bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-content morphological profiling by Cell Painting in 3D spheroids
Authors: Ringers Christa , Holmberg David , Flobak Åsmund , Georgieva Polina , Jarvius Malin , Johansson Martin , Larsson Anders , Rosén Dan , Seashore–Ludlow Brinton , Visnes Torkild , Carreras Puigvert Jordi , Spjuth Ola 
Published: February 2025

AbstractCell Painting is a popular assay for morphological profiling of multi-labeled 2D monolayer cell cultures used in a wide range of applications. Culturing cells in 3D has potential for higher physiological relevance, such as when studying effects of perturbations. Robust and scalable 3D models can be challenging to characterize through imaging – particularly because light has difficulty penetrating cell multilayers. We introduce a scalable method where the Cell Painting assay is combined with tissue-clearing and applied to 3D spheroids generated in a ULA microplate format. Multi-channel images are acquired using confocal microscopy, and cells can be segmented inside those spheroids allowing for relevant morphological features to be extracted. Our end-to-end analysis pipeline comprises cell segmentation, morphological feature extraction, and between-spheroids and within-spheroid normalization. We demonstrate the method using spheroids cultured from two colorectal cancer cell lines and successfully detect distinct phenotypic changes upon compound treatments, on both spheroid-level using maximum intensity projections and on single cell-level. We show that drugs group by mechanism of action, with biologically relevant clusters especially evident with single-cell data. Finally, we contrast our method to results from 2D Cell Painting and discover a different pattern in DNA damaging drugs in HCT116 colorectal cancer cells. This work lays the foundation for multi-channel image-based screening in 3D spheroids.
Investigating the dynamics of the aquatic community in Oslofjord through time series analysis of eDNA
Authors: Mahlangu Sibusiso , Ewers Isabelle , Carvalho Cintia Oliveira , Schrøder-Nielsen Audun , Dunthorn Micah , Karlsen Hans Erik , Sørnes Grete , Chavarie Louise , Endresen Dag , Ready Jonathan Stuart , de Boer Hugo J , Mauvisseau Quentin 
Published: February 2025

AbstractUnderstanding temporal dynamics of marine communities is critical for assessing ecosystem health and guiding conservation efforts. Here, we conducted a survey using environmental DNA (eDNA) metabarcoding with two primer sets, MiFish and Elas02, to investigate seasonal and interannual changes in the fish community of Oslofjord (Norway) over two consecutive years. Using the MitoFish reference database through the GBIF querying tool, we identified 61 fish species and found significant changes in the dominant taxa between seasons and years.Clupea harengus(Atlantic herring) consistently peaked in early spring, whileScomber scombrus(Atlantic mackerel) dominated winter months in the second year. The MiFish primer set showed increased species richness in the second year, whereas the Elas02 primer set showed stable richness despite compositional turnover. Non-metric multidimensional scaling (NMDS) revealed distinct community separation between years in presence/absence data, driven by species turnover rather than abundance read changes. Our findings support the use of eDNA metabarcoding to capture fine-scale temporal dynamics and emphasise the importance of multi-year datasets for distinguishing ecological trends from stochastic changes. This strategy improves monitoring practices for marine ecosystems under anthropogenic stressors.
The G-protein coupled receptor OXER1 is a tissue redox sensor essential for intestinal epithelial barrier integrity
Authors: Lengyel Miklos , Ma Yanan , Gelashvili Zaza , Peng Siyang , Quraishi Meysoon , Niethammer Philipp 
Published: February 2025

