bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microfiber-Templated Porogel Bioinks Enable Tubular Interfaces and Microvascularization Down to the Building Blocks for 3D Bioprinting
Authors: Guo Yuzhi , Wang Ziyu , Zhang Xuening , Li Jinghang , Ouyang Liliang 
Published: December 2024

AbstractVascularization is key to the biofabrication of large-scale tissues. Despite the progress, there remain some outstanding challenges, such as limited vessel density, difficulty in fabricating microvasculatures, and inhomogeneity of post-seeding cells. Here, we introduce a new form of bioink called microfiber-templated porogel (μFTP) bioink to engineer vasculatures down to the filament building blocks of 3D bioprinted hydrogels. The cell-laden sacrificial microfibers (diameter ranges from 50-150 μm) are embedded in the bioink to template tubular voids and deliver endothelial cells forin-situendothelialization. The inclusion of softening hydrogel microfibers retains the desirable rheological properties of the bioink for extrusion-based bioprinting. Such bioinks can be printed into a well-defined 3D structure with tunable tubular porosities up to 55%. Compared to the conventional bulk bioink counterpart, the μFTP bioink supports the significant growth and spread of endothelial cells either embedded in the matrix or sacrificial fibers, free of the post-cell seeding procedure. Furthermore, the bioprinted scaffolds based on μFTP bioink are seen to significantly promote the in-growth of blood vessels and native tissuesin vivo. The μFTP bioink approach enables the engineering of tubular bio-interfaces within the building blocks and contributes to thein-situendothelialization of microvasculatures, providing a versatile tool for the construction of customized vascularized tissue models.
Microvascular preservation and cardiomyocyte hyperplasia underlie adaptive right ventricular development in congenital heart disease-associated pulmonary arterial hypertension
Authors: Smith Michael A. , Guardado Eleana Stephanie , Boehme Jason , Datar Sanjeev A. , Maltepe Emin , Swami Naveen , Raff Gary W. , Bodansky Aaron , Moreno Joseph , Prince Annelise , Powers Nevan , Huang Guo N. , de Jesus Perez Vinicio , Fineman Jeffrey R. 
Published: December 2024

AbstractBackgroundRight ventricular (RV) failure is the primary cause of death among patients with pulmonary arterial hypertension (PAH). Patients with congenital heart disease- associated PAH (CHD-PAH) demonstrate improved outcomes compared to patients with other forms of PAH, which is related to the maintenance of an adaptively hypertrophied RV. In an ovine model of CHD-PAH, we aimed to elucidate the cellular, microvascular, and transcriptional adaptations to congenital pressure overload that support RV function in CHD-PAH.MethodsFetal surgery was performed on late gestation lambs to insert a large aortopulmonary graft, leading to a persistent congenital left-right shunt and RV pressure load. At 3 days and 4-6 weeks of life, shunt RV microvasculature, cardiomyocyte structure, and myocardial growth mechanisms were compared to age-matched controls and unoperated fetal RV. RNA sequencing was performed to assess differences in the RV transcriptomes.ResultsAt 4-6 weeks of age, shunt lambs demonstrate significant RV enlargement (shunt 37.1 ± 2.9g vs control 15.9 ± 1.0g, p<0.001) but maintain stable microvascular density (fetal 3.0 ± 0.6 vs shunt 2.9 ± 0.3 vs control 3.1 ± 0.6 capillaries per 1000 µm3, p>0.05). Shunt RV cardiomyocytes are significantly smaller by cross-sectional area and more numerous than age-matched controls (shunt 73.3 ± 5.5 µm2vs control 99.2 ± 4.9 µm2, p=0.013). At 3 days, shunt RV cardiomyocytes show evidence of increased proliferative capacity and ongoing hyperplasia compared to controls. RNA sequencing analyses reveal a distinct gene expression profile in shunt RV consistent with a delay in terminal differentiation and metabolic adaptations to support adaptive function.ConclusionsThis study provides novel insights into the development of adaptive RV hypertrophy in CHD-PAH, demonstrating roles for preserved microvascular density and increased postnatal cardiomyocyte hyperplasia in supporting RV performance. Future investigations into the mechanisms underlying these changes could have significant implications for the development of novel therapeutic strategies for supporting RV function.
Essential strategies for the detection of constitutive and ligand-dependent Gi-directed activity of 7TM receptors using bioluminescence resonance energy transfer
Authors: Endzhievskaya Sofia , Chahal Kirti , Resnick Julie , Khare Ekta , Roy Suchismita , Handel Tracy M. , Kufareva Irina 
Published: December 2024

