Data in Brief
○ Elsevier BV
Preprints posted in the last 90 days, ranked by how well they match Data in Brief's content profile, based on 14 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.
Asres, Y. H.; Mathuth, M.
Show abstract
Botanical dietary supplements (like wheat, barley, teff, oats, white lupin, pumpkin seed, and chickpeas) may contain trace amounts of toxicants in addition to important micronutrients. Developing and validating a reliable protocol for the simultaneous quantification of Cu, Fe, Zn, Mo, Se, Mn, Pb, Al, Ni, and Cr using a PerkinElmer (NexIONTM2000 model) quadrupole ICP MS (including a He collision and reaction cell when needed) with closed vessel microwave digestion using (HNO3 + H2O2) was the aim of this study.The method was subsequently utilized in a sample survey, and the outcomes were evaluated against WHO/JECFA standards. From five study regions, twenty-seven farm-collected botanical powder samples representing seven species were acquired. To create one composite per species, field subsamples were cleaned, air dried, ground, and blended (nine subsamples per botanical: three grabs from each of three farms). HNO3/H2O2 was used to digest aliquots (0.250-0.500gm) in closed microwave containers. Internal standards, multi-point external calibration, procedural blanks, verified reference materials, matrix spikes, and duplicates were all used in ICP MSs multi-element quantitation. Method LODs/LOQs, accuracy (CRM recoveries), and precision (RSD) were calculated.The technique produced low LODs that were suitable for dietary evaluation (typical LOD ranges: Cu, Fe, Zn, Mn, Ni, Cr (0.001-0.01) mg/kg; Mo, Se, Pb, Al (0.002-0.05) mg/kg. For the majority of analytes, within-run RSDs were less than 5%, while CRM recoveries ranged from 88.9 to 110%. The concentrations of essential elements varied greatly (average mg/kg: Fe (280.7{+/-}25.6); Zn (6.0{+/-}0.541); Cu (2.8{+/-}0.269); Mn (398.3{+/-}23.8); {micro}gm/kg: Se (0.061{+/-}0.006); Mo (1.0 {+/-}0.022). Although some composites approached or exceeded conservative intake thresholds for Pb and Al under high consumption scenarios, toxic elements were generally low (mean mg/kg: Pb (0.062{+/-}0.007); Al(185.2{+/-}18.5); Ni(1.6{+/-}0.163); Cr(1.8{+/-}0.171).For the simultaneous nutritional and contaminant profiling of supplements derived from cereals and those not, the validated ICP- MS workflow with microwave HNO3 and H2O2 digestion is suitable. Accurate labeling and consumer safety can be supported by routine screening and supply chain controls.
Wienbrandt, L.; Priess, C.; Schmöhl, M.; Neff, V.; Gretsova, M.; Torres, G.; Wacker, E. M.; Franke, A.; Ellinghaus, D.
Show abstract
We constructed a genotype imputation reference panel from whole-genome sequence data of 490,319 UK Biobank participants and enabled both standalone and cloud-based phasing and imputation through EagleImp and EagleImp-RAP within the UK Biobank Research Analysis Platform. The UK Biobank reference panel achieves lower phasing switch error rates than the widely used TOPMed r3 panel (133,597 individuals) for all global superpopulations except AMR and for 25 of 26 1000 Genomes Project subpopulations. Imputation accuracy, measured by mean absolute error, improved for four of five superpopulations and 12 subpopulations for variants with minor allele frequencies down to 0.01%. Estimated squared correlation further improved across all five superpopulations and 22 subpopulations, with the largest gains in East and South Asian populations. Re-imputation of COVID-19 GWAS datasets from Italy, Germany, Spain and Norway demonstrated that common-variant imputation remains unsaturated, enhancing the discovery of genome-wide significant loci and improving fine-mapping resolution.
Spilioti, E.; Spyropoulou, A.; Gate, L.; Lorcin, M.; Machera, K.; Nestora, A.; Repouskou, A.; Theologidis, I.; Marko, D.; Behr, A.-C.
