bluuebunny/crossref_metadata_2025_split huggingface dataset:
brainlife.io: a decentralized and open-source cloud platform to support neuroscience research
Authors: Hayashi Soichi , Caron Bradley A. , Heinsfeld Anibal Sólon , Vinci-Booher Sophia , McPherson Brent , Bullock Daniel N. , Bertò Giulia , Niso Guiomar , Hanekamp Sandra , Levitas Daniel , Ray Kimberly , MacKenzie Anne , Avesani Paolo , Kitchell Lindsey , Leong Josiah K. , Nascimento-Silva Filipi , Koudoro Serge , Willis Hanna , Jolly Jasleen K. , Pisner Derek , Zuidema Taylor R. , Kurzawski Jan W. , Mikellidou Kyriaki , Bussalb Aurore , Chaumon Maximilien , George Nathalie , Rorden Christopher , Victory Conner , Bhatia Dheeraj , Aydogan Dogu Baran , Yeh Fang-Cheng F. , Delogu Franco , Guaje Javier , Veraart Jelle , Fischer Jeremy , Faskowitz Joshua , Fabrega Ricardo , Hunt David , McKee Shawn , Brown Shawn T. , Heyman Stephanie , Iacovella Vittorio , Mejia Amanda F. , Marinazzo Daniele , Craddock R. Cameron , Olivetti Emanuale , Hanson Jamie L. , Garyfallidis Eleftherios , Stanzione Dan , Carson James , Henschel Robert , Hancock David Y. , Stewart Craig A. , Schnyer David , Eke Damian O. , Poldrack Russell A. , Bollmann Steffen , Stewart Ashley , Bridge Holly , Sani Ilaria , Freiwald Winrich A. , Puce Aina , Port Nicholas L. , Pestilli Franco 
Published: April 2024

AbstractNeuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants.
High-resolution freshwater dissolved calcium and pH data layers for Canada and the United States
Authors: Guerin Andrew J. , Weise Andréa M. , Chu Jackson W. F. , Wilcox Mark A. , Greene Erin Sowerby , Therriault Thomas W. 
Published: April 2024

AbstractFreshwater ecosystems are biologically important habitats that provide many ecosystem services. Calcium concentration and pH are two key variables that are linked to multiple chemical processes in these environments, influence the biology of organisms from diverse taxa, and can be important factors affecting the distribution of native and non-native species. However, it can be challenging to obtain high-resolution data for these variables at regional and national scales. To address this data gap, water quality data for lakes and rivers in Canada and the continental USA were compiled and used to generate high-resolution (10 × 10 km) interpolated raster layers, after comparing multiple spatial interpolation approaches. This is the first time that such data have been made available at this scale and resolution, providing a valuable resource for research, including projects evaluating risks from environmental change, pollution, and invasive species. This will aid the development of conservation and management strategies for these vital habitats.
An open source knowledge graph ecosystem for the life sciences
Authors: Callahan Tiffany J. , Tripodi Ignacio J. , Stefanski Adrianne L. , Cappelletti Luca , Taneja Sanya B. , Wyrwa Jordan M. , Casiraghi Elena , Matentzoglu Nicolas A. , Reese Justin , Silverstein Jonathan C. , Hoyt Charles Tapley , Boyce Richard D. , Malec Scott A. , Unni Deepak R. , Joachimiak Marcin P. , Robinson Peter N. , Mungall Christopher J. , Cavalleri Emanuele , Fontana Tommaso , Valentini Giorgio , Mesiti Marco , Gillenwater Lucas A. , Santangelo Brook , Vasilevsky Nicole A. , Hoehndorf Robert , Bennett Tellen D. , Ryan Patrick B. , Hripcsak George , Kahn Michael G. , Bada Michael , Baumgartner William A. , Hunter Lawrence E. 
Published: April 2024

