Biology subjects

Dalman, M.

Publications and source records attributed to Dalman, M..

4 recordsLinked to original sources

bioRxiv2026

Assessing chemical toxicity across Eukaryota using multimodal transformers

Biodiversity is globally threatened by chemical pollution, yet toxicity data remain unavailable for millions of species and tens of thousands of chemicals, severely limiting our ability to assess ecological impacts. Here we present TRIDENT-2, a multimodal artificial intelligence model for predicting chemical toxicity across evolutionarily diverse eukaryotic species. Trained on 560,780 toxicity assays spanning 82,775 chemicals, 6,793 species, and multiple exposure scenarios, TRIDENT-2 accurately predicts toxicity across Eukaryota with an average median absolute error ranging from 1.76 to 3.80. By jointly learning from chemical, biological, and experimental information, it remains accurate across broad chemical and taxonomic distances, allowing for toxicity assessment for species and chemicals beyond the current experimental evidence. Our findings demonstrate that artificial intelligence can help overcome longstanding data limitations in ecotoxicology, paving the way for improved decision-making and reducing chemical impacts on biodiversity and ecosystems.

pharmacology and toxicology↗

bioRxiv2026

Spatial and functional mapping of the human pancreas reveals endocrine and exocrine cell states in health and metabolic disease

The human pancreas contains diverse endocrine and exocrine cell populations whose spatial organization is essential for tissue physiology. While single-cell and spatial transcriptomics revealed molecular heterogeneity across pancreatic cell types, linking these states to physiological activity in situ has remained challenging. Here, we combined single-nucleus RNA sequencing, spatial transcriptomics, and functional calcium imaging across pancreatic samples in health and metabolic disease. We identified heterogeneous endocrine and exocrine cell states associated with obesity and diabetes, including inflammatory remodeling of acinar and ductal populations. To directly couple tissue physiology with molecular state, we developed Slice-seq, which integrates calcium imaging with spatial transcriptomics in acute pancreatic slices. Slice-seq linked local endocrine composition and transcriptional programs with {beta} cell activity and identified extra-islet {beta} cells with reduced glucose responsiveness and mitochondrial oxidative metabolism. Together, our study provides a framework for linking pancreatic cell states to tissue organization and physiological activity in health and disease.

genomics↗

bioRxiv2017

The Nasal And Oropharyngeal Microbiomes Of Healthy Livestock Workers

Little information exists on the microbiomes of livestock workers. A cross-sectional, epidemiological study was conducted enrolling 59 participants (26 of which had livestock contact) in Iowa. Participants were enrolled in one of four ways: from an existing prospective cohort study (n=38), from the Iowa Department of Natural Resources Animal Feeding Operations database (n=17), through Iowa county fairs (n=3), and through snowball sampling (n=1). We collected two sets of swabs from the nares and oropharynx of each participant. The first set of swabs was used to assess the microbiome via 16s rRNA sequencing and the second was used to culture S. aureus. We observed livestock workers to have greater diversity in their microbiomes compared to those with no livestock contact. In the nares, there were 26 operational taxonomic units found to be different between livestock workers and non-livestock workers with the greatest difference seen with Streptococcus and Proteobacteria. In the oropharynx, livestock workers with swine exposure were more likely to carry several pathogenic organisms. The results of this study are the first to characterize the livestock worker nasal and oropharyngeal microbiomes.

epidemiology↗

bioRxiv2017

A Cross-Sectional Study Of Staphylococcus aureus Colonization And The Nasal And Oropharyngeal Microbiomes

BackgroundStaphylococcus aureus is a frequent cause of both infections globally. Colonization with the organism is known to increase the risk of developing infections and occurs in roughly one third of the general population. While many factors influence colonization, it has been demonstrated other members of the microbiome influence colonization with S. aureus. Here, we assessed the nasal and oropharyngeal microbiomes of healthy participants in relation to S. aureus colonization in a cross-sectional study using 16s rRNA sequencing of the v1-v3 region. As livestock workers have also been shown to be at an increased risk of carriage, we have also assessed microbiota differences in colonization status in a population of livestock workers.\n\nResultsIn both the nares and oropharynx, there were no microbiota differentially abundant between colonized and non-colonized persons. However, there was a significant difference in the beta diversity (Bray-Curtis distances) between carriers and non-carriers (P=0.002). When considering carriage stratified by livestock exposure, there were a number of differences. Most notably, colonized livestock workers had significantly more Porphyomonas (2-fold change = -8.54, P = 0.03) than the non-colonized livestock workers.\n\nConclusionsS. aureus is a frequent colonizer of the human upper respiratory tract, including the nares and oropharynx and causes a wide range of infections. Livestock workers are at increased risk for carriage. Interventions such as improving oral hygiene may lead to decreased S. aureus carriage by reducing other bacterial species such as Porphyomonas. Larger, longitudinal studies are needed to better explore what microorganisms may be associated with S. aureus colonization.

epidemiology↗