bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations
Authors: Lecomte Laurie , Árnyasi Mariann , Ferchaud Anne-Laure , Kent Matthew , Lien Sigbjørn , Stenløkk Kristina , Sylvestre Florent , Mérot Claire , Bernatchez Louis 
Published: September 2023

AbstractGenomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (< 50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and at smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns ofFSTand density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large-scale SV characterization and highlights its relevance for salmonid population genomics.
Unpacking Unstructured Data: A Pilot Study on Extracting Insights from Neuropathological Reports of Parkinson’s Disease Patients using Large Language Models
Authors: Stroganov Oleg , Schedlbauer Amber , Lorenzen Emily , Kadhim Alex , Lobanova Anna , Lewis David A. , Glausier Jill R. 
Published: September 2023

ABSTRACTObjectiveThe aim of this study was to make unstructured neuropathological data, located in the NeuroBioBank (NBB), follow FAIR principles, and investigate the potential of Large Language Models (LLMs) in wrangling unstructured neuropathological reports. By making the currently inconsistent and disparate data findable, our overarching goal was to enhance research output and speed.Materials and MethodsThe NBB catalog currently includes information from medical records, interview results, and neuropathological reports. These reports contain crucial information necessary for conducting in-depth analysis of NBB data but have multiple formats that vary across different NBB biorepositories and change over time. In this study we focused on a subset of 822 donors with Parkinson’s disease (PD) from 7 NBB biorepositories. We developed a data model with combined Brain Region and Pathological Findings data at its core. This approach made it easier to build an extraction pipeline and was flexible enough to convert resulting data to Common Data Elements (CDEs), a standardized data collection tools used by the neuroscience community to improve consistency and facilitate data sharing across studies.ResultsThis pilot study demonstrated the potential of LLMs in structuring unstructured neuropathological reports of PD patients available in the NBB. The pipeline enabled successful extraction of detailed tissue-level (microscopic) and gross anatomical (macroscopic) observations, along with staging information from pathology reports, with extraction quality comparable to manual curation results. To our knowledge, this is the first attempt to automatically standardize neuropathological information at this scale. The collected data has the potential to serve as a valuable resource for PD researchers, facilitating integration with clinical information and genetic data (such as genome-wide genotyping and whole genome sequencing) available through the NBB, hereby enabling a more comprehensive understanding of the disease.
OBIA: An Open Biomedical Imaging Archive
Authors: Jin Enhui , Zhao Dongli , Wu Gangao , Zhu Junwei , Wang Zhonghuang , Wei Zhiyao , Zhang Sisi , Wang Anke , Tang Bixia , Chen Xu , Sun Yanling , Zhang Zhe , Zhao Wenming , Meng Yuanguang 
Published: September 2023

AbstractWith the development of artificial intelligence (AI) technologies, biomedical imaging data play an important role in scientific research and clinical application, but the available resources are limited. Here we present Open Biomedical Imaging Archive (OBIA), a repository for archiving biomedical imaging and related clinical data. OBIA adopts five data objects (Collection, Individual, Study, Series, and Image) for data organization, accepts the submission of biomedical images of multiple modalities, organs, and diseases. In order to protect personal privacy, OBIA has formulated a unified de-identification and quality control process. In addition, OBIA provides friendly and intuitive web interface for data submission, browsing and retrieval, as well as image retrieval. As of September 2023, OBIA has housed data for a total of 937 individuals, 4136 studies, 24,701 series, and 1,938,309 images covering 9 modalities and 30 anatomical sites. Collectively, OBIA provides a reliable platform for biomedical imaging data management and offers free open access to all publicly available data to support research activities throughout the world. OBIA can be accessed athttps://ngdc.cncb.ac.cn/obia.
Resilience assessment in complex natural systems
Authors: Sguotti Camilla , Vasilakopoulos Paraskevas , Tzanatos Evangelos , Frelat Romain 
Published: September 2023

