bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis
Authors: Franzén Lovisa , Olsson Lindvall Martina , Hühn Michael , Ptasinski Victoria , Setyo Laura , Keith Benjamin P. , Collin Astrid , Oag Steven , Volckaert Thomas , Borde Annika , Lundeberg Joakim , Lindgren Julia , Belfield Graham , Jackson Sonya , Ollerstam Anna , Stamou Marianna , Ståhl Patrik L. , Hornberg Jorrit J. 
Published: July 2024

AbstractIdiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and limited treatment options. Efforts to identify effective treatments are thwarted by limited understanding of IPF pathogenesis and poor translatability of available preclinical models. Here we generated spatially resolved transcriptome maps of human IPF (n = 4) and bleomycin-induced mouse pulmonary fibrosis (n = 6) to address these limitations. We uncovered distinct fibrotic niches in the IPF lung, characterized by aberrant alveolar epithelial cells in a microenvironment dominated by transforming growth factor beta signaling alongside predicted regulators, such as TP53 and APOE. We also identified a clear divergence between the arrested alveolar regeneration in the IPF fibrotic niches and the active tissue repair in the acutely fibrotic mouse lung. Our study offers in-depth insights into the IPF transcriptional landscape and proposes alveolar regeneration as a promising therapeutic strategy for IPF.
Continuous neural control of a bionic limb restores biomimetic gait after amputation
Authors: Song Hyungeun , Hsieh Tsung-Han , Yeon Seong Ho , Shu Tony , Nawrot Michael , Landis Christian F. , Friedman Gabriel N. , Israel Erica A. , Gutierrez-Arango Samantha , Carty Matthew J. , Freed Lisa E. , Herr Hugh M. 
Published: July 2024

AbstractFor centuries scientists and technologists have sought artificial leg replacements that fully capture the versatility of their intact biological counterparts. However, biological gait requires coordinated volitional and reflexive motor control by complex afferent and efferent neural interplay, making its neuroprosthetic emulation challenging after limb amputation. Here we hypothesize that continuous neural control of a bionic limb can restore biomimetic gait after below-knee amputation when residual muscle afferents are augmented. To test this hypothesis, we present a neuroprosthetic interface consisting of surgically connected, agonist–antagonist muscles including muscle-sensing electrodes. In a cohort of seven leg amputees, the interface is shown to augment residual muscle afferents by 18% of biologically intact values. Compared with a matched amputee cohort without the afferent augmentation, the maximum neuroprosthetic walking speed is increased by 41%, enabling equivalent peak speeds to persons without leg amputation. Further, this level of afferent augmentation enables biomimetic adaptation to various walking speeds and real-world environments, including slopes, stairs and obstructed pathways. Our results suggest that even a small augmentation of residual muscle afferents restores biomimetic gait under continuous neuromodulation in individuals with leg amputation.
Predicting glycan structure from tandem mass spectrometry via deep learning
Authors: Urban James , Jin Chunsheng , Thomsson Kristina A. , Karlsson Niclas G. , Ives Callum M. , Fadda Elisa , Bojar Daniel 
Published: July 2024

AbstractGlycans constitute the most complicated post-translational modification, modulating protein activity in health and disease. However, structural annotation from tandem mass spectrometry (MS/MS) data is a bottleneck in glycomics, preventing high-throughput endeavors and relegating glycomics to a few experts. Trained on a newly curated set of 500,000 annotated MS/MS spectra, here we present CandyCrunch, a dilated residual neural network predicting glycan structure from raw liquid chromatography–MS/MS data in seconds (top-1 accuracy: 90.3%). We developed an open-access Python-based workflow of raw data conversion and prediction, followed by automated curation and fragment annotation, with predictions recapitulating and extending expert annotation. We demonstrate that this can be used for de novo annotation, diagnostic fragment identification and high-throughput glycomics. For maximum impact, this entire pipeline is tightly interlaced with our glycowork platform and can be easily tested at https://colab.research.google.com/github/BojarLab/CandyCrunch/blob/main/CandyCrunch.ipynb. We envision CandyCrunch to democratize structural glycomics and the elucidation of biological roles of glycans.
A Phanerozoic gridded dataset for palaeogeographic reconstructions
Authors: Jones Lewis A. , Domeier Mathew 
Published: July 2024