AbstractThe constitutive (ligand-independent) signaling of G protein-coupled receptors (GPCRs) is being increasingly appreciated as an integral aspect of their function; however, it can be technically hard to detect for poorly characterized, e.g. orphan, receptors of the cAMP-inhibitory Gi-coupled (GiPCR) family. In this study, we delineate the optimal strategies for the detection of such activity across several GiPCRs in two cell lines. As our study examples, we chose two canonical GiPCRs - the constitutively active Smoothened and the ligand-activated CXCR4,-and one atypical GPCRs, the chemokine receptor ACKR3. We verified the applicability of three Bioluminescence Resonance Energy Transfer (BRET)-based assays - one measuring changes in intracellular cAMP, another in Gβγ/GRK3ct association and third in Gαi-Gβγ dissociation, - for assessing both constitutive and ligand-modulated activity of these receptors. We also revealed the possible caveats and sources of false positives, and proposed optimization strategies. All three types of assays confirmed the ligand-dependent activity of CXCR4, the controversial G protein incompetence of ACKR3, the constitutive Gi-directed activity of SMO, and its modulation by PTCH1. We also demonstrated that PTCH1 promotes SMO localization to the cell surface, thus enhancing its responsiveness not only to agonists but also to antagonists, which is a novel mechanism of regulation of a Class F GiPCR Smoothened.
Regulation of B cell migration to the Bursa of Fabricius by CCR7 and cell adhesion molecules in chicken embryonic development
Authors: Brunner Milena , Cavaleiro Catarina L. C. T. , Berghof Tom V. L. , Wurmser Christine , Elleder Daniel , von Heyl Theresa , Schusser Benjamin 
Published: December 2024

AbstractThe development of functional B lymphocytes during chicken embryogenesis relies on a series of tightly regulated processes. Precursor B cells migrate from the spleen via the blood to the bursa of Fabricius, where they colonize the bursal follicles to undergo further maturation and differentiation. To better understand the molecular mechanisms underlying early B cell migration in the chicken embryo, transcriptome analysis of B cells isolated from the spleen, blood, and bursa at embryonic days (ED) 12, ED14, and ED16 was performed. These findings suggest that sphingosine-1-phosphate (S1P) and its receptors regulate B cell presence in the bloodstream, while CCR7 and CXCR4 guide B cells to the bursa. Additionally, integrins and cell adhesion molecules, such as PECAM1, appear to facilitate transendothelial migration into the bursal mesenchyme. This study highlights a coordinated interplay between chemokines, integrins and cell adhesion molecules involved in B cell recruitment and colonization of the bursa microenvironment. These findings enhance our understanding of early B cell migration and shed light on the mechanisms governing B cell trafficking during chicken embryonic development.
Modeling and predicting single-cell multi-gene perturbation responses with scLAMBDA
Authors: Wang Gefei , Liu Tianyu , Zhao Jia , Cheng Youshu , Zhao Hongyu 
Published: December 2024

AbstractUnderstanding cellular responses to genetic perturbations is essential for understanding gene regulation and phenotype formation. While high-throughput single-cell RNA-sequencing has facilitated detailed profiling of heterogeneous transcriptional responses to perturbations at the single-cell level, there remains a pressing need for computational models that can decode the mechanisms driving these responses and accurately predict outcomes to prioritize target genes for experimental design. Here, we present scLAMBDA, a deep generative learning framework designed to model and predict single-cell transcriptional responses to genetic perturbations, including single-gene and combinatorial multi-gene perturbations. By leveraging gene embeddings derived from large language models, scLAMBDA effectively integrates prior biological knowledge and disentangles basal cell states from perturbation-specific salient representations. Through comprehensive evaluations on multiple single-cell CRISPR Perturb-seq datasets, scLAMBDA consistently outperformed state-of-the-art methods in predicting perturbation outcomes, achieving higher prediction accuracy. Notably, scLAMBDA demonstrated robust generalization to unseen target genes and perturbations, and its predictions captured both average expression changes and the heterogeneity of single-cell responses. Furthermore, its predictions enable diverse downstream analyses, including the identification of differentially expressed genes and the exploration of genetic interactions, demonstrating its utility and versatility.
SpatioMark: Quantifying the impact of spatial proximity on cell phenotype
Authors: Iyengar Sourish S , Qin Alex R , Robertson Nicholas , Harman Andrew N , Patrick Ellis 
Published: December 2024