AbstractEcological resilience is the capability of an ecosystem to maintain the same structure and function and to avoid crossing catastrophic tipping points. While fundamental for management, concrete ways to estimate and interpret resilience in real ecosystems are still lacking. Here, we develop an empirical approach to estimate resilience based on the stochasticcuspmodel derived from catastrophe theory. OurCusp Resilience Assessment(CUSPRA) has three characteristics: i) it provides estimates on how likely a system is to cross a tipping point characterized by hysteresis, ii) it assesses resilience in relation to multiple external drivers, and iii) it produces straightforward results for ecosystem-based management. We validated our approach using simulated data and demonstrated its application using empirical time-series of an Atlantic cod population and of marine ecosystems in the North and the Mediterranean Sea. We show that CUSPRA provides a powerful method to empirically estimate resilience in support of a sustainable management of our constantly adapting ecosystems under global climate change.
Cancer-associated Fibroblast Spatial Heterogeneity andEMILIN1Expression in Cancer Stroma Modulate TGF-β Activity and CD8+T-Cell Infiltration in Breast Cancer
Authors: Honda Chikako , Kurozumi Sasagu , Fujii Takaaki , Pourquier Didier , Khellaf Lakhdar , Boissiere Florence , Horiguchi Jun , Oyama Tetsunari , Shirabe Ken , Colinge Jacques , Yokobori Takehiko , Turtoi Andrei 
Published: September 2023

ABSTRACTThe tumor microenvironment (TME) and its multifaceted interactions with cancer cells are major targets for cancer treatment. Single-cell technologies have brought major insights into the TME, but the resulting complexity frequently precludes conclusions on function. Therefore, we combined single-cell RNA sequencing and spatial transcriptomic data to explore the relationship between different cancer-associated fibroblast (CAF) populations and immune cell exclusion in breast tumors. Our data show for the first time the degree of spatial organization of different CAF populations in breast cancer. We found that IL-iCAFs, Detox-iCAFs, and IFNγ-iCAFs tended to cluster together, while Wound-myCAFs, TGFβ-myCAFs, and ECM-myCAFs formed another group that overlapped with elevated TGF-β signaling. Differential gene expression analysis of areas with CD8+T-cell infiltration/exclusion within the TGF-β signaling-rich zones identified elastin microfibrillar interface protein 1 (EMILIN1) as a top modulated gene.EMILIN1, a TGF-β inhibitor, was upregulated in IFNγ-iCAFs directly modulating TGFβ immunosuppressive function. Histological analysis of 74 breast cancer samples confirmed that high EMILIN-1 expression in the tumor margins was related to high CD8+T-cell infiltration, consistent with our spatial gene expression analysis. High EMILIN-1 expression was also associated with better prognosis of patients with breast cancer, underscoring its functional significance for the recruitment of cytotoxic T cells into the tumor area. In conclusion, our data show that correlating TGF-β signaling to a CAF subpopulation is not enough because proteins with TGF-β-modulating activity originating from other CAF subpopulations can alter its activity. Therefore, therapeutic targeting should remain focused on biological processes rather than on specific CAF subtypes.
Enkephalin-mediated modulation of basal somatic sensitivity by regulatory T cells in mice
Authors: Aubert Nicolas , Purcarea Madeleine , Novarino Julien , Schopp Julien , Audibert Alexis , Li Wangtianrui , Fornier Marie , Cagnet Léonie , Naturel Marie , Casrouge Armanda , Dieu-Nosjean Marie-Caroline , Blanchard Nicolas , Dietrich Gilles , Peirs Cedric , Marodon Gilles 
Published: September 2023

AbstractCD4+CD25+Foxp3+regulatory T cells (Treg) have been implicated in pain modulation in various inflammatory conditions. However, whether Treg cells hamper pain at steady state and by which mechanism is still unclear. From a meta-analysis of the transcriptomes of murine Treg and conventional T cells (Tconv), we observe that the proenkephalin gene (Penk), encoding the precursor of analgesic opioid peptides, ranks among the top 25 genes most enriched in Treg cells. We then present various evidence suggesting thatPenkis regulated in part by members of the TNF receptor family and the transcription factor Batf. Using mice in which the promoter activity ofPenkcan be tracked with a fluorescent reporter, we also show thatPenkexpression is mostly detected in Treg and activated Tconv in non-inflammatory conditions in the colon and skin. Functionally, Treg cells proficient or deficient forPenksuppress equally well the proliferation of effector T cellsin vitroand autoimmune colitisin vivo. In contrast, inducible ablation ofPenkin Treg leads to heat hyperalgesia in both male and female mice. Overall, our results indicate that Treg might play a key role at modulating basal somatic sensitivity in mice through the production of analgesic opioid peptides.
Non fire-adapted dry forest of Northwestern Madagascar: escalating and devastating trends revealed by remote-sensing data
Authors: Percival Joseph Emile Honour , Sato Hiroki , Razanaparany Tojotanjona Patrick , Harilalao Ando Rakotomamonjy , Razafiarison Zo Lalaina , Kitajima Kaoru 
Published: September 2023

