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Life Sciences

185 items

  1. bioRxiv

    After a 2011 marine heatwave wiped out seagrass, Shark Bay bottlenose dolphin adult survival fell from 0.99 to 0.85 and the two gulf populations declined by 39% and 36%

    Using 20 years (2003-2023) of dolphin photo-identification data, the study fitted a Bayesian Hidden Markov Model to estimate annual, age-class-specific survival probabilities, abundance and recruitment rate for Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the western (WSB) and eastern (ESB) gulfs of Shark Bay, and related them to seagrass loss following the 2011 marine heatwave, finding adult survival fell from 0.99 (0.98-1.00) pre-MHW to 0.85 (0.79-0.90) post-MHW in WSB and from 0.96 (0.92-0.98) to 0.89 (0.85-0.
  2. Journal of Intelligent Media Computing

    Extracting heart girth and body length from 2D images with age and sex, XGBoost predicts body weight in unseen Surti goats at R²=0.7955

    This study used Mask R-CNN to segment goats from two-dimensional images and extract heart girth and body length, combined these with age and sex metadata, trained XGBoost, Random Forest and CatBoost and integrated them with weights of 0.5/0.3/0.2; on a validation set split by Animal ID (37 goats) XGBoost reached R²=0.8514 (RMSE=4.26 kg, MAE=3.47 kg, MAPE=16.27%), and on a completely unseen test set (37 goats) XGBoost performed best with R²=0.7955 (MSE=29.15 kg², RMSE=5.40 kg, MAE=4.01 kg, MAPE=16.38%) while the weighted ensemble recorded R²=0.7713 (MSE=32.60 kg², RMSE=5.71 kg, MAE=4.13 kg, MAPE=16.60%), indicating that combining visual and morphometric information under strict group-based evaluation provides reliable non-contact body weight estimation on unseen livestock.
  3. bioRxiv

    RNASeek uses a 1.6B-parameter cross-phyla transcriptomic model for RNA function prediction and GRPO-guided design, yielding ribozymes at wild-type activity and 3′ UTRs beyond the training data

    The authors present RNASeek, a 1.6-billion-parameter generative foundation model built on a DeepSeek architecture and trained on a cross-phyla transcriptomic corpus, using natural-language tokens for conditional prediction and sequence design; it captures species-specific transcript features and intron–exon boundaries in a zero-shot setting, can be fine-tuned to predict ribozyme self-cleavage activity and viral mRNA stability while revealing interpretable features such as loop flexibility, stem stability, and AU-rich motifs, and these functional predictors then serve as reward models for GRPO updates to the generation policy, producing faster-cleaving ribozymes and stability-enhancing 3′ UTRs under user-specified IUPAC constraints, with experimentally validated generated ribozymes reaching
  4. Research Square

    Transcriptomic and single-cell sequencing identify lipotoxicity-related COPD biomarkers APRT and S100A8, validated by RT-qPCR and a nomogram

    Using COPD-related datasets from a public database, this study applied differential expression analysis, machine learning, and gene expression analysis to identify APRT and S100A8 as lipotoxicity-related COPD biomarkers (APRT notably lower and S100A8 notably higher in COPD samples), supported by RT-qPCR, built and validated a nomogram for predicting COPD risk (P = 0.395 in the Hosmer-Lemeshow test), found both biomarkers co-enriched in the "focal adhesion" pathway and significantly correlated with neutrophils, predicted 27 drugs targeting APRT (such as alteplase and relaxin) and methotrexate targeting S100A8, and used scRNA-seq to identify macrophages as a key cell type in COPD with dynamic expression patterns of both biomarkers during macrophage differentiation.
  5. Frontiers in Cellular and Infection Microbiology

    Knocking out M. tuberculosis small RNAs MTS0997 and MTS1338 shortens mouse survival without changing lung bacterial burden