AbstractGeneration of reactive oxygen species is an important part of the innate immune response. Generating microbicidal levels of reactive oxygen species (ROS) requires adaptation of mucosal barriers. High tolerance of ROS provides improved innate immune defenses against pathogens, whereas low tolerance renders host cells prone to chronic toxicity and mutagenesis, which can promote inflammation (e.g., in asthma and Crohn’s disease) and cancerogenesis. The mechanisms that sense and mediate host tolerance to ROS are little understood. In this study, we discover an unexpected role for the redox-sensitive, chemokine-like lipid 5-oxo-eicosatetraenoic acid (5-KETE) in redox adaptation. 5-KETE is known to attract leukocytes to damaged/infected mucosal barriers by signaling through its receptor, OXER1. Suggestive of a distinct non-immune function, we here report that the loss of the OXER1 ortholog Hcar1-4 causes barrier defects and baseline inflammation in the intestine of live zebrafish larvae. In zebrafish and cultured human cells, OXER1 signaling protects against oxidative nucleotide lesions by inducing DNA-protective Nudix hydrolases. Our data reveal the oxoeicosanoid pathway as a conserved ROS resilience mechanism that fortifies pathogen-exposed mucosal linings against increased oxidative stressin vivo.
scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics
Authors: Wang Chloe , Cui Haotian , Zhang Andrew , Xie Ronald , Goodarzi Hani , Wang Bo 
Published: February 2025

AbstractSpatial transcriptomics has emerged as a pivotal technology for profiling gene expression of cells within their spatial context. The rapid growth of publicly available spatial data presents an opportunity to further our understanding of microenvironments that drive cell fate decisions and disease progression. However, existing foundation models, largely pretrained on single-cell RNA sequencing (scRNA-seq) data, fail to resolve the spatial relationships among samples or capture the unique distributions from various sequencing protocols. We introducescGPT-spatial, a specialized foundation model for spatial transcriptomics continually pretrained on our previously published scGPT scRNA-seq foundation model. We also curate SpatialHuman30M, a comprehensive spatial transcriptomics dataset comprising of 30 million spatial transcriptomic profiles, encompassing both imaging- and sequencing-based protocols. To facilitate integration, scGPT-spatial introduces a novel MoE (Mixture of Experts) decoder that adaptively routes samples for protocol-aware decoding of gene expression profiles. Moreover, scGPT-spatial employs a spatially-aware sampling strategy and a novel neighborhood-based training objective to better capture spatial co-localization patterns among cell states within tissue. Empirical evaluations demonstrate that scGPT-spatial robustly integrates spatial data in mulit-slide and multi-modal settings, and effectively supports cell-type deconvolution and contextualized missing gene expression imputation, outperforming many existing methods. The scGPT-spatial codebase is publicly available athttps://github.com/bowang-lab/scGPT-spatial.
Chromosome-level genome assembly ofProtandrena(Anthemurgus)passiflorae(Hymenoptera: Andrenidae), a host-plant specialist bee
Authors: Parys Katherine A. , Schweizer Rena M. , Benavides Ligia , Geib Scott , Sim Sheina , Evans Jay D. , Branstetter Michael G. 
Published: February 2025

AbstractThe passion flower bee,Protandrena(Anthemurgus)passiflorae(Robertson) is a monolectic, host-plant specialist of the passionflower plantPassiflora luteaL. Using a single adult male individual, we generated long-read PacBio HiFi, HiC, and short-read RNA sequencing data to build a well-annotated, chromosome-level genome assembly for this species. The final nuclear genome is 249 Mb with 150x coverage and with most of the genome scaffolding into 12 chromosomes. The scaffold N50 is 21.4 Mb and the genome has a Benchmarking Universal Single-Copy Ortholog (BUSCO) score of 97.2% for 5991 hymenopteran genes. BRAKER3 annotation of the genome identified 12,098 genes and 15,353 total transcripts and found that 20.27% of the genome is made up of repetitive elements. We resolved a mitochondrial genome of 12.7 kb. TheP. passifloraegenome represents one of only a few published andrenid bee genomes and one of the first monolectic bees. This new high-quality genome will serve as a valuable resource for investigating the genomic basis of specialization and for providing a useful resource for studying pollinator health and conservation.
DHRS7 Integrates NADP+/NADPH Redox Sensing with Inflammatory Lipid Signalling via the Oxoeicosanoid Pathway
Authors: Ma Yanan , Hui King Lam , Ambaw Yohannes A. , Walther Tobias C. , Farese Robert V. , Lengyel Miklos , Gelashvili Zaza , Lu Dajun , Niethammer Philipp 
Published: February 2025