AbstractTranslational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoint resources and abstraction algorithms), and benchmarks (e.g., prebuilt KGs). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 different large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.
OCTDL: Optical Coherence Tomography Dataset for Image-Based Deep Learning Methods
Authors: Kulyabin Mikhail , Zhdanov Aleksei , Nikiforova Anastasia , Stepichev Andrey , Kuznetsova Anna , Ronkin Mikhail , Borisov Vasilii , Bogachev Alexander , Korotkich Sergey , Constable Paul A. , Maier Andreas 
Published: April 2024

AbstractOptical coherence tomography (OCT) is a non-invasive imaging technique with extensive clinical applications in ophthalmology. OCT enables the visualization of the retinal layers, playing a vital role in the early detection and monitoring of retinal diseases. OCT uses the principle of light wave interference to create detailed images of the retinal microstructures, making it a valuable tool for diagnosing ocular conditions. This work presents an open-access OCT dataset (OCTDL) comprising over 2000 OCT images labeled according to disease group and retinal pathology. The dataset consists of OCT records of patients with Age-related Macular Degeneration (AMD), Diabetic Macular Edema (DME), Epiretinal Membrane (ERM), Retinal Artery Occlusion (RAO), Retinal Vein Occlusion (RVO), and Vitreomacular Interface Disease (VID). The images were acquired with an Optovue Avanti RTVue XR using raster scanning protocols with dynamic scan length and image resolution. Each retinal b-scan was acquired by centering on the fovea and interpreted and cataloged by an experienced retinal specialist. In this work, we applied Deep Learning classification techniques to this new open-access dataset.
Transcriptome profiling of aerial and subterranean peanut pod development
Authors: Peng Zhenying , Jia Kai-Hua , Meng Jingjing , Wang Jianguo , Zhang Jialei , Li Xinguo , Wan Shubo 
Published: April 2024

AbstractPeanut (Arachis hypogaea) showcases geocarpic behavior, transitioning from aerial flowering to subterranean seed development. We recently obtained an atavistic variant of this species, capable of producing aerial and subterranean pods on a single plant. Notably, although these pod types share similar vigor levels, they exhibit distinct differences in their physical aspects, such as pod size, color, and shell thickness. We constructed 63 RNA-sequencing datasets, comprising three biological replicates for each of 21 distinct tissues spanning six developmental stages for both pod types, providing a rich tapestry of the pod development process. This comprehensive analysis yielded an impressive 409.36 Gb of clean bases, facilitating the detection of 42,401 expressed genes. By comparing the transcriptomic data of the aerial and subterranean pods, we identified many differentially expressed genes (DEGs), highlighting their distinct developmental pathways. By providing a detailed workflow from the initial sampling to the final DEGs, this study serves as an important resource, paving the way for future research into peanut pod development and aiding transcriptome-based expression profiling and candidate gene identification.
Automated BigSMILES conversion workflow and dataset for homopolymeric macromolecules
Authors: Choi Sunho , Lee Joonbum , Seo Jangwon , Han Sung Won , Lee Sang Hyun , Seo Ji-Hun , Seok Junhee 
Published: April 2024

AbstractThe simplified molecular-input line-entry system (SMILES) has been utilized in a variety of artificial intelligence analyses owing to its capability of representing chemical structures using line notation. However, its ease of representation is limited, which has led to the proposal of BigSMILES as an alternative method suitable for the representation of macromolecules. Nevertheless, research on BigSMILES remains limited due to its preprocessing requirements. Thus, this study proposes a conversion workflow of BigSMILES, focusing on its automated generation from SMILES representations of homopolymers. BigSMILES representations for 4,927,181 records are provided, thereby enabling its immediate use for various research and development applications. Our study presents detailed descriptions on a validation process to ensure the accuracy, interchangeability, and robustness of the conversion. Additionally, a systematic overview of utilized codes and functions that emphasizes their relevance in the context of BigSMILES generation are produced. This advancement is anticipated to significantly aid researchers and facilitate further studies in BigSMILES representation, including potential applications in deep learning and further extension to complex structures such as copolymers.
Three de novo assembled wild cacao genomes from the Upper Amazon
Authors: Nousias Orestis , Zheng Jinfang , Li Tang , Meinhardt Lyndel W. , Bailey Bryan , Gutierrez Osman , Baruah Indrani K. , Cohen Stephen P. , Zhang Dapeng , Yin Yanbin 
Published: April 2024