Show abstract
Alternaria mycotoxins represent an emerging concern due to their frequent occurrence in food and feed. However, available toxicological data remain limited. Under the current EU regulatory framework, and in line with the EFSA/ECHA/JRC guidance for the identification of endocrine disruptors (EDs), assessment of endocrine activity relies on standardized assays performed according to OECD Test Guidelines (TGs) for the estrogen-, androgen- and steroidogenesis- (EAS) modalities. Within the framework of the European Partnership for the Assessment of Risks from Chemicals (PARC), standardized in vitro methods of regulatory relevance were performed for six chemically characterized Alternaria toxins, aiming to address current regulatory gaps on EAS-mediated activity. Alternariol (AOH), alternariol monomethyl ether (AME), tenuazonic acid (TeA), altertoxin-I (ATX-I), tentoxin (TEN) and altenuene (ALT) were assessed over a broad concentration range, from 0.001 up to 60 M, depending on cytotoxicity and solubility profile of each compound. Our findings indicate estrogenic activity for AOH (PC50: 3.9 - 4.6 {micro}M) and AME (PC50: 5.2 - 8.5 {micro}M) in the estrogen receptor transactivation assay (OECD TG 455), as well as an anti-estrogenic activity for ATX-I (IC30: 0.27 - 0.37 {micro}M). Minimal positive responses were observed at high concentrations for AOH (from the dose of 3 {micro}M) and for AME (from the dose of 10 {micro}M) in the agonistic part of the androgen receptor transactivation assay (OECD TG 458), which may also reflect glucocorticoid receptor activation. No effects on estradiol or testosterone production were observed for any of the tested Alternaria compounds in the steroidogenesis assay (OECD TG 456).
Sun, V. L.; Wang, K.; Kelly, E. J.; Arnold, S. L. M.
Show abstract
Transporters localized to the small intestinal epithelium govern the absorption of many orally administered drugs and nutrients, and thorough characterization of transporter protein abundance is key to accurate prediction of small molecule absorption. Previous studies have reported more than 100 solute carrier and ATP-binding cassette superfamilies expressed in the intestine, but only a small subset of these transporter proteins have been quantified in native intestinal tissue. In addition, a majority of published transporter abundance data for the intestine was collected with adult tissue. Here, we report the identification and relative quantification of 87 solute carrier and 18 ATP-binding cassette superfamily transporters by intestinal region in neonatal, pediatric, and adult small intestinal mucosa using data-independent acquisition mass spectrometry. This study identified transporters uniquely expressed by intestinal region in all three age groups and region-associated abundance for 23 SLC/ABC transporters in pediatrics and adults. The protein abundance data reported here provide a valuable resource for the prediction of nutrient and drug absorption and efflux across age and will inform future studies of specific transporters and age-associated differences in transporter abundance. Significance statementWe report the relative abundance of key xenobiotic transporters along the length of the small intestine in neonates, pediatrics, and adults based on data-independent acquisition mass spectrometry. Intestinal region-associated transporter expression was observed for drug transporters and under-studied nutrient transporters across age groups.
Ogata, N.; MATSUDA, T.
Show abstract
Human hair is a common contaminant in GMP-controlled manufacturing environments, and its identification is important for contamination source investigation and corrective action. Because human hair can originate from multiple body sites, it is often necessary to determine not only the species of origin but also the anatomical source of the hair. Conventional forensic approaches distinguish scalp hair from body hair by microscopic examination of cuticle patterns, medullary structure, cross-sectional morphology, and pigment distribution. However, these methods depend on examiner expertise, are difficult to apply to damaged specimens, and provide limited quantitative information. In this study, we developed a proteomics-based approach for distinguishing scalp hair from pubic hair using identical sample preparation and analytical workflows. Comparative proteomic analysis identified keratin-associated proteins KAP 4-3 and KAP 9-6 as enriched in scalp hair, whereas cuticular keratins Ha7 and Ha8 were strongly enriched in pubic hair. Amino acid composition analysis further revealed that scalp hair-enriched proteins were highly cysteine-rich, consistent with sulfur-rich cross-linking matrix proteins, whereas pubic hair-enriched proteins exhibited characteristics of structural keratin filaments. These results demonstrate that proteomic signatures can provide a quantitative and objective means of determining the anatomical origin of human hair and may contribute to contamination source tracing in GMP manufacturing and forensic investigations.