AbstractDuring the innate immune response at epithelial wound sites, oxidative stress acts microbicidal and—mechanistically less well understood—as an immune and resilience signal. The reversible sulfhydryl (SH) oxidation of kinases, phosphatases, and transcription factors constitute the perhaps best-known redox signalling paradigm, whereas mechanisms that transduce metabolic redox cues, such as redox cofactor balance, remain little explored.Here, using mammalian cells, microsomes, and live zebrafish, we identify DHRS7, a short-chain fatty acid dehydrogenase/reductase (SDR), as conserved, 5-hydroxyeicosanoid dehydrogenase (5-HEDH). Under oxidative stress, DHRS7 consumes NADP+to convert arachidonic acid (AA)-derived 5(S)-HETE into the inflammatory lipid 5-KETE, which activates leukocyte chemotaxis via the OXER1 receptor. While Dhrs7 acts as a NADPH-dependent 5-KETE sink in unstressed, healthy tissue, it promotes rapid, 5-KETE dependent leukocytic inflammation in wounded zebrafish skin.Thus, DHRS7 epitomizes an underappreciated mode of redox signalling—beyond classic SH oxidation—that leverages NADPH metabolism to generate or quench a paracrine lipid signal. Metabolic redox sensors like DHRS7 might be promising therapeutic targets in diseases characterized by disturbed redox balance.
Proteoform identification using multiplexed top-down mass spectra
Authors: Wang Zhige , Xiong Xingzhao , Liu Xiaowen 
Published: February 2025

AbstractTop-down mass spectrometry (TDMS) is the method of choice for analyzing intact proteoforms, as well as their post-translational modifications and sequence variations. In TDMS experiments, multiple proteoforms are often co-fragmented in tandem mass spectrometry (MS/MS) analysis, resulting in multiplexed TD-MS/MS spectra. Since multiplexed TD-MS/MS spectra are more complex than common spectra generated from single proteoforms, these spectra pose a significant challenge for proteoform identification and quantification. Here we present TopMPI, a new computational tool specifically designed for the identification of multiplexed TD-MS/MS spectra. Experimental results demonstrate that TopMPI significantly increases proteoform identifications and reduces identification errors in multiplexed TD-MS/MS spectral analysis compared to existing tools.
Skin microbiomes of frogs vary among individuals and body regions, revealing differences that reflect known patterns of chytrid infection
Authors: Ghose Sonia L. , Eisen Jonathan A. 
Published: February 2025

AbstractThe amphibian skin microbiome is an important line of defense against pathogens including the deadly chytrid fungus,Batrachochytrium dendrobatidis(Bd). Intra-species variation in disease susceptibility and intra-individual variation in infection distribution across the skin, therefore, may relate to differences in skin microbiomes. However, characterization of microbiome variation within and among amphibian individuals is needed. We utilized 16S rRNA gene amplicon sequencing to compare microbiomes of ten body regions from nine captiveR. sierraeindividuals and their tank environments. While frogs harbored distinct microbial communities compared to their tank environments, tank identity was associated with more variation in frog microbiomes than individual frog identity. Within individuals, we detected differences between microbiomes of body regions whereBdinfection would be expected compared to regions that infrequently experience infection. Notably, the bacterial families Burkholderiaceae (phylum Proteobacteria) and Rubritaleaceae (phylum Verrucomicrobia) were dominant on frog skin, and the relative abundances of undescribed members of these families were important to describing differences among and within individuals. Two undescribed Burkholderiaceae taxa were found to be putativelyBd-inhibitory, and both showed higher relative abundance on body regions whereBdinfection is often localized. These findings highlight the importance of considering intrapopulation and intraindividual heterogeneities, which could provide insights relevant to predicting localized interactions with pathogens.
Φ-Space ST: a platform-agnostic method to identify cell states in spatial transcriptomics studies
Authors: Mao Jiadong , Choi Jarny , Lê Cao Kim-Anh 
Published: February 2025