AbstractAs research advances in spatially resolving the biological archetype of various diseases, technologies that capture the spatial relationships between cells are demonstrating increasing value. Whilst there are an increasing number of analytical methods being developed to identify the complex web of interactions between cells, the downstream impacts of these cell-cell relationships are under explored. Here, we present SpatioMark, a statistical framework that simplifies the assessment of gene or protein expression in relation to the spatial proximity of different cell types. We demonstrate its performance across spatial proteomics and transcriptomics datasets and link identified relationships with differences in patient survival. We highlight key challenges in identifying changes in molecular markers associated with the localisation of cells and propose corrections which reduce artefact induced relationships. SpatioMark is implemented in the Statial R package hosted on the Bioconductor Project, ensuring interoperability with existing spatial analysis tools. Ultimately, this work highlights strategies for identifying and interpreting changes in cell phenotype associated with cellular relationships in spatial omics data, with broad applicability across various multiplexed imaging platforms.
Transcriptomic Landscape and Immune Microenvironment Around Wound Bed Define Regenerative versus Non-regenerative Outcomes in Mouse Digit Amputation
Authors: Prabahar Archana , Chamberlain Connie S. , Vanderby Ray , Murphy William L. , Dangelo William , Mangesh Kulkarni , Brown Bryan , Mazumder Barsanjit , Badylak Stephen , Jiang Peng 
Published: December 2024

AbstractIn the mouse distal terminal phalanx (P3), it remains unclear why amputation at less than 33% of the digit results in regeneration, while amputation exceeding 67% leads to non-regeneration. Unraveling the molecular mechanisms underlying this disparity could provide crucial insights for regenerative medicine. In this study, we aim to investigate the tissues within the wound bed to understand the tissue microenvironment associated with regenerative versus non-regenerative outcomes. We employed a P3-specific amputation model in mice, integrated with time-series RNA-seq and a macrophage assay challenged with pro- and anti-inflammatory cytokines, to explore these mechanisms. Our findings revealed that non-regenerative digits exhibit a greater intense early transcriptional response in the wound bed compared to regenerative ones. Furthermore, early macrophage phenotypes differ distinctly between regenerative and non-regenerative outcomes. Regenerative digits also display unique co-expression modules related to Bone Morphogenetic Protein 2 (BMP2). The differentially expressed genes (DEGs) between regenerative and non-regenerative digits are enriched in targets of several transcription factors, such as HOXA11 and HOXD11 from the HOX gene family, showing a time-dependent pattern of enrichment. These transcription factors, known for their roles in bone regeneration, skeletal patterning, osteoblast activity, fracture healing, angiogenesis, and key signaling pathways, may act as master regulators of the regenerative gene signatures. Additionally, we developed a deep learning AI model capable of predicting post-amputation time and level from RNA-seq data, with potential applications in personalized treatment strategies and assessing the impact of interventions on regenerative outcomes.
Motivators and Barriers to Mouthguard Compliance by Adult Gaelic Football Athletes
Authors: Burke Aoife , O’Connor Niall , Duffy Niall , Holohan Katie , Whyte Enda F , O’Connor Siobhán 
Published: December 2024