Madgaonkar, S. R.; Vashishth, S.; Ayyanar, E.; Srirama, S.; Samal, A.
Show abstract
Ticks transmit pathogens across wildlife, domestic animals, and humans, and are therefore considered important vectors under the One Health framework. In India, the burden of tick-borne diseases, such as Kyasanur Forest Disease and Crimean-Congo Hemorrhagic Fever, remains poorly quantified due to fragmented surveillance and limited spatial data. Here, we present TickMapKB, a curated spatial knowledgebase documenting 72 tick species across more than 600 georeferenced locations in India. The majority of the species belonged to the genera Haemaphysalis, Rhipicephalus, and Hyalomma. Additionally, the resource integrates host associations, pathogen and disease information, morphological identification keys, acaricide resistance profiles, and protein annotations into a single, interactive platform accessible at https://cb.imsc.res.in/tickmapkb/. Specifically, the resource captures 53 pathogens, over 3000 protein annotations, and morphological keys from 26 published resources. TickMapKB thus provides researchers, clinicians, and other stakeholders with integrated spatial, biological, and resistance information to support surveillance planning, resistance management, and tick-borne disease risk assessment.
Antunes, D. F.; Liu, Z.; Ringler, E.
Show abstract
Parental care can have pervasive effects on offsprings neurodevelopment. Parent-offspring interactions are often modulated by the neuropeptide oxytocin, which is responsible for the development of social bonds. The development of the oxytocinergic system is dependent on the quality of parental care during the post-natal phase. However, it is yet unknown how post-natal direct interactions can influence the development of the oxytocinergic pathway. Here we tested how an obligate parental care behaviour, tadpole transport in poison frogs, influences the development of the oxytocinergic pathway. To this end, we quantified whole brain expression of oxytocin receptor and oxytocin precursor throughout three developmental stages of A. femoralis tadpoles, before, during and after tadpole transport. Our results show an overall downregulation during tadpole transport, which indicates that during transport tadpoles enter a dormant state to slow down development until they are placed in water. Interestingly, the expression of oxytocin precursor did not vary between the three developmental stages. This might indicate that oxytocin is being recruited during transport, but does not lead to neurodevelopmental changes. In sum, here we present the first evidence of a dormant state during tadpole transport which might be an adaptive response to the terrestrial reproduction in poison frogs.
Charnley, G. E. C.; Kotz, M.; Kawiecki Peralta, A.; Grayson, K. M.
Show abstract
Climate change detection and attribution (D&A) methods have become vital for quantifying the influence of anthropogenic forcing on the Earth's systems, including human health. Health impact attribution (HIA) studies seek to disentangle climate-driven health effects from natural variability yet are often constrained by the availability of accessible counterfactual climate scenarios. This tutorial paper presents a flexible, reproducible framework for developing counterfactual climates without reliance on computationally intensive global circulation models. We provide practical, R-based methodologies for constructing both trend-based (temperature and non-temperature) and event-based counterfactual, using a variety of techniques including model residual detrending, data-driven decomposition (e.g., Singular Spectrum Analysis and Empirical Mode Decomposition) and stochastic weather generators. The tutorial also explores the incorporation of greenhouse gas concentrations as forcing variables, rather than global mean temperature anomalies. By operationalising these methods through worked examples and an open code repository, this paper aims to build capacity within the HIA community, enhance methodological transparency, and foster interdisciplinary collaboration between climate and health researchers.
Dewi, Y. K.; Chudori, Y. N.
Show abstract
Reliable DNA isolation is a critical prerequisite for PCR-based food authentication, particularly for meat products where complex matrices may compromise DNA quality and amplification efficiency. This study aimed to analytically validate an automated DNA extraction method from meat matrices using Qiagen QIAcube Connect in combination with the DNeasy(R) Mericon Food Kit. Validation parameters included DNA concentration, total yield, purity, integrity, and assessment of PCR inhibitors using real-time PCR targeting the porcine cytochrome b gene. The method produced a mean DNA concentration of 219.5 ng/{micro}L with an average yield of 21,519.7 ng, exceeding predefined acceptance criteria. Agarose gel electrophoresis confirmed DNA fragment sizes larger than the target amplicon, indicating suitability for PCR analysis. Real-time PCR evaluation demonstrated excellent linearity (R2 = 0.99-1.00), amplification efficiencies between 90.34% and 99.84%, and mean {Delta}Ct values of 0.10, confirming the absence of PCR inhibition. These results indicate that the validated automated method is robust, reproducible, and suitable for routine PCR-based meat species authentication in food control laboratories.