AbstractWe introduce Φ-Space ST, a platform-agnostic method to identify continuous cell states in spatial transcriptomics (ST) data using multiple scRNA-seq references. For ST with supercellular resolution, Φ-Space ST achieves interpretable cell type deconvolution with significantly faster computation. For subcellular resolution, Φ-Space ST annotates cell states without cell segmentation, leading to highly insightful spatial niche identification. Φ-Space ST harmonises annotations derived from multiple scRNA-seq references, and provides interpretable characterisations of disease cell states by leveraging healthy references. We validate Φ-Space ST in three case studies involving CosMx, Visium and Stereo-seq platforms for various cancer tissues. Our method revealed niche-specific enriched cell types and distinct cell type co-presence patterns that distinguish tumour from non-tumour tissue regions. These findings highlight the potential of Φ-Space ST as a robust and scalable tool for ST data analysis for understanding complex tissues and pathologies.
Draft Genome of the Endangered Visayan Spotted Deer (Rusa alfredi), a Philippine Endemic Species
Authors: Javier Ma. Carmel F. , Noblezada Albert C. , Sienes Persie Mark Q. , Guino-o Robert S. , Palomar-Abesamis Nadia , Malay Maria Celia D. , del Castillo Carmelo S. , Ferriols Victor Marco Emmanuel N. 
Published: February 2025

ABSTRACTThe Visayan Spotted Deer (Rusa alfredi) is an endangered and endemic species in the Philippines facing significant threats from habitat loss and hunting. It is considered as the world’s most threatened deer species by the International Union for Conservation of Nature (IUCN) thus its conservation has been a top priority. Despite its status, there is a notable lack of genomic information available forR. alfrediand the genusRusain general. This study presents the first draft genome assembly of the Visayan Spotted Deer (VSD),Rusa alfredi, using Illumina short-read sequencing technology. The RusAlf_1.1 assembly has a 2.52 Gb total length with a contig N50 of 46 Kb and scaffold N50 size of 75 Mb. The assembly has a BUSCO complete score of 95.5%, demonstrating the genome’s completeness, and includes the annotation of 24,531 genes. Phylogenetic analysis based on single-copy orthologs reveals a close evolutionary relationship between theR. alfrediand the genusCervus. The availability of the RusAlf_1.1 genome assembly represents a significant advancement in our understanding of the VSD. It opens opportunities for further research in population genetics and evolutionary biology, which could contribute to more effective conservation and management strategies for this endangered species. This genomic resource can help in assuring the survival ofRusa alfrediin the country.
Phosphatidylinositol (4,5)-bisphosphate Impacts Ectosome Shedding fromC. elegansCiliated Sensory Neurons
Authors: Elsayyid Malek , Semmel Alexis E. , Prova Nahin Siara , Parekh Krisha D. , Tanis Jessica E. 
Published: February 2025

