomics uses sequencing for culture-independent identification of pathogens directly from clinical specimens. While a number of protocols claim to be pathogen agnostic, sensitivity for RNA viruses is likely lower than for bacteria or fungi, as it requires additional processing steps including conversion to cDNA. Sequence-independent, single-primer amplification (SISPA) was first described in 1991, yet how it preferentially enriches viral molecules has never been described. Here we propose that single-primer amplification exploits the PCR suppression effect, which selectively amplifies longer viral molecules over shorter host-derived cDNA fragments on the basis of size. This model predicts that any upstream processing step that disrupts fragment length will prevent this enrichment occurring. To test this, we systematically compared two adapter introduction strategies - during cDNA synthesis and via tagmentation - followed by single primer amplification, using the ZeptoMetrix Respiratory Panel 2.1 containing 16 RNA and 3 DNA virus strains. SISPA-based approaches recovered all of the viral genomes in the control, whereas using tagmentation to amplify cDNA recovered none. We then spiked the controls into extracted clinical samples and found that SISPA-based methods performed best in all background settings, however in high-background settings no viral genomes were recovered by any approach. Finally, using a modified SMART-9N protocol, we demonstrated that single-primer PCR is critical to overall performance, indicating that direct tagmentation of cDNA and dual-primer PCR should be avoided in protocols for clinical metagenomics where high sensitivity for RNA viruses is critical. These findings demonstrate that library preparation strategy fundamentally determines RNA virus sensitivity and offer mechanistic insights for protocol optimisation with direct relevance to clinical metagenomics.

We investigate the effects of skin pigmentation and light source characteristics on the performance of reflective Pulse oximetry (PO) devices used in healthcare and well-being applications. We use Monte Carlo (MC) simulations to compare ideal monochromatic and realistic LED spectral emission profiles and tolerance-related wavelength shifts. The simulation covers photon transport in skin models with melanin concentrations (2.55% to 30.5%) and arterial oxygen saturations SaO2 (70% to 100%.) Accuracy was assessed by SpO2 error, root-mean-square error RMSE (Arms), and percentile tail-errors (P90, P95, and P99). Monochromatic spectral emission yielded the lowest SpO2 error (RMSE = 1.32), while LED spectral emission profiles increased errors (RMSE = 2.10). Infrared wavelength tolerances increased SpO2 RMSE by 1.1 {+/-} 0.3. SpO2 error increased with melanin concentration, from underestimation (-1.8 {+/-} 0.1%) at 2.55% melanin concentration to overestimation (+3.9 {+/-} 1.2%) at 30.5% for low SaO2 (70%) and LED spectral emission profiles. At 30.5% melanin concentration, P95 and P99 exceeded FDA and DIN EN ISO 80601-2-61 thresholds, in particular at low SaO2 (70%). Clipping SpO2 estimates at 100% resulted in an apparent RMSE decrease of up to 3%, reflecting error masking rather than real error reduction. In conclusion, LED spectral emission profiles and wavelength tolerances can amplify melanin-related bias in SpO2 estimates. Monochromatic emission and tighter wavelength control can reduce SpO2 error and should be considered in device design and regulation. Regulatory standards should discourage clipping SpO2 estimates at 100% and mandate additional metrics as RMSE fails to reflect clinically critical percentile error thresholds, i.e. P95 and P99.

Shared sleeping quarters are commonplace in contexts such as athletes at major sporting events, academic dormitories, and military barracks, yet mismatched sleep preferences can undermine rest and ultimately, human behaviour and performance. We introduce the Roommate Sleep Preference Questionnaire (ROOMPREF), a brief eight-question survey capturing preferences for noise, lighting, and temperature tolerances, snoring behaviour, and chronotype. Responses feed into a free, web-based clustering tool built in Python, which flags preference conflicts, and implements adaptive K-Means clustering within sex-chronotype subgroups. A post-cluster swapping algorithm further mitigates residual mismatches, enhancing the room-matching process. The resource includes distribution charts, group summaries, and optional automated room allocations, with downloadable CSV outputs. We demonstrate its application in a pilot cohort, highlighting its potential to improve sleep outcomes across various use-cases. This free resource has the potential to alleviate mismatched rooming partners, resulting in enhanced sleep and wellbeing outcomes.

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 childrens 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.