Skouloudaki, K.; Denecke, S.; Vogelsang, K.; Pergantis, S.; Vontas, J.
Show abstract
Intestinal insect cells are integral to pharmacokinetic research, unfortunately they do not serve as cell models for more advanced studies comparable to transport studies typically conducted in mammalian models. To overcome this limitation, in this study, we developed a Caco-2 cell line that has been genetically modified to mimic insect-like characteristics, providing a robust insectified screening platform to monitor transport processes of xenobiotics. This platform consists of Wild Type (Pgpwild type) cells, an Pgp Knockout (PgpKO) line to eliminate endogenous background interference, and species-specific P-gp rescue lines. These rescue lines allow for the stable expression of human (Hs Pgp), cotton bollworm (Ha Pgp), and malaria mosquito (Ag Pgp) homologs, enabling a direct comparative analysis of efflux kinetics across different pesticide target and non-target biological systems. Functional validation using the substrate Digoxin confirmed high P-gp dependency within the platform. Methyl-parathion, an organophospate insecticide, was recognised and transported by both insect and human Pgps. This is consistent with the low mammalian selectivity of the compound. In contrast, Triflumezopyrim exhibited a high efflux ratio that remained remarkably stable even in the absence of MDR1, indicating that the uptake and pharmacokinetics of this compound are not Pgp-dependent. By successfully differentiating between transporter-specific and independent pathways these cell lines can serve as a high-fidelity screening tool for predicting novel pesticide selectivity and possibly validating the potential role of transporters in resistance. The system can be expanded and exploit also other transporters.
Zhang, R.;Zhang, Y.;Zang, H.;Lou, J.;Li, Y.;Jiang, J.;Chen, D.;Yan, T.;Guo, R.
Show abstract
Melittin, the principal bioactive peptide of bee venom, exerts potent antitumor activity against hepatocellular carcinoma (HCC). However, the comprehensive transcriptomic alterations it elicits in hepatoma cells remain poorly characterized. Here, we present an integrated transcriptome dataset from melittin- and un-treated murine Hepa 1-6 hepatoma cells, encompassing messenger RNA (mRNA) and microRNA (miRNA) expression profiles. Cells were exposed to 4 g/mL melittin in serum-free DMEM for 20 min, and total RNA was subjected to ribosomal RNA-depleted strand-specific RNA sequencing on an Illumina NovaSeq6000 platform (paired-end 150 bp) and small RNA sequencing on an Illumina HiSeq2500 platform (single-end 50 bp). Raw data were processed using Cutadapt to remove adapters and low-quality reads, yielding clean datasets with Q20 [≥] 99.85%, Q30 [≥] 98.48%, and valid data ratios exceeding 85%. All raw and processed sequencing data are publicly available. This transcriptomic resource provides a valuable resource and basis for elucidating the regulatory networks underlying melittin-induced anti-hepatoma effects. DatasetThe dataset can be accessed through the National Genomics Data Center, China National Center website by searching with the BioProject accession number PRJCA065485 Reviewers may use this link for anonymous access during the review process. Direct URL to data: Genome Sequence Archive-CNCB-NGDC. Dataset LicenseCC BY 4.0
Kavil, S.; Jinmi, D.; Alphey, L.; Anderson, M. A. E.