AbstractSmall secreted extracellular vesicles (EVs) mediate the intercellular transport of bioactive macromolecules during physiological processes and propagation of pathological conditions. The primary cilium, a sensory organelle protruding from most non-dividing cells, transmits signals by shedding EVs called ectosomes. Although the ciliary membrane is continuous with the plasma membrane, it exhibits unique phospholipid distribution, with levels of phosphatidylinositol 4,5-bisphosphate PI(4,5)P2high in the periciliary membrane compartment (PCMC), but low in the cilium proper and distal tip. The functional impact of PI(4,5)P2on ectosome biogenesis is not known. InC. eleganssensory neurons, different populations of ectosomes are shed from the PCMC and cilium distal tip. We used a genetic approach to increase PI(4,5)P2in the PCMC by overexpressing the type I phosphatidylinositol 4-phosphate 5-kinase (PIP5K1) PPK-1 or in the cilium proper through deletion of the phosphoinositide 5-phosphatase (INPP5E)inpp-1, then imaged released EVs that carried different fluorescently-tagged cargos. We discovered that high PI(4,5)P2differentially affected shedding of distinct ectosome populations from ciliary subcompartments, decreasing biogenesis of EVs from the PCMC, but increasing budding from the cilium distal tip. While manipulating PI(4,5)P2also impacted the trafficking, localization, and abundance of EV cargos in the cilium, localization of these proteins to distinct subsets of ectosome was unchanged, suggesting that PI(4,5)P2does not impact cargo sorting. Further, the PI(4,5)P2-dependent increase in ectosome shedding from the distal tip did not alter cilium length. Thus, altering PI(4,5)P2serves as a mechanism to specifically regulate biogenesis of ectosomes shed in response to physiological stimulus.SignificanceThe membrane lipid phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2) plays a critical role in many cellular processes including endocytosis, protein trafficking, cytoskeletal dynamics, ion channel activity, and cell polarity. Here we used a genetic approach to manipulate PI(4,5)P2levels in the primary cilium, a specialized sensory organelle that serves as a platform not only for organizing signal transduction, but also signal transmission via shedding of a class of extracellular vesicles, termed ectosomes. We discovered that high PI(4,5)P2differentially impacted shedding of two distinct EV subpopulations, decreasing biogenesis of ectosomes derived from the periciliary membrane compartment, but increasing budding from the cilium distal tip. This work defines a new role for PI(4,5)P2in the regulation of ectosome biogenesis and ciliary biology.
Checkerboard synergistic data analysis using a Hill function-based approach
Authors: Gutheil William G. 
Published: February 2025

ABSTRACTThis study presents a checkerboard data analysis approach using a Hill function (y = 1/(1+(x/K)n) to fit each column and row of checkerboard assay data. Column fits give a K (MIC) value in units of row concentration for each column antibiotic concentration (MIC_row vs [Col]), and row fits give an MIC_col value for each row antibiotic (MIC_row vs [Row]). Since the corresponding row and column concentrations are themselves MICs, this provides two sets of MIC vs MIC data pairs which can be plotted together as an isobologram. These MIC_A vs MIC_B values can be subjected to a second round of Hill function fitting, separately in x-y and y-x directions. Finally, a fit based on overlapping Hill functions is developed that allows x-y and y-x dimension fits to be performed simultaneously. Formula for fractional inhibitory concentrations (FICIs) as a function of fit parameters, and other features of these curves, are derived. This analysis also provides “n” (steepness) values from column and row fits, which are themselves dependent on the other antibiotic concentration and can be exceptionally, as in the case of ceftobiprole alone (n>10). This synergistic checkerboard analysis approach is implemented in MATLAB, which performs the fits and provides statistics variable values and alternative models significance.
Dissecting dynamic gene regulatory network using transformer-based temporal causality analysis
Authors: Peng Rui , Qi Juntian , Lu Yuxing , Wu Wei , Sun Qichen , Zhang Chi , Chen Yihan , Wang Jinzhuo 
Published: February 2025

AbstractGene regulatory networks (GRNs) dynamically regulate gene activation and repression, driving cellular differentiation. Despite advancements in GRN inference, challenges remain in capturing differentiation dynamics and causal inference. To address these limitations, we developed TRIGON, a Transformer-based model that infers dynamic GRN through learning temporal causality among genes. TRIGON achieved state-of-the-art performance, improving accuracy by 204% over the latest methods across four developmental datasets. When applied to well-established paradigms, including mouse embryonic stem cell and hematopoietic stem cell differentiation, TRIGON identified key transcription factors (TFs) that were not detectable by differential expression analysis and revealed potential TFs associated with primitive endoderm differentiation. Furthermore, TRIGON constructed dynamic GRN across varying time resolutions, enabling the analysis of GRN dynamics from diverse time scales. Through in silico perturbation, TRIGON accurately recapitulated cell fate changes following Gata1 and Spi1 knockout and accurately predicted gene expression changes.