AbstractAnkarafantsika National Park (ANP), the last significant remnant of Northwestern Madagascar’s tropical dry forests, is facing rapid degradation due to increased incidences of fire. This poses severe threats to biodiversity, local livelihoods, and vital ecosystem services. Our study, conducted on 3052 ha of ANP’s pristine forests, employed advanced remote-sensing techniques to assess fire impacts during the past 37 years. Our aims were to understand historical fire patterns and evaluate forest recovery and susceptibility to repeated fires following initial burns. Using data from multiple Landsat satellite sensors, we constructed a time series of fire events since 1985, which revealed no fire activity before 2014. The Global Ecosystem Dynamics Investigation (GEDI) lidar sensor data were used to observe forest structure in both post-fire areas and undisturbed zones for comparison. We recorded six fire incidents from 2014-2021, during which the fire-affected area exponentially grew. A significant fire incident in October 2021 impacted 1052 hectares, 59% of which had experienced at least one fire in 2-4 years prior, with 60% experiencing 2 preceding incidents: one in 2017 and another in 2019. The initial fire drastically reduced plant cover and tree height, with subsequent fires causing minor additional loss. Post-fire recovery was negligible within the initial four years, even in patches without recurrent fires. The likelihood for an initial burn to trigger subsequent fires within a few years was high, leading to larger, more severe fires. We conclude that ANP’s dry forests exhibit high vulnerability and low resilience to anthropogenic fires. Prompt preventive measures are essential to halt further fire spread and conserve the park’s unique and invaluable biodiversity.
Engineering an artificial catch bond using mechanical anisotropy
Authors: Liu Zhaowei , Liu Haipei , Vera Andrés M. , Yang Byeongseon , Tinnefeld Philip , Nash Michael A. 
Published: September 2023

AbstractCatch bonds are a rare class of protein-protein interactions where the bond lifetime increases under an external pulling force. Here, we report how modification of anchor geometry generates catch bonding behavior for the mechanostable Dockerin G:Cohesin E (DocG:CohE) adhesion complex found on human gut bacteria. Using AFM single-molecule force spectroscopy in combination with bioorthogonal click chemistry, we mechanically dissociated the complex using five precisely controlled anchor geometries. When tension was applied through residue #13 on CohE and the N-terminus of DocG, the complex behaved as a two-state catch bond, while in all other tested pulling geometries, including the native configuration, it behaved as a slip bond. We used a kinetic Monte Carlo model with experimentally derived parameters to simulate rupture force and lifetime distributions, achieving strong agreement with experiments. Single-molecule FRET measurements further demonstrated that the complex does not exhibit dual binding mode behavior at equilibrium but unbinds along multiple pathways under force. Together, these results show how mechanical anisotropy and anchor point selection can be used to engineer artificial catch bonds.
Rampant Reticulation in a Rapid Radiation of Tropical Trees - Insights fromInga(Fabaceae)
Authors: Schley Rowan J. , Piñeiro Rosalía , Nicholls James A. , Pezzini Flávia Fonseca , Kidner Catherine , Farbos Audrey , Ringelberg Jens J. , Twyford Alex D. , Dexter Kyle G. , Pennington R. Toby 
Published: September 2023

AbstractEvolutionary radiations underlie much of the species diversity of life on Earth, particularly within the world’s most species-rich tree flora – that of the Amazon rainforest. Hybridisation occurs in many radiations, with effects ranging from homogenisation of species to generation of genetic and phenotypic novelty that fuels speciation, but the influence of hybridisation on Amazonian tree radiations has been little studied. We address this using the ubiquitous, species-rich, neotropical tree genusInga, which typifies rapid radiations of rainforest trees. We assess patterns of gene tree incongruence to ascertain whether hybridisation was associated with rapid radiation inInga.Given the importance of insect herbivory in structuring rainforest tree communities (and hence the potential for hybridisation to promote adaptation through admixture of defence traits), we also test whether introgression of loci underlying chemical defences against herbivory occurred during the radiation ofInga.Our phylogenomic analyses of 189/288Ingaspecies using >1300 target capture loci showed widespread introgression inInga. Specifically, we found widespread phylogenetic incongruence explained by introgression, with phylogenetic networks recovering multiple introgression events acrossIngaand up to 20% of shared, likely introgressed, genetic variation between some species. In addition, most defence chemistry loci showed evidence of positive selection and marginally higher levels of introgression. Overall, our results suggest that introgression has occurred widely over the course ofInga’shistory, likely facilitated by extensive dispersal across Amazonia, and that in some cases introgression of chemical defence loci may influence adaptation inInga.
Syntrichia ruralis: Emerging model moss genome reveals a conserved and previously unknown regulator of desiccation in flowering plants
Authors: Zhang Xiaodan , Ekwealor Jenna T. B. , Silva Anderson T. , Yu Li’ang , Jones Andrea K. , Mishler Brent D. , Nelson Andrew D. L. , Oliver Melvin J. 
Published: September 2023