Show abstract
BackgroundMalaria control is increasingly challenged by the urban-adapted vector Anopheles stephensi, yet molecular and cellular tools for this species remain scarce, restricting functional genomic studies and the development of genetic control strategies. To help address this gap, we established a new embryo-derived Anopheles stephensi cell line. ResultsWe generated and characterised a novel embryo-derived Anopheles stephensi (SDA-500) cell line capable of sustained growth in vitro. Species identity was confirmed by mitochondrial COI barcoding, and karyotypic analysis revealed a diploid chromosome complement with the presence of a Y chromosome, confirming that at least some cells are of male origin. Transfection conditions were optimized, with TransIT-PRO showing higher efficiency than Lipofectamine-based reagents. Using a dual-luciferase reporter assay, of several promoters tested the Anopheles gambiae polyubiquitin promoter exhibited the strongest and most consistent transcriptional activity in SDA-500 cells. ConclusionsThe SDA-500 cell line provides a stable and genetically validated in vitro platform that supports efficient transgene expression. This resource provides a useful system for functional genomics and molecular manipulation in Anopheles stephensi and is expected to facilitate studies of mosquito biology and contribute to the development of novel malaria control strategies.
Pain, M.; Boulain, M.; Cardoit, L.; Cabirol, M.-J.; Forgue, J.; Gorges, M.; Courtand, G.; Glasauer, S.; Lambert, F. M.
Show abstract
Extraocular motoneurons are the final neuronal relay implicated in gaze motor control and are known to be subdivided in functional subgroups, differently implicated in ocular motion dynamics. However, the maturation of these functional populations of extraocular motoneurons, in relation with the development of gaze-stabilizing reflexes remains largely unexplored. In amphibian tadpoles, the angular vestibulo-ocular reflex (VOR) appears later than other visuo-vestibular ocular reflexes and matures until the metamorphosis climax. Two types of Abducens motoneurons have been described to participate to the angular VOR in larval frog: spontaneous motor units, exhibiting a robust resting activity and silent motor units recruited only during head motion. The aim of this study was to investigate the maturation of these two types of Abducens motor units in relation with the development of the angular VOR by evaluating their discharge dynamic in response to head rotation in semi-intact preparations of larval Xenopus laevis. During larval life, the discharge modulation during sinusoidal head rotations increases significantly for silent units only, demonstrating a better sensitivity of this Abducens motoneuron sub-population to horizontal semicircular canal activation. In addition, this functional maturation was accompanied by an increase of the myelination in the lateral rectus motor nerve, promoting a faster conductivity in late larval stages than in early one. These findings showed that the development of the angular VOR is supported by a selective maturation of extraocular motoneurons subpopulations, specifically implicated in the improvement of the ocular kinematic during the reflex.
Sheldon, D.; Winner, K.; Deznabi, I.; Bernstein, G.; Bhambhani, P.; Lin, T.-Y.; Desmet, P.; Dokter, A. M.; Horton, K. G.; Nilsson, C.; Van Doren, B. M.; Farnsworth, A.; La Sorte, F. A.; Maji, S.
Show abstract
The US NEXRAD radar network has monitored the aerosphere over the US and its territories continuously since the 1990s and archived nearly 300 million radar volume scans. These data contain a wealth of information about the movements of birds, bats, and insects. Historically, this biological information was difficult to access due to the amount of data and challenges in analyzing it. In the last 15 years, fueled by computational and methodological advances, large-scale aeroecology research has blossomed. However, comprehensive analyses of the NEXRAD archive remain very costly. We collected measurements of biological activity from every volume scan in the NEXRAD archive--nearly 300 million data files total--to assemble a dataset of aerial biomass over the US from 1995 to 2025. The core data are vertical profiles, which summarize biological activity at different heights above the radar station for each volume scan. We also provide time series data products that aggregate vertical profiles to point measurements at radar stations across time. These data products can support a range of aeroecology analyses at significantly reduced effort.
Morvan, M.
