bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Deep Learning Pipeline for Morphological and Viability Assessment of 3D Cancer Cell Spheroids
Authors: Mali Ajay K. , Murugappan Sivasubramanian , Prasad Jayashree Rajesh , Tofail Syed A. M. , Thorat Nanasaheb D. 
Published: January 2025

AbstractThree-dimensional (3D) spheroid models have advanced cancer research by better mimicking the tumour microenvironment compared to traditional 2D dimensional (2D) cell cultures. However, challenges persist in high-throughput analysis of morphological characteristics and cell viability, as traditional methods like manual fluorescence analysis are labour-intensive and inconsistent. Existing AI-based approaches often address segmentation or classification in isolation, lacking an integrated workflow.We propose a scalable, two-stage deep learning pipeline to address these gaps: (1) a U-Net model for precise detection and segmentation of 3D spheroids from microscopic images, achieving 95% prediction accuracy, and (2) a CNN Regression Hybrid method for estimating live/dead cell percentages and classifying spheroids, with anR2value of 98%. This end-to-end pipeline automates cell viability quantification and generates key morphological parameters for spheroid growth kinetics.By integrating segmentation and analysis, our method addresses environmental variability and morphological characterization challenges, offering a robust tool for drug discovery, toxicity screening, and clinical research. This approach significantly improves efficiency and scalability of 3D spheroid evaluations, paving the way for advancements in cancer therapeutics.
Wing Hinge Dynamics Influence Stroke Amplitudes in Flapping Wing Insects: A Frequency Response Approach
Authors: Casey Cailin , Cote Braden , Heveran Chelsea , Jankauski Mark 
Published: January 2025

AbstractFlapping insects are thought to leverage resonance or vibration amplification to reduce the energetic costs of flight. However, precisely where resonance occurs within their flight systems remains unclear. We hypothesized that most insects flap near a resonance where elastic deformation occurs primarily within the wing hinge rather than the flexible thorax. To test this, we measured the linear frequency response relating thorax deformation to wing stroke angle in sacrificed honeybees and army cutworm moths. Using experimental data, we developed a linear model of the flight system, which we then extended to incorporate nonlinear effects associated with large wing stroke angles. Our findings revealed that both species flap below the linear resonance of the wing hinge. At large wing stroke angles, nonlinear aerodynamic damping reduces the resonant frequency, causing both species to flap above resonance. However, the wing-hinge resonant frequency varied significantly depending on whether angular position, velocity or acceleration was considered as the frequency response output. Based on these observations, we hypothesized that cutworm moths flap between angular position and velocity resonances, whereas honeybees flap at the angular velocity resonance. The collective results suggest that insects flap in proximity to a wing hinge resonance rather than a thorax resonance.
Aging directs the differential evolution of KRAS-driven lung adenocarcinoma
Authors: Lazure Felicia , Drapela Stanislav , Liu Xiaoxian , Lockhart John H. , Kashfi Hossein , Sarigul Nadir , Ilter Didem , Flores Elsa R. , Wang Xuefeng , Smalley Inna , Jaeger Alex , Yu Xiaoqing , Gomes Ana P. 
Published: January 2025

AbstractLung adenocarcinoma (LUAD), the most common histological subtype of lung cancer(1, 2), is a disease of the elderly, with an average age of diagnosis of about 70 years of age(3). Older age is associated with an increased incidence of KRAS-driven LUAD(4), a particularly deadly type of LUAD characterized by treatment resistance and relapse. Despite this, our understanding of how old age shapes KRAS-driven LUAD evolution remains incomplete. While the age-related increase in cancer risk was previously ascribed to the accumulation of mutations over time, we are now beginning to consider the role of host biology as an independent factor influencing cancer. Here, we use single-cell RNA-Sequencing of KP (KrasG12D/+; Trp53flox/flox) LUAD transplanted into young and old mice to define how old age affects LUAD evolution and map the changes that old age imposes onto LUAD’s microenvironment. Our data demonstrates that the aged lung environment steers LUAD evolution towards a primitive stem-like state that is associated with poor prognosis. We ascribe this differential evolution, at least in part, to a population of rare and highly secretory damage-associated alveolar differentiation intermediate (ADI) cells that accumulate in the aged tumor microenvironment (TME) and that dominate the niche signaling received by LUAD cells. Overall, our data puts aging center stage in coordinating LUAD evolution, highlighting the need to model LUAD in its most common context and creating a framework to tailor future cancer therapeutic strategies to the age of the patient to improve outcomes in the largest and most vulnerable LUAD patient population, the elderly.
Deep Modeling of Gain-of-Function Mutations on Androgen Receptor
Authors: You Jiaying , Foo Jane , Lallous Nada , Cherkasov Artem 
Published: January 2025