AbstractTheobroma cacao, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. Recent advancement in plant genomics highlights the importance of de novo sequencing of multiple reference genomes to capture the genome diversity present in different cacao populations. In this study, three high-quality chromosome-level genomes of wild cacao were constructed, de novo assembled with HiFi long reads sequencing, and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. The five cacao genetic clusters were inferred to have diverged in the early and middle Pleistocene period, approximately 1.83–0.69 million years ago. The results shown here serve as an example of understanding how the Amazonian biodiversity was developed. The three wild cacao genomes provide valuable resources for studying genetic diversity and advancing genetic improvement of this species.
AI and narrative embeddings detect PTSD following childbirth via birth stories
Authors: Bartal Alon , Jagodnik Kathleen M. , Chan Sabrina J. , Dekel Sharon 
Published: April 2024

AbstractFree-text analysis using machine learning (ML)-based natural language processing (NLP) shows promise for diagnosing psychiatric conditions. Chat Generative Pre-trained Transformer (ChatGPT) has demonstrated preliminary initial feasibility for this purpose; however, whether it can accurately assess mental illness remains to be determined. This study evaluates the effectiveness of ChatGPT and the text-embedding-ada-002 (ADA) model in detecting post-traumatic stress disorder following childbirth (CB-PTSD), a maternal postpartum mental illness affecting millions of women annually, with no standard screening protocol. Using a sample of 1295 women who gave birth in the last six months and were 18+ years old, recruited through hospital announcements, social media, and professional organizations, we explore ChatGPT’s and ADA’s potential to screen for CB-PTSD by analyzing maternal childbirth narratives. The PTSD Checklist for DSM-5 (PCL-5; cutoff 31) was used to assess CB-PTSD. By developing an ML model that utilizes numerical vector representation of the ADA model, we identify CB-PTSD via narrative classification. Our model outperformed (F1 score: 0.81) ChatGPT and six previously published large text-embedding models trained on mental health or clinical domains data, suggesting that the ADA model can be harnessed to identify CB-PTSD. Our modeling approach could be generalized to assess other mental health disorders.
Mitochondrial Ca2+ signaling is a hallmark of specific adipose tissue-cancer crosstalk
Authors: De Mario Agnese , Trevellin Elisabetta , Piazza Ilaria , Vindigni Vincenzo , Foletto Mirto , Rizzuto Rosario , Vettor Roberto , Mammucari Cristina 
Published: April 2024

AbstractObesity is associated with increased risk and worse prognosis of many tumours including those of the breast and of the esophagus. Adipokines released from the peritumoural adipose tissue promote the metastatic potential of cancer cells, suggesting the existence of a crosstalk between the adipose tissue and the surrounding tumour. Mitochondrial Ca2+signaling contributes to the progression of carcinoma of different origins. However, whether adipocyte-derived factors modulate mitochondrial Ca2+signaling in tumours is unknown. Here, we show that conditioned media derived from adipose tissue cultures (ADCM) enriched in precursor cells impinge on mitochondrial Ca2+homeostasis of target cells. Moreover, in modulating mitochondrial Ca2+responses, a univocal crosstalk exists between visceral adipose tissue-derived preadipocytes and esophageal cancer cells, and between subcutaneous adipose tissue-derived preadipocytes and triple-negative breast cancer cells. An unbiased metabolomic analysis of ADCM identified creatine and creatinine for their ability to modulate mitochondrial Ca2+uptake, migration and proliferation of esophageal and breast tumour cells, respectively.
Effects of foetal size, sex and developmental stage on adaptive transcriptional responses of skeletal muscle to intrauterine growth restriction in pigs
Authors: Cortes-Araya Y. , Cheung S. , Ho W. , Stenhouse C. , Ashworth C. J. , Esteves C. L. , Donadeu F. X. 
Published: April 2024