Show abstract
Accurate biological sex estimation is a key objective in archaeological and bioanthropological research but remains challenging when skeletal remains are fragmented, juvenile, or poorly preserved. Paleoproteomics approaches based on the detection of sex-specific amelogenin peptides (AMELX/AMELY) have emerged as a powerful alternative to osteological and genetic methods. However, current workflows often lack standardized criteria for peptide-level confidence assessment, potentially affecting the reproducibility and reliability of sex assignments. In this study, I evaluated the impact of peptide-level confidence filtering on paleoproteomics-based sex estimation through the reanalysis of 164 Homo sapiens individuals from 10 published datasets and 26 Bos taurus individuals from 3 datasets, spanning contexts from the Pleistocene to the present. To address methodological inconsistencies, I developed SexPeptID, an R/Shiny-based framework that integrates Posterior Error Probability (PEP) filtering, standardized peptide selection, and explicit uncertainty assessment. Application of SexPeptID revealed that peptide-level filtering substantially affects sex assignment outcomes: 17 previously classified males (10.4%) were reclassified as non-conclusive, while 5 individuals (3.1%) were identified as potentially female. Despite this sensitivity, AMELX/AMELY-based sex estimation remained robust overall, with stable signal ratios observed across archaeological periods. Variability in peptide intensities was primarily associated with dataset-specific factors rather than temporal differences, highlighting the influence of analytical workflows and preservation conditions. By incorporating confidence-based filtering and a non-conclusive classification category, SexPeptID improves the transparency, reproducibility, and reliability of palaeoproteomics sex estimation, providing a standardized framework for future archaeological and bioanthropological studies. HighlightsO_LISexPeptID provides a reproducible framework for amelogenin-based sex estimation. C_LIO_LIPeptide-level confidence filtering significantly affects paleoproteomics sex estimates. C_LIO_LI13.4% of published male assignments were revised after confidence filtering. C_LIO_LIAMELX/AMELY ratios show temporal stability from modern to Pleistocene samples. C_LIO_LIStandardized uncertainty assessment strengthens palaeoproteomics inference. C_LI
Norekian, T. P.; Moroz, L. L.
Show abstract
Hydrozoa is a group of relatively simple animals with a well-developed nervous system. The nervous system in all hydrozoan medusae is highly conserved and includes outer and inner nerve rings at the bell margin, a neural network in the manubrium, and radial neural pathways that connect them. However, one element of the nervous system shows substantial variability among species: the subumbrella neural network. We examined the structure of the nervous and muscular systems in the subumbrella of 14 species of hydrozoan medusae. The main conclusion of this study is that the distribution of neural networks in the subumbrella strongly correlates with the distribution of smooth radial muscles. This correlation suggests that smooth radial muscles are the primary target of the subumbrella nervous system. Most species in the order Anthoathecata show a trend toward secondary loss of the neural networks and radial smooth muscle fibers in the subumbrella region, concentrating neural elements and smooth muscles only in the radial pathways along the radial canals. By contrast, all studied species in the order Leptothecata have neural networks in the subumbrella area, as well as radial smooth muscle fibers spread throughout the entire subumbrella region. The correlation between radial smooth muscles and the nervous system is also observed in the radial pathways along the radial canals. All species with thick bundles of smooth radial muscles along the radial canals have clearly defined, dense neural pathways running along or even embedded within the smooth muscle bundles.
Frisoni, F.; Carrard, T.; U. Gruebler, M.; S. Hatzl, J.; Safi, K.; A. Sprenger, M.; Sumasgutner, P.; Wikelski, M.; Scacco, M.
Show abstract
Understanding how animals respond to their physical environment requires environmental observations at the scale at which behavioural decisions are made. For soaring birds, the coarse resolution of weather products has long hindered the analysis of their behavioural response to fine-scale atmospheric dynamics, forcing uplift sources to be inferred largely from behaviour itself. Here, we combined high-resolution movement data from 24 golden eagles with the kilometre-scale COSMO weather model. We first classified thermal, orographic, and gravity-wave uplifts using independent atmospheric predictors and then quantified the birds' use of each uplift type and their fine-scale behavioural responses. Eagles relied predominantly on thermals, but opportunistically adjusted their use of uplift sources seasonally. The birds' flight behaviour could not reliably indicate which uplift type was primarily used, and thus suggests that both atmospheric processes and behavioural responses are better described as continua than discrete categories. Finally, we compared vertical wind velocities derived from eagles soaring behaviour with those modelled by the COSMO weather model, showing that most of the thermals exploited by eagles remain unresolved at kilometre-scale model resolution. Our results demonstrate how high-resolution weather models provide new insights into bird movement decisions, while also highlighting the potential of soaring birds as biologically embedded atmospheric sensors that could help closing the resolution gap in atmospheric models.