AbstractThe efficiency of Androgen Receptor (AR) pathway inhibitors for prostate cancer (PCa) is on decline due to resistance mechanisms including the occurrence of gain-of-function mutations on human androgen receptor (AR). Hence, understanding and predicting such mutations is crucial for developing effective PCa treatment strategies. Leveraging accumulated data on clinically relevant AR mutants with recent advances in deep modeling techniques, this study aims to unveil and quantify critical AR mutation-drug relationships. By incorporating molecular descriptors for drugs and mutated genes sequences, this work represented these features as single vectors and demonstrates their effectiveness in modeling AR mutant responses to conventional antiandrogens. The developed approach achieves up to 80% accuracy in predicting the gain-of-function behavior of AR mutants and therefore can potentially uncover unknown agonist/antagonist relationships among mutant-drug pairs.
Shear stress inhibits adipocyte differentiation via downregulating lncRNA MALAT1
Authors: Caron Justin , Marino Madison , Wang Bo , Wang Shue 
Published: January 2025

AbstractAdipocyte differentiation plays an important role in bone remodeling due to secretory factors that can directly modulate osteoblast and osteoclast, thus affecting overall bone mass and skeletal integrity. Excessive adipocyte differentiation within bone marrow microenvironment can lead to decreased bone mass, eventually causing osteoporosis. Mechanical microenvironment of bone marrow, including fluid shear, maintains the balance of adipocyte and osteoblast differentiation during bone remodeling. However, how mechanical cues interact with long noncoding RNA (lncRNA) and regulating adipocyte differentiation remains unexplored. In this study, we investigated the mechanosensitive role of lncRNA MALAT1 during mesenchymal stem cells (MSCs) adipocyte differentiation. By applying physiologically relevant shear stress, MSCs experienced morphological changes and adipocyte differentiation differences. Shear stress inhibits MSCs adipocyte differentiation with reduced oil-red-o-stained lipid droplets. Silencing MALATs results in reduced adipocyte differentiation. By leveraging a novel gapmer double stranded locked nuclei acid (dsLNA) nanobiosensor, we showed that shear stress inhibits MALAT1 expression with significantly reduced fluorescence intensity. Our findings suggest that shear stress influences adipocyte differentiation primarily through the downregulation of MALAT1, highlighting a significant interplay between biophysical cues and lncRNAs. This interaction is crucial for understanding the complexities of bone remodeling and the potential therapeutic targeting of lncRNAs to treat bone-related disorders.
Druggable genome CRISPRi screen in 3D hydrogels reveals regulators of cortactin-driven actin remodeling in invading glioblastoma cells
Authors: Hu Mufeng , Weldy Anna , Lovalvo Isabella , Akins Erin , Jain Saket , Chang Alexander , Sati Ankita , Lad Meeki , Lui Austin , Rajidi Akhil , Kothekar Ameya , Ding Erika , Kumar Sanjay , Aghi Manish K. 
Published: January 2025