AbstractIntrauterine growth restriction (IUGR) occurs both in humans and domestic species. It has a particularly high incidence in pigs, and is a leading cause of neonatal morbidity and mortality as well as impaired postnatal growth. A key feature of IUGR is impaired muscle development, resulting in decreased meat quality. Understanding the developmental origins of IUGR, particularly at the molecular level, is important for developing effective strategies to mitigate its economic impact on the pig industry and animal welfare. The aim of this study was to characterise transcriptional profiles in the muscle of growth restricted pig foetuses at different gestational days (GD; gestational length ~ 115 days), focusing on selected genes (related to development, tissue injury and metabolism) that were previously identified as dysregulated in muscle of GD90 fetuses. Muscle samples were collected from the lightest foetus (L) and the sex-matched foetus with weight closest to the litter average (AW) from each of 22 Landrace x Large White litters corresponding to GD45 (n = 6), GD60 (n = 8) or GD90 (n = 8), followed by analyses, using RT-PCR and protein immunohistochemistry, of selected gene targets. Expression of the developmental genes, MYOD, RET and ACTN3 were markedly lower, whereas MSTN expression was higher, in the muscle of L relative to AW littermates beginning on GD45. Levels of all tissue injury-associated transcripts analysed (F5, PLG, KNG1, SELL, CCL16) were increased in L muscle on GD60 and, most prominently, on GD90. Among genes involved in metabolic regulation, KLB was expressed at higher levels in L than AW littermates beginning on GD60, whereas both IGFBP1 and AHSG were higher in L littermates on GD90 but only in males. Furthermore, the expression of genes specifically involved in lipid, hexose sugar or iron metabolism increased or, in the case of UCP3, decreased in L littermates on GD60 (UCP3, APOB, ALDOB) or GD90 (PNPLA3, TF), albeit in the case of ALDOB this only involved females. In conclusion, marked dysregulation of genes with critical roles in development in L foetuses can be observed from GD45, whereas for a majority of transcripts associated with tissue injury and metabolism differences between L and AW foetuses were apparent by GD60 or only at GD90, thus identifying different developmental windows for different types of adaptive responses to IUGR in the muscle of porcine foetuses.
Gut-associated microbes are present and active in the pig nasal cavity
Authors: Obregon-Gutierrez Pau , Bonillo-Lopez Laura , Correa-Fiz Florencia , Sibila Marina , Segalés Joaquim , Kochanowski Karl , Aragon Virginia 
Published: April 2024

AbstractThe nasal microbiota is a key contributor to animal health, and characterizing the nasal microbiota composition is an important step towards elucidating the role of its different members. Efforts to characterize the nasal microbiota composition of domestic pigs and other farm animals frequently report the presence of bacteria that are typically found in the gut, including many anaerobes from the Bacteroidales and Clostridiales orders. However, the in vivo role of these gut-microbiota associated taxa is currently unclear. Here, we tackled this issue by examining the prevalence, origin, and activity of these taxa in the nasal microbiota of piglets. First, analysis of the nasal microbiota of farm piglets sampled in this study, as well as various publicly available data sets, revealed that gut-microbiota associated taxa indeed constitute a substantial fraction of the pig nasal microbiota that is highly variable across individual animals. Second, comparison of herd-matched nasal and rectal samples at amplicon sequencing variant (ASV) level showed that these taxa are largely shared in the nasal and rectal microbiota, suggesting a common origin driven presumably by the transfer of fecal matter. Third, surgical sampling of the inner nasal tract showed that gut-microbiota associated taxa are found throughout the nasal cavity, indicating that these taxa do not stem from contaminations introduced during sampling with conventional nasal swabs. Finally, analysis of cDNA from the 16S rRNA gene in these nasal samples indicated that gut-microbiota associated taxa are indeed active in the pig nasal cavity. This study shows that gut-microbiota associated taxa are not only present, but also active, in the nasal cavity of domestic pigs, and paves the way for future efforts to elucidate the function of these taxa within the nasal microbiota.
Hypoxia enhances autophagy level of human sperms
Authors: Hu Jie , Wu Jiwei , Liu Xinge , Zhang Yan , Mo Linfeng , Liu Liangzhao , Liu Shengxue , Ou Chaoyan , He Yonghua 
Published: April 2024