AbstractWater scarcity poses a significant threat to ecosystems in the face of global climate change.Syntrichia ruralis, a dryland moss known for its desiccation tolerance, provides valuable insights into surviving water-limited conditions. In this study, the genome ofS. ruraliswas sequenced and assembled into 12 chromosomes encompassing 21,169 protein-coding genes. Additionally, 3,199 unplaced scaffolds were identified as non-nuclear and symbiont DNA. Transposable elements (TEs) constitute 51.24% of the genome. Notably, chromosome 12, the largest in size due to its high TE load, was identified as the putative sex chromosome. Comparative analysis with the closely relatedSyntrichia caninervisgenome reveals significant large-scale synteny yet some rearrangements, as well as the occurrence of older duplication events that are shared by both. Desiccation and drought tolerance associated gene families, such as early light-inducible proteins (ELIPs) and late embryogenesis abundant (LEA) proteins, were characterized. In addition to a subset of LEA genes being species-specific, a comparative transcriptomic analysis revealed that some shared LEA genes respond differently to dehydration in these two species. Many ELIPs (9 out of 30) are the product of tandem duplication events. As expected, our analyses revealed the importance of the phytohormone abscisic acid (ABA) in the desiccation response ofS. ruralis. A significant number of ABA responsive genes were found to be regulated byS. ruralisorthologs of ABA insensitive 3 (ABI3) and abscisic acid responsive element binding factor 2 (AREB2). Markedly, an uncharacterized, but deeply conserved MYB transcription factor, appears to act as a negative regulator of AREB2 inS. ruralis. Interestingly, we determined that the orthologous MYB TF is also involved in an ABA-dependent stress response in the model flowering plantA. thaliana. In sum, the new genomic resources from this emerging model moss offer new insights into the evolution of desiccation tolerance in land plants.
Nanopore translocation reveals electrophoretic force on non-canonical RNA:DNA double helix
Authors: Bošković Filip , Maffeo Christopher , Patiño-Guillén Gerardo , Tivony Ran , Aksimentiev Aleksei , Keyser Ulrich F. 
Published: September 2023

ABSTRACTElectrophoretic transport plays a pivotal role in advancing sensing technologies. So far, systematic studies have focused on translocation of canonical B-form or A-form nucleic acids, while direct RNA analysis is emerging as the new frontier for nanopore sensing and sequencing. Here, we compare the less-explored dynamics of non-canonical RNA:DNA hybrids in electrophoretic transport with the well-researched transport of B-form DNA. Using DNA/RNA nanotechnology and solid-state nanopores, the translocation of RNA:DNA (RD) and DNA:DNA (DD) duplexes was examined. Notably, RD duplexes were found to translocate through nanopores faster than DD duplexes, despite containing the same number of base pairs. Our experiments reveal that RD duplexes present a non-canonical helix with distinct transport properties from B-form DD molecules. We find RD and DD molecules with the same contour length move with comparable velocity through nanopores. We examined the physical characteristics of both duplex forms using atomic force microscopy, atomistic molecular dynamics simulations, agarose gel electrophoresis, and dynamic light scattering measurements. With the help of coarse-grained and molecular dynamics simulations, we find the effective force per unit length applied by the electric field to a fragment of RD or DD duplex in nanopores with various geometries or shapes to be approximately the same within experimental errors. Our results shed light on the significance of helical form in nucleic acid translocation, with implications for RNA sensing, sequencing, and molecular understanding of electrophoretic transport.
Approaches to Species Distribution Modelling in Dinosaurs and Other Fossil Organisms
Authors: Stockdale Maximilian T. 
Published: September 2023

AbstractSDM describes a family of methods aiming to predict the geographic distribution of organisms using environmental data such as climate variables. It is a versatile tool in estimating ecological communities and interactions both spatially and through time. However, it has had limited utility in predicting the geographic distribution of fossil organisms. Due to preservation and sampling biases, fossil data does not satisfy the assumptions of species distribution models. Here is presented an analysis proposing a new methodology, which substitutes the conventional pseudoabsence data for fossil occurrences from non-target species. This approach eliminates variation in preservation and sampling, and returns a SDM which performs better than a conventional example. This model concludes that the ceratopsian Triceratops may have been widespread across North America, and beyond the region where its fossils have been recovered. The geographic distribution of Triceratops appears to have been governed by seasonality in temperature and temperature of the coldest month.