ABSTRACTTo identify new therapeutic targets that limit glioblastoma (GBM) invasion, we applied druggable-genome CRISPR screens to patient-derived GBM cells in micro-dissectible biomimetic 3D hydrogel platforms that permit separation and independent analysis of core vs. invasive fractions. We identified 12 targets whose suppression limited invasion, of which ACP1 (LMW-PTP) and Aurora Kinase B (AURKB) were validated in neurosphere assays. Proximity labeling analysis identified cortactin as an ACP1- AURKB link, as cortactin undergoes serine phosphorylation by AURKB and tyrosine dephosphorylation by ACP1. Suppression of ACP1 or AURKB in culture andin vivoshifted the balance of cortactin phosphorylation in GBM and reduced actin polymerization and actin-cortactin co-localization. Additional biophysical analysis implicated AURKB in GBM cell adhesion and cortical stiffness, and ACP1 in resistance to mechanical stress and shape plasticity needed for 3D migration. These findings reveal a novel targetable axis that balances kinase and phosphatase activities to regulate actin polymerization during GBM invasion.
Multiple, not single, recipient muscle tendon transfers produce well-directed thumb-tip forces in lateral pinch grasp: a simulation study with application to restoration of improved grasp after tetraplegia
Authors: Garcia Oliver , Towles Joseph D 
Published: January 2025

ABSTRACTThumb tendon transfer surgical procedures in patients with cervical spinal injury engage the paralyzed flexor pollicis longus (FPL) muscle to enable lateral pinch grasp. However, functional outcomes are mixed, in part because the FPL cannot produce force at the thumb tip to promote a stable grasp. We used simulation to investigate whether a multi-site tendon transfer, targeting sets of paralyzed muscles driven by a single donor muscle, could outperform a single-site tendon transfer with the FPL alone and restore lateral pinch. We formed 36 groups of 2 muscles, 84 groups of 3 muscles, and 126 groups of 4 muscles. We used nonlinear optimization and in-situ measurements of endpoint forces in 3 lateral pinch postures. We found that 116 of the 246 muscle groups outperformed the FPL for wide and narrow lateral pinch postures and a posture in between. On average, the 116 muscle groups produced endpoint forces 8° to 40° better directed than the FPL, and groups of four muscles statistically significantly outperformed the FPL’s force production. Our findings highlight the possibility of using multi-insertion site tendon transfers to restore grasp following cervical spinal cord injury.
ResolVI - addressing noise and bias in spatial transcriptomics
Authors: Ergen Can , Yosef Nir 
Published: January 2025

AbstractTechnologies for estimating RNA expression at high throughput, in intact tissue slices, and with high spatial resolution (spatial transcriptomics; ST) shed new light on how cells communicate and tissues function. A fundamental step common to all ST protocols is quantification, namely segmenting the plane into regions, each approximating a cell, and then collating the molecules inside each region to estimate the cellular expression profile. Despite many advances in this area, a persisting problem is that of wrong assignment of molecules to cells, which limits most current applications to the level of a priori defined cell subsets and complicates the discovery of novel cell states. Here, we develop resolVI, a model that operates downstream of any segmentation algorithm to generate a probabilistic representation, correcting for misassignment of molecules, as well as for batch effects and other nuisance factors. We demonstrate that resolVI improves our ability to distinguish between cell states, to identify subtle expression changes in space, and to perform integrated analysis across datasets. ResolVI is available as open source software within scvi-tools.
Development of metagenomic methods for non-invasive health monitoring of endangered species: Unveiling hidden microbial threats in fecal samples
Authors: Sapino Román , Fernández-González Ángel , Castresana Jose 
Published: January 2025

AbstractMetagenomic analysis of feces is emerging as a powerful tool for improving the monitoring of endangered species. A critical aspect in assessing the extinction risk of a species is the analysis of the burden of parasites and pathogens that can negatively affect the health of individuals. However, the identification of pathogens in non-model species using metagenomics is a major challenge due to the lack of reference genome sequences or data limited to distantly related species. In this study, we developed a pipeline for detecting potentially pathogenic bacteria from metagenomic sequences by mapping unassembled reads to available reference genomes. The approach uses the breadth of genome coverage rather than the number of mapped reads for species identification, thereby minimizing false positives due to conserved or repetitive genomic regions. We applied this method to fresh fecal samples of the Iberian desman (Galemys pyrenaicus), a critically endangered semi-aquatic mammal. Our analysis revealed the presence of 19 potentially pathogenic bacterial species, with prevalences ranging from a single individual to 30% of the samples. We also detected some desmans with elevated or altered pathogen loads, suggesting variations in individual health status or different environmental exposures. This work represents a novel application of metagenomic methods for species-level pathogen detection in wildlife using fecal samples. Application of this method across populations and over time for endangered species may provide essential health and epidemiological information to improve conservation strategies.
AlphaCross-XL: a seamless tool for automated and proteome-scale mapping of crosslinked peptides onto three-dimensional protein structures
Authors: Shenoy Sanjyot Vinayak , Biswas Deeptarup , Mandal Kamal , Zalevsky Arthur , Kishishita Audrey , Verma Ayushi , Upadhay Ishan , He Yi , Sali Andrej , Viner Rosa , Srivastava Sanjeeva , Wiita Arun P. 
Published: January 2025