AbstractIntroductionDental injuries contribute to 57% of reported maxillofacial injuries in Gaelic Football, with associated psychological and economic impacts on the affected athletes. Mouthguards have been developed in efforts to mitigate the incidence and severity of dental injuries, and use is mandatory in Gaelic Football. Dental claims have reduced by over 50% since mouthguards became mandatory, but costs of dental injuries are still prevalent. The aim of this study was to determine the mouthguard compliance rates in adult Gaelic Football players, as well as the motivations and barriers to compliance.MethodsThis cross-sectional study utilised an online survey to determine the self-reported compliance of adult Gaelic Footballers with mouthguard use, the perceived peer compliance, and the motivations and barriers to compliance. Chi-square tests were used to examine differences between sex and between elite and sub-elite players.ResultsA total of 545 Gaelic Footballers completed the survey. During training, 22% of players reported to always wear a mouthguard, with 48% never wearing it, and 30% occasionally wearing it. For games, 48% of players reported to wear a mouthguard, with 11% never wearing it and 41% occasionally wearing it. Motivating factors included teeth protection, gum protection and the rules of the game. The main barriers were discomfort, difficulty breathing and difficulty speaking. Females had significantly poorer compliance in training, but had significantly better compliance in games when compared to males.ConclusionMouthguard compliance is relatively poor amongst adult Gaelic Football players. Although compliance improves for games compared to training, there are still 1 in 2 players not wearing a mouthguard for games. Discomfort and challenges with breathing and speaking suggest that players may benefit from having a custom-fit mouthguard. Coaches, refereeing officials and governing bodies should strive to implement the rules more often and improve education around the benefits of mouthguard use within the sport.
Associations Between Menstrual Cycle Phases and Heart Rate, Well-Being, and Perceived Exertion in Female Football Players
Authors: Lipková Lucie , Beníčková Michaela , Wagner Adam , Kumstát Michal 
Published: December 2024

AbstractThis study aimed to investigate potential associations between menstrual cycle (MC) phases and heart rate (HR), perceived exertion (RPE), and subjective well-being in female football players. Data were collected from 11 players (aged 17–29 years) across 10 competitive matches. HR metrics, subjective well-being, and RPE were monitored in the pre-match, during-match, and post-match periods, as was the menstrual cycle in detail. Key findings revealed that during the early luteal (EL) phase, players spent significantly more time in moderate-intensity HR zones (Zone 4) in both the first (p = 0.046) and second halves (p = 0.051), while spending less time in high-intensity zones (Zone 5) during the first half (p = 0.012). Subjective measures highlighted elevated energy levels in the EL phase compared to the late luteal phase (p = 0.001), underscoring the influence of different menstrual cycle phases on well-being. However, RPE and maximum HR were predominantly shaped by external factors such as opponent strength (p < 0.001) and match outcome (p = 0.035). These results underscore the importance of exploring individual and contextual factors in understanding performance and well-being in female football players.
High resolution kinematic approach for quantifying impaired mobility of dystrophic zebrafish larvae
Authors: Widrick Jeffrey J. , Lambert Matthias R. , de Souza Leite Felipe , Jung Youngsook Lucy , Park Junseok , Conner James R. , Lee Eunjung Alice , Beggs Alan H. , Kunkel Louis M. 
Published: December 2024

AbstractDystrophin-deficient zebrafish larvae are a small, genetically tractable vertebrate model of Duchenne muscular dystrophy well suited for early stage therapeutic development. However, current approaches for evaluating their impaired mobility, a physiologically relevant therapeutic target, are characterized by low resolution and high variability. To address this, we used high speed videography and deep learning-based markerless motion capture to develop linked-segment models of larval escape response (ER) swimming. Kinematic models provided repeatable, high precision estimates of larval ER performance. Effect sizes for ER peak instantaneous acceleration and speed, final displacement, and ER distance were 2 to 3.5 standard deviations less for dystrophin-deficient mutants vs. wild-types. Further analysis revealed that mutants swam slower because of a reduction in their tail stroke frequency with little change in tail stroke amplitude. Kinematic variables were highly predictive of the dystrophic phenotype with ≤ 3% of larvae misclassified by random forest and support vector machine models. Tail kinematics also performed as well asin vitroassessments of tail muscle contractility in classifying larvae as mutants or wild-type, suggesting that ER kinematics could serve as a non-lethal proxy for direct measurements of muscle function. In summary, ER kinematics can be used as precise, physiologically relevant, non-lethal biomarkers of the dystrophic phenotype. The open-source approach described here may have applications not only for studies of skeletal muscle disease but for other disciplines that use larval mobility as an experimental outcome.
Gaze Following in Pigeons Increases with the Number of Demonstrators
Authors: Delacoux Mathilde , Itahara Akihiro , Kano Fumihiro 
Published: December 2024