AbstractThe relationship between oxygen sensing and autophagy in human sperms was explored in this study. Health semen and asthenozoospermia (astheno) semen were incubated with hypoxia-inducible factor-1α (HIF-1α) interferents, i.e., lificiguat (YC-1) or cobalt chloride (CoCl2), respectively. Label-free quantitative proteomic technology was used to identify the differentially expressed proteins in human semen under the hypoxia condition. Selected proteins were detected with ELISA. It was found that the autophagy levels of sperm in the YC-1 + health group or CoCl2 + astheno group increased while the vitality decreased. A total of 17, 34 and 35 differentially expressed proteins were observed in the Astheno group, the YC-1 + health group and the CoCl2 + astheno group, respectively. These proteins were primarily associated with protein processing in endoplasmic reticulum, Th17 cell differentiation, progesterone-mediated oocyte maturation, glycolysis/gluconeogenesis, HIF-1 signaling pathway, biosynthesis of amino acids, and carbon metabolism. The expression levels of protein HIF-1α, LC3B, histone H4, cathepsin L and ENO1 changed significantly in the groups. The study suggests that hypoxia can increase sperm autophagy level and reduce their vitality through HIF-1 signaling pathway and glycolysis/gluconeogenesis signaling pathway. Furthermore, proteins histone H4, cathepsin L, glutathione synthetase and ENO1 are proposed as potential biomarkers of autophagy and vitality in asthenozoospermia sperm.
Whole-heart electromechanical simulations using Latent Neural Ordinary Differential Equations
Authors: Salvador Matteo , Strocchi Marina , Regazzoni Francesco , Augustin Christoph M. , Dede’ Luca , Niederer Steven A. , Quarteroni Alfio 
Published: April 2024

AbstractCardiac digital twins provide a physics and physiology informed framework to deliver personalized medicine. However, high-fidelity multi-scale cardiac models remain a barrier to adoption due to their extensive computational costs. Artificial Intelligence-based methods can make the creation of fast and accurate whole-heart digital twins feasible. We use Latent Neural Ordinary Differential Equations (LNODEs) to learn the pressure-volume dynamics of a heart failure patient. Our surrogate model is trained from 400 simulations while accounting for 43 parameters describing cell-to-organ cardiac electromechanics and cardiovascular hemodynamics. LNODEs provide a compact representation of the 3D-0D model in a latent space by means of an Artificial Neural Network that retains only 3 hidden layers with 13 neurons per layer and allows for numerical simulations of cardiac function on a single processor. We employ LNODEs to perform global sensitivity analysis and parameter estimation with uncertainty quantification in 3 hours of computations, still on a single processor.
A unified analysis of evolutionary and population constraint in protein domains highlights structural features and pathogenic sites
Authors: MacGowan Stuart A. , Madeira Fábio , Britto-Borges Thiago , Barton Geoffrey J. 
Published: April 2024

AbstractProtein evolution is constrained by structure and function, creating patterns in residue conservation that are routinely exploited to predict structure and other features. Similar constraints should affect variation across individuals, but it is only with the growth of human population sequencing that this has been tested at scale. Now, human population constraint has established applications in pathogenicity prediction, but it has not yet been explored for structural inference. Here, we map 2.4 million population variants to 5885 protein families and quantify residue-level constraint with a new Missense Enrichment Score (MES). Analysis of 61,214 structures from the PDB spanning 3661 families shows that missense depleted sites are enriched in buried residues or those involved in small-molecule or protein binding. MES is complementary to evolutionary conservation and a combined analysis allows a new classification of residues according to a conservation plane. This approach finds functional residues that are evolutionarily diverse, which can be related to specificity, as well as family-wide conserved sites that are critical for folding or function. We also find a possible contrast between lethal and non-lethal pathogenic sites, and a surprising clinical variant hot spot at a subset of missense enriched positions.