ABSTRACTCrosslinking mass spectrometry (XL-MS) is an exciting proteomics technology to capture native protein conformations in real time within biological systems. Historically, however, implementation of this technology has typically been limited to single purified recombinant proteins orin vitroassembled protein complexes. These limitations are associated with inherent challenges in XL-MS analysis, including extremely low abundance of crosslinked (XL) peptides and complex deconvolution of XL peptide-derived spectral data. However, impressive recent developments in computation and instrumentation have now made it feasible to address biological questions using proteome-wide XL-MS analysis. Although some XL mapping software tools exist, these require manual input of specific Protein Data Bank (PDB) structures at the single protein level, and do not function at the high throughput scale required to analyze datasets derived from thousands of proteins. To address this need, we therefore sought to develop a strategy enabling automated mapping of XL peptides onto the three-dimensional (3D) structures of proteins, at a proteome-wide scale. Herein we describe AlphaCross-XL, a first-in-class seamless computational tool for automated mapping of XL peptides onto the protein structures for intra-protein crosslinks and loop-links. The AlphaCross-XL software first retrieves protein structures from the AlphaFold Protein Structure Database and maps all the identified crosslinks onto the 3D structure. It also calculates the Euclidian distance between the crosslinked residues and reports the violated and satisfied crosslink distances based on a user-defined distance threshold, which is visually discriminated by color in PyMOL. Lastly, the tool also supports further validation of user-submitted protein structures, that can include any computer-predicted protein structure and experimentally derived protein structures (i.e., from PDB). AlphaCross-XL is available athttps://github.com/sanjyotshenoy/alphacross-xl.
High cholesterol increases myeloma tumour burden and promotes resistance to bortezomib
Authors: Gámez Beatriz , Whipp Danielle , Rao Srinivasa , Morris Emma V. , Park Young Eun , Kaya Zeynep , Edwards Claire M. 
Published: January 2025

ABSTRACTMultiple myeloma (MM) is an incurable hematologic cancer where malignant plasma cells accumulate in the bone marrow (BM), with disease progression highly dependent on cellular interactions. Obesity is a major risk factor for myeloma, however the underlying mechanisms are unclear. Here we used a murine myeloma model to show that a high cholesterol diet increases local and circulating levels of low density lipoprotein cholesterol (LDL), increasing bone marrow tumour burden in vivo. Exogenous LDL induced bortezomib-specific drug resistance in metabolically stressed myeloma cells in vitro and ex vivo. RNA-seq analysis revealed bortezomib-induced changes in the cholesterol biosynthesis/homeostasis pathway that were completely reverted with LDL pretreatment. In silico analysis of patient data supported a role for cholesterol in response to bortezomib-based therapies. Targeted proteome profiling revealed changes in expression of the adipokine resistin in the bone marrow of cholesterol-treated or myeloma-bearing mice, with elevated resistin expression observed in MGUS patients. Bone marrow adipocytes were found to be a major source of resistin, which was further increased in response to LDL. In summary, we demonstrate that high cholesterol promotes both myeloma development and bortezomib resistance, identifying resistin as a potential mediator so revealing new mechanisms underlying myeloma pathogenesis.
Epigenetic clocks and inflammaging: pitfalls caused by ignoring cell-type heterogeneity
Authors: Guo Xiaolong , Teschendorff Andrew E. 
Published: January 2025