Rhesus macaques (Macaca mulatta) are widely used as non-human primate models for biomedical research. When housed in captivity, it is essential to provide an environment that supports their natural behaviours; otherwise, they risk developing mood disorders, stereotypies, and other behavioural issues that may lead to physical harm. The objective of this preliminary study was to monitor the behaviour of three aged rhesus macaques ([&ge;] 20 y.o.), relocated from a laboratory to a Rescue Centre for Exotic Animals (Italy), and to assess the impact of novel food enrichments. Behavioural data were collected over 18 weeks, beginning at their arrival, using continuous focal sampling from video recordings. Simultaneously, faecal samples were gathered for cortisol analysis. The study was divided into three phases: a control phase without enrichments, a feeding enrichment phase (divided into two periods), and a final control phase without enrichments. Each phase comprised 900 minutes of observations for each subject. Data were analysed using generalized linear mixed models. Results showed an increase in locomotion during the enrichment and final phase compared to the initial phase. Additionally, a reduction in scratching and body-shaking behaviours was observed in the final phase compared to the initial phase. These findings suggest that implementing an enrichment program can enhance the welfare of aged non-human primates and can be considered a valuable tool in the rehabilitation of non-human primates previously housed in laboratories. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/719840v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@152a3a1org.highwire.dtl.DTLVardef@74b53forg.highwire.dtl.DTLVardef@275b21org.highwire.dtl.DTLVardef@1d004d8_HPS_FORMAT_FIGEXP M_FIG C_FIG RESEARCH HIGHLIGHTSO_LIEnvironmental enrichment positively affected activity and stress indicators in aged ex-laboratory rhesus macaques. C_LIO_LILocomotion rates increased while scratching, body-shaking, and cortisol levels decreased. C_LIO_LIEnrichment enhance welfare during rehabilitation, even in older individuals. C_LI

Compassion fatigue is a well-documented hazard among healthcare and veterinary professionals, yet the psychological toll on informal caregivers of feral cat colonies, likely numbering several tens of thousands in Portugal, remains largely unexplored. This cross-sectional study examines internal and external factors associated with the secondary traumatic stress component of compassion fatigue among 172 informal caregivers in Portugal. Secondary traumatic stress refers to work-related secondary exposure to individuals who have experienced extremely stressful or traumatic events. Structured telephone interviews assessed sociodemographics, colony management, compassion satisfaction, resilience, spiritual well-being, and perceived social support. Univariate and multivariable linear regression identified predictors of secondary traumatic stress. Results indicate that 47% of participants experienced moderate secondary traumatic stress, and 10% reported high levels. Multivariable analysis revealed that caring for large colonies (more than 25 cats) and being unemployed were significantly associated with higher fatigue. Conversely, older age, higher perceived family support, and the resilience dimension of serenity served as protective factors. Interestingly, finding meaning in life was positively correlated with fatigue, suggesting that caregivers who perceive their role as central to their life purpose may become more emotionally invested, increasing vulnerability to distress when unable to help animals. Official colony registration and formal institutional support did not significantly alleviate fatigue. These findings highlight that institutional support alone is insufficient to mitigate fatigue among informal caregivers, who experience significant distress driven by both practical burdens and profound emotional involvement. The most frequently reported concern among caregivers was the inability to cover the costs of feeding and veterinary care for the cats. Interventions must address both external needs (e.g., support to cover veterinary and feeding expenses for the cats) and internal coping mechanisms. Implementing psychosocial support alongside trap-neuter-return programs may also improve caregiver well-being and foster sustainable urban feral cat management. This underscores a One Health perspective, demonstrating that animal health is closely interconnected with human well-being and environmental health.

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.

BackgroundSickle cell disease (SCD) is the most common recessive genetic disorder, caused by pathogenic variants of the HBB gene. SCD is associated with a range of clinical manifestations, including vaso-occlusive crises, infections, and severe anaemia, which contribute to increased morbidity and mortality. The frequency of pathogenic alleles is high in Sub-Saharan African countries, with heterozygous carriers reaching up to 25% of the population. Several methods can be employed for molecular diagnostics, with HBB gene sequencing being the most precise. However, access to DNA analyses and sequencing in Low- and Middle-Income Countries (LMICs), where SCD prevalence is high, is limited. Understanding genetic profiles is crucial at both individual and population levels, as it can guide public health strategies and facilitate accurate genetic counselling. AimThis feasibility study aimed to demonstrate that a portable medical genetic laboratory (in suitcases) can be used to genotype individuals for the HBB A, S, and C alleles and their combinations within a few hours outside of a laboratory setting. Methods and resultsWe established a portable medical genetics laboratory capable of DNA extraction and isothermal DNA amplification using a commercially available kit for the A, S, and C alleles of the HBB gene. During one single study day, this portable lab was set up in a room where the Swiss Association of Patients with SCD was holding its annual meeting. We analysed the samples of 27 participants who were aware of their A, S, or C status. We collected buccal swabs and dried blood samples for genotyping. Genotype results for all participants were obtained within five hours after sample collection. In four cases, we observed discrepancies between the buccal swab and blood genotypes; three were resolved upon repeat testing, and one reflected donor chimerism following hematopoietic stem-cell transplantation. ConclusionsThis study demonstrates the feasibility and efficiency of using a portable medical genetics laboratory for rapid genotyping of HBB SCD alleles in community settings.This approach can improve access to molecular diagnostics in resource-limited environments. Such tools have the potential to significantly enhance local capabilities for genetic screening, counselling, and public health planning in regions heavily affected by SCD.