Schecter, D. R.; Lee, S. S.; Vimal, T.; Lahoti, Y.; Goncalves, V. F.; Retallick-Townsley, K.; Pang, J.; Guvenek, A.; Preuss, M.; Tinker, R. J.; Morava, E.; Kozicz, T.; Hirano, M.; Ganesh, J.; Naini, A.; Liang, J.; Davis, L.
Show abstract
Mitochondrial DNA (mtDNA) is increasingly recognized as an important contributor to human disease and population variation, yet most genomic biobanks do not provide standardized mtDNA variant datasets despite abundant mitochondrial sequencing reads in existing whole exome and whole-genome sequencing data. We developed a scalable framework based on the Mitoverse mtDNA Server 2 Fusion workflow to generate harmonized, analysis-ready mtDNA resources across diverse biobank infrastructures. The framework was implemented in the Mount Sinai Million Health Discoveries Program (54,151 participants) using the native Nextflow workflow and adapted for the All of Us Research Program (197,361 participants) using a custom cloud implementation that preserved the same analytical strategy. Across 251,512 participants, the framework generated standardized mtDNA datasets containing 12.9 million variant observations suitable for downstream genomic and electronic health record linked analyses. This framework enables reproducible, population-scale mitochondrial genomics across institutional and national biobanks without requiring additional sequencing or development of new variant calling methods.
Gross, A.; Singleton, C.; Gross, S.
Show abstract
Gastroesophageal reflux disease (GERD) is a prevalent chronic disorder where dietary modifications, particularly reducing spicy foods, are a primary management strategy. Salsa, a widely consumed condiment whose spiciness comes from capsaicin, lacks standardized heat labelling, potentially leading to inconsistent capsaicin exposure for consumers. To address this, our study aimed to develop and apply an LC-MS workflow for accurate capsaicin quantification in commercially available salsas. This approach seeks to provide objective "reflux-conscious" spice classification, supporting evidence-based dietary recommendations for individuals with GERD. In the eight commercial brands we examined, we found that products labelled "mild" had significantly lower capsaicin levels as compared to "medium" or "hot", but that there was an almost 15-fold range of capsaicin within this group. Surprisingly, there was no statistical difference in capsaicin content between those groups labelled "medium" or "hot" facilitating unambiguous assignment to either category, revealing that product labelling alone is insufficient to guide consumers seeking to control capsaicin exposure in their food. The results in this study enable improved brand-specific recommendations for GERD symptom management.
Kobara, S.; Huang, M.; Ilhamsyah, R.; Struk, D.; Dimandja, J.; Hesketh, P. J.; Arrubla, D. C.; Fensore, C.; Polito, C.; Kamaleswaran, R.; Esper, A.
Show abstract
Background/ObjectivesPolydimethylsiloxane (PDMS) is a non-invasive and versatile material often used for non-invasive collection of skin-emitted volatile organic compounds (VOCs), with potential applicability in acute and pre-critical care settings. However, most existing PDMS-based methodologies rely on extensive sample preparation and environmental control, limiting their feasibility in time-sensitive clinical contexts. MethodsWe conducted a proof-of-concept pilot study in four healthy volunteers to evaluate whether a simplified skin-contact PDMS sampling procedure can capture detectable VOCs and preserve individual-level variation. PDMS strips were applied directly to the skin with minimal preparation, and collected VOCs were analyzed using gas chromatography-mass spectrometry. Donor-associated variability was assessed using Bray-Curtis dissimilarity, and variability in VOC detection was evaluated across body sites. ResultsSkin-contact PDMS sampling detected 160 VOCs across four participants. The mean within-donor Bray-Curtis dissimilarity was 0.308, compared with a mean between-donor dissimilarity of 0.347. Preliminary permutation testing showed distinguishable donor profiles (p-value = 0.004). VOC detection variability differed across body sites, with lower coefficients of variation at the forehead, neck, and wrist than at the ankle. ConclusionsUnder simplified sampling conditions, skin-contact PDMS captured individual-associated VOC profiles with lower within-donor variability than between-donor variability. These findings support the feasibility of PDMS-based skin VOC sampling in minimally controlled settings. Further validation in larger and clinically relevant cohorts is warranted to assess the utility of PDMS-sampled skin VOCs as potential biomarkers for early disease detection.