AbstractGaze following, orienting one’s gaze in the same direction as another individual, is widespread across species and well-studied in terms of cognitive mechanisms. However, the role of collective context on this behavior is less understood. This study tested whether the number of conspecifics looking in a particular direction facilitates gaze following in pigeons (Columba livia). We presented attention-getting stimuli to subsets of pigeons (demonstrators), while other pigeons (observers) could not see the stimuli directly. We used a motion-capture system to track fine-scale movements of head and body orientations. Observer pigeons followed the gaze of demonstrators, specifically toward the target object rather than a perceptually similar distractor. Critically, the likelihood and frequency of gaze following increased with the number of demonstrators looking at the target. We observed no nonlinear effects, such as saturation or quorum thresholds, in this increasing trend, at least under our experimental conditions. In group-living species like pigeons, multiple individuals looking in the same direction may serve as a more reliable social signal. To our knowledge, this is the first study to demonstrate that the number of demonstrators influences gaze following in non- human animals, highlighting the critical role of collective context in animal social cognition.
deepBlastoid: A Deep Learning-Based High-Throughput Classifier for Human Blastoids Using Brightfield Images with Confidence Assessment
Authors: Fan Zejun , Li Zhenyu , Jin Yiqing , Chandrasekaran Arun Pandian , Shakir Ismail M. , Zhang Yingzi , Siddique Aisha , Wang Mengge , Zhou Xuan , Tian Yeteng , Wonka Peter , Li Mo 
Published: December 2024

AbstractRecent advances in human blastoids have opened new avenues for modeling early human development and implantation. Human blastoids can be generated in large numbers, making them suitable for high-throughput screening, which often involves analyzing vast numbers of images. However, automated methods for evaluating and characterizing blastoid morphology are still underdeveloped. We developed a deep-learning model capable of recognizing and classifying blastoid brightfield images into five distinct quality categories. The model processes 53.2 images per second with an average accuracy of 87%, without signs of overfitting or batch eHects. By integrating a Confidence Rate (CR) metric, the accuracy was further improved to 97%, with low-CR images flagged for human review. In a comparison with human experts, the model matched their accuracy while significantly outperforming them in throughput. We demonstrate the value of the model in two real-world applications: (1) systematic assessment of the eHect of lysophosphatidic acid (LPA) concentration on blastoid formation, and (2) evaluating the impact of dimethyl sulfoxide (DMSO) on blastoids for drug screening. In the applications involving over 10,000 images, the model identified significant eHects of LPA and DMSO, which may have been overlooked in manual assessments. The deepBlastoid model is publicly available and researchers can train their own model according to their imaging conditions and blastoid culture protocol. deepBlastoid thus oHers a precise, automated approach for blastoid classification, with significant potential for advancing mechanism research, drug screening, and clinical in vitro fertilization (IVF) applications.
Plant recruitment six years after theSamarco’s tailings-dam disaster: Impacts on species richness and plant growth
Authors: Araújo da Paz André , Aleixo Diego Shimizu , Wittmann Astrid de Oliveira , Wittmann Florian , Ribeiro Cleberson , Ildefonso de Campos Ricardo 
Published: December 2024

AbstractOne of the greatest tragedies in Brazilian mining history occurred in November 2015 in Mariana, Minas Gerais state, when a dam from the mining companySamarcowas breached. Millions of mine tailings from this upstream embankment were dumped over theDoceRiver basin, impacting an area of approximately 1469 ha of riparian vegetation. Our objective was to experimentally investigate whether plant recruitment and establishment are impaired in areas affected by tailings six years after the deposition. To achieve this goal, in 2021 we compared soil chemical properties between affected and unaffected areas, performed a soil seed bank experiment in controlled conditions, and conducted a greenhouse growth experiment using the two most abundant plant species. Affected soils presented lower fertility and organic matter content. At the same time, the mean abundance and richness of emerging plants did not differ between soils. Still, affected areas exhibited approximately 35% lower accumulated species richness (gamma diversity) than unaffected ones. The three most abundant species in both areas represented 34% of the individuals, beingMarsypianthes chamaedrys(Vahl) Kuntze,Ludwigia octovalvis(Jacq.) P.H. Raven andAgeratum conyzoidesL. In the growth experiment, plants growing in affected soils presented reduced height and stem diameter increment (L. octovalvis) or allocated fewer resources to root production than aerial parts (M. chamaedrys), potentially in response to soil infertility and density. Even after six years, our results showed that tailings- affected areas continue to experience negative impacts on plant recruitment, highlighting its adverse effects on ecosystem functions and services.