A fermented-food intervention trial conducted in Pakistan suggested beneficial changes in the composition of the gut microbiota in healthy women. Using a subset (n=17) of the same participants, this study further investigates the impact of fermented food (onion pickle) on gene expression levels using RNA transcriptomics, with a focus on host-microbiome interactions. After consuming pickles (50g/day) for eight weeks, blood and stool samples of participants were collected at baseline and post-intervention to assess inflammatory markers, 16S rRNA gene sequencing, clinical parameters, and RNA sequencing. Among inflammatory biomarkers, lipocalin (LCN-2) levels significantly decreased (pre=86.5{+/-}80.1ng/mL, post=61.0{+/-}59.0 ng/mL, p=0.04, paired T-test). Additionally, the intervention downregulated pathways (p<0.05) involved host responses to microbial stimuli, including response to bacterial origin, chemotaxis, and response to lipopolysaccharide. In gut microbiota, observed -diversity significantly increased post-intervention (p=0.02). Linear discriminant analysis effect size (LEfSe) revealed differential expressions (LDA [&ge;] 2.0) of Olsenella and Coriobacteriales at week-8, where Olsenella sp. showed a significant negative correlation with LCN-2 (R=-0.36, p<0.05, Spearmans correlation). These findings suggest that fermented onion pickle consumption for eight weeks modestly alters gut microbial diversity and composition and is associated with reduced inflammatory markers and altered host immune-related gene expression, potentially improving intestinal health. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/711246v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1be865eorg.highwire.dtl.DTLVardef@167b253org.highwire.dtl.DTLVardef@ec763aorg.highwire.dtl.DTLVardef@45db55_HPS_FORMAT_FIGEXP M_FIG C_FIG

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.

Celiac disease (CD) is strongly associated with specific HLA DQ heterodimers, formed by HLA DQA1 and HLA DQB1 proteins. In particular DQ2.5 (DQB1*02 associated to DQA1*05) and DQ8 (DQB1*03:02 with DQA1*03) are present in virtually all celiac patients. HLA DQB1*02 is considered the main single genetic susceptibility marker and has been reported in 90 to 95% of CD patients. However, the distribution of these alleles may vary across populations, potentially impacting the performance of genetic screening strategies. In this study, we evaluated the prevalence of HLA DQ2.5 and DQ8 genotypes in celiac patients (n = 41) and an unbiased general population cohort (n = 60) from San Luis, Argentina, using a PCR-based genotyping approach. In addition, we assessed the feasibility of a simplified saliva direct PCR protocol for large scale testing. Overall, 95.1% of CD patients carried DQ2.5 and/or DQ8. Notably, 41.5% of patients were DQ8(+)/DQ2.5(-), and 36.6% lacked the DQB1*02 allele, indicating that DQB1*02 based screening alone would have reduced sensitivity in this population. In the general population, 53.3% of individuals carried CD associated genotypes, with a markedly higher prevalence of DQ8 compared to European cohorts. Genotype distributions deviated from Hardy Weinberg equilibrium in CD patients but not in the general population. We show that DQB1*03:02 is a reliable proxy for DQ8, allowing simplification of genotyping strategies, whereas DQA1*05 typing remains essential to discriminate DQ2.5 from other lower risk DQB1*02 carrying heterodimers. We also describe a saliva direct PCR approach showing a performance comparable to purified DNA based assays. These findings highlight the importance of population specific genetic data for optimizing CD screening strategies and foster the development of simplified, cost effective genotyping approaches for large scale applications.

Close to 50% of all bird species are reservoirs of potentially pathogenic fungi, including those listed as priority by the World Health Organization. In Malawi, data on diversity, pathogenic potential, and ecological avian sources of medically important yeast are scarce. A cross-sectional study using a descriptive approach was conducted in Blantyre, Southern Malawi, to characterise medically important yeasts recovered from environments contaminated with excreta/guano from synanthropic pigeons. A total of 20 samples were collected from 4 peri-urban areas, which yielded 71 yeast isolates. To assess the pathogenic potential of the environmental isolates, we compared their phenotypic virulence traits with those of 21 clinical yeast isolates collected from referral hospital laboratories. Pichia kudriavzevii (39%) and Candida orthopsilosis (30%) were the commonly isolated species in the pigeon-guano-contaminated environments. Candida parapsilosis sensu stricto (29%) and Candida albicans (24%) constituted most of the clinical yeast isolates. Half of the species isolated in the pigeon-guano-contaminated environments were also identified among the clinical isolates. A majority of the environmental isolates showed virulence traits similar to or stronger than clinical isolates. The findings underscore the critical need for integrated surveillance under the One Health framework, especially in bird-inhabited spaces close to human settlements.