AbstractEpigenetic clocks are machine learning predictors of chronological age that have consistently been shown to be also informative of biological age measures, such as all-cause mortality. A recent study has argued against the use of machine learning methods for building epigenetic clocks, on grounds that these predictors do not enrich for features that correlate with disease. In particular, it argues that standard epigenetic clocks can’t measure inflammaging, an age-related trait, proposing an ad-hoc ‘feature rectification’ strategy and an ‘inflammation clock’ that predicts age-acceleration in inflammatory diseases. Here we demonstrate that this inflammation clock only captures an increase in the neutrophil to lymphocyte ratio associated with inflammatory diseases like rheumatoid arthritis, and that it fails to capture the shift from naïve to mature lymphocytes, which is a key feature of inflammaging. As such, their clock does not measure inflammaging, and is subsumed and outperformed by an ordinary cell-type deconvolution algorithm. Our analysis underscores the critical importance for epigenetic clock and epigenome-wide association studies to always estimate cell-type fractions in the tissue of consideration, and to adjust for its variation, in order to disentangle effects due to changing cell-type composition from DNA methylation changes that happen in specific cell-types.
Mechanical efficiency during sub-maximal cycling is underestimated because negative muscular power is ignored
Authors: Vos Roeland T. , Bobbert Maarten F. , Kistemaker Dinant A. 
Published: January 2025

AbstractThein vivomechanical efficiency of muscles has often been estimated during sub-maximal cycling. In this approach, it has implicitly been assumed that the average amount of positive mechanical muscle power equals the average mechanical power output, i.e., that no power is dissipated by muscles. Here, we investigated the validity of this assumption using an optimal control musculoskeletal model. We identified optimal muscle stimulation patterns for 4 cadences (60, 80, 100 and 120RPM) and 5 levels of average mechanical power output (50, 100, 150, 200 and 250W). We found that the amount of negative mechanical muscular power was substantial, with the average across all conditions being -84,6W (56,4%). The amount of negative mechanical muscular power was found to increase with increasing cadence and was independent of the average mechanical power output. To investigate the effect of negative muscular power onin vivoestimates of the muscular efficiency, we used our simulation results to correct gross efficiencies measured during sub-maximal cycling. The resulting increases in the gross efficiency were substantial, with the average increasing from 16.9% to 27.5%. These results suggest that current estimates of the muscular efficiency during sub-maximal cycling underestimate the true muscular efficiency.
Mitochondrial ATP-Sensitive K+Channels (MitoKATP) Regulate Brown Adipocyte Differentiation and Metabolism
Authors: Pereira Osvaldo R. , Serna Julian D.C. , Caldeira da Silva Camille C. , Camara Henrique , Kodani Sean D. , Festuccia William T. , Tseng Yu-Hua , Kowaltowski Alicia J. 
Published: January 2025

AbstractBrown adipose tissue (BAT) plays a central role in mammalian non-shivering thermogenesis, dissipating mitochondrial membrane potentials through the activity of uncoupling protein UCP1 to release heat. Inner membranes of mitochondria are known to be permeable to potassium ions (K+), which enter the matrix either through ATP-sensitive channels (MitoKATP) or leakage across the bilayer driven by inner membrane potentials. Mitochondrial K+influx is associated with increased osmotic pressure, promoting water influx and increasing matrix volume. Since BAT mitochondria have lower inner membrane potentials due to uncoupling protein 1 (UCP1) activity, we hypothesized this could involve compensatory changes in MitoKATP activity, and thus tested MitoKATP involvement in brown adipocyte activities under basal and stimulated conditions. We find that cold exposure and adrenergic stimulation in mice modulate BAT MitoK levels, the channel portion of MitoKATP. Genetic ablation of the gene that codes for the pore-forming subunit of MitoKATP in human pre-adipocytes decreased cellular respiration and proliferation, compromising differentiation into mature adipocytes. In mouse cell lines, the absence of the protein limited cellular oxygen consumption in the precursor stage, but not in mature adipocytes. Interestingly, inhibition of MitoKATP in mature adipocytes increased adrenergic-stimulated oxygen consumption, indicating that shutdown of this pathway is important for full BAT thermogenesis. Similarly, MitoKATP inhibition increased oxygen consumption in BAT mitochondria isolated from mice treated with beta 3 adrenergic receptor agonist CL316,243. Overall, our results suggest that the activity of MitoKATP regulates differentiation and metabolism of brown adipocytes, impacting on thermogenesis.