    The authors built unmarked single- and double-knockout Mycobacterium tuberculosis strains lacking MTS0997, MTS1338, or both, profiled whole-genome expression during culture growth, in IFN-γ-activated and non-activated murine bone marrow-derived macrophages, and in infection of highly TB-susceptible I/St mice, and found that MTS0997 deletion had the larger impact on bacterial biology (altered succinate/fumarate respiration, up-regulated ESX-1 secretion genes, increased virulence in mice, reduced lung pro-inflammatory cytokine production), that all three knockout strains killed mice significantly faster than wild type while lung CFU counts at 6 weeks did not differ, and that B-cell and MHC-II-expressing lung cell populations differed between single- and double-knockout infections, suggesting
  6. Frontiers in Immunology

    Paeonol reduced lesions in LL-37-induced rosacea-like mice, correlating with suppressed S100A9-NF-κB signaling

    Using network pharmacology to predict shared targets of paeonol and rosacea, then validating in an LL-37-induced rosacea-like BALB/c mouse model, the study found that 150 mg/kg paeonol markedly lowered redness area and score, reduced inflammatory cell and CD4+ T-cell infiltration and angiogenesis, and downregulated S100A9 and p65 phosphorylation, indicating its effects correlate with suppressed S100A9-NF-κB signaling.
  7. Nature News

    China dominates in vivo CAR-T trials while a pancreatic cancer study shows how the liver feeds metastases with serine

    Nature reports that 82% of the 140 in vivo CAR-T cell drugs being tested in animals and people are being developed by groups in China, which has become a fast mover to the clinic through investigator-initiated trials; a Nature study in the same evidence bundle shows that PHGDH-deficient pancreatic cancer cells reprogram neighbouring hepatocytes through a CXCL5–CXCR2–PI3K–AKT–FOXO3A axis, driving hepatocyte PHGDH expression and serine secretion that supports liver metastatic outgrowth.
  8. Nature News

    Transplanted hearts shift their biological age toward the host: mouse grafts and 11 human transplants show donor hearts ageing or rejuvenating

    Jesse Poganik's team at Harvard grafted hearts from young, middle-aged and old mice into mice of all three age groups and measured DNA methylation across roughly 320,000 genomic regions, finding that grafted hearts shifted their biological age toward the recipient; the same effect appeared in biopsy samples from 11 historical heart transplants at Brigham and Women's Hospital with large donor-recipient age gaps, while some functional measures such as heart rate, posterior wall thickness and exercise capacity tracked recipient age rather than donor age.
  9. bioRxiv

    Team builds a single-nucleus multi-omic atlas across 21 adult human tissues, profiling 459,856 transcriptomic and chromatin accessibility profiles and identifying 161,270 novel regulatory elements

    The study presents a single-nucleus multi-omic atlas comprising 459,856 transcriptomic and chromatin accessibility profiles from 21 adult human tissues and four donors, including paired measurements from 160,688 nuclei, resolving nine cell lineages, 61 broad cell types and 313 subclusters, identifying 1,085,062 candidate cis-regulatory elements (including 161,270 novel elements absent from ENCODE), and using the dataset to train sequence-to-function models that predict chromatin-accessibility effects for 548,656 fine-mapped variants, identifying 18,133 high-effect variants including 1,120 broadly active variants.
  10. arXiv

    On MoleculeNet BBBP (n=2039), Dynamic Random Forest with combined features reached the highest mean AUC of 0.970, while after orthogonalization no conditional LogP–BBB permeability effects remained significant

    Using the MoleculeNet BBBP dataset (n = 2039), this study systematically ablated three molecular feature families (Morgan fingerprints, RDKit physicochemical descriptors, SMILES bigrams) across four learning algorithms, finding that Dynamic Random Forest with combined features achieved the highest mean AUC (0.970, 95% CI: 0.963-0.977), and then constructed a pseudo-treatment from a LogP median split and applied double/debiased machine learning for exploratory heterogeneity estimation, showing that orthogonalization substantially attenuated the heterogeneity detected by naive causal forests, with no conditional effects remaining significant after false discovery rate correction (smallest adjusted p = 0.

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