AbstractGlobal Plate Models are widely used in the Earth Sciences to reconstruct the past geographic position of geological and palaeontological samples. However, the application of Global Plate Models to retrieve ‘palaeocoordinates’ is not trivial. Different Global Plate Models exist which vary in their complexity, spatiotemporal coverage, reference frame, and intended use. Consequently, careful consideration of which models are appropriate for any given research question is required. Here, we document and provide access to reconstruction datasets for five Global Plate Models in the palaeomagnetic reference frame. These datasets provide ‘true’ palaeolatitudes for three discrete global grids reconstructed at one-million-year intervals throughout the Phanerozoic (540–0 Ma), offering three key benefits for the Earth Science community: (1) allow users to look up palaeocoordinates for their samples (e.g. fossil occurrences) through simple indexing without having to learn additional software packages; (2) provide palaeocoordinates which have been generated consistently with thorough documentation; (3) provide static files which preserve model output and which can be used to evaluate palaeogeographic differences between Global Plate Models.
Chromosome-level genome assembly of Guide Black-Fur sheep (Ovis aries)
Authors: Lu Zengkui , Yuan Chao , An Xuejiao , Chen Zhixiang , Guo Tingting , Liu Jianbin 
Published: July 2024

AbstractGuide Black-Fur sheep (GD) is a breed of Tibetan sheep (Ovis aries) that lives in the Qinghai–Tibetan plateau region at an altitude of over 4,000 m. However, a lack of genomic information has made it difficult to understand the high-altitude adaptation of these sheep. We sequenced and assembled the GD reference genome using PacBio, Hi-C, and Illumina sequencing technologies. The final assembled genome size was 2.73 Gb, with a contig N50 of 20.30 Mb and a scaffold N50 of 107.63 Mb. The genome is predicted to contain 20,759 protein-coding genes, of which 98.42 have functional annotations. Repeat elements account for approximately 52.2% of the genomic landscape. The completeness of the GD genome assembly is highlighted by a BUSCO score of 93.1%. This high-quality genome assembly provides a critical resource for future molecular breeding and genetic improvement of Tibetan sheep.
A systematic review and dose–response meta-analysis of prospective cohort studies on coffee consumption and risk of lung cancer
Authors: Jabbari Maedeh , Salari-Moghaddam Asma , Bagheri Amir , Larijani Bagher , Esmaillzadeh Ahmad 
Published: July 2024

AbstractStudies on the association between coffee consumption and risk of lung cancer have been conflicting. The aim of this study was to systematically review the current evidence on the association between coffee consumption and risk of lung cancer and to quantify this association by performing a meta-analysis. A comprehensive systematic search was performed on online databases up to July 2023 investigating the association between coffee consumption and risk of lung cancer. All prospective cohort studies reporting odds ratios (ORs), rate or risk ratios (RRs), or hazard ratios (HRs) and 95% confidence intervals (CIs) in this context were included. The overall effect size was calculated using the random-effects model and statistical between-studies heterogeneity was examined using Cochrane’s Q test and I2. A total of 14 prospective cohort studies were included in this systematic review and meta-analysis. We found a significant positive association between coffee consumption and risk of lung cancer (RR: 1.28; 95% CI: 1.12, 1.47). This association remained significant when we included a pooled analysis paper and excluded 5 cohort studies (RR: 1.37; 95% CI: 1.12, 1.66). We observed no proof of significant publication bias using Egger’s test (P = 0.58). Moreover, dose–response analysis showed that each one cup/day increase in coffee consumption was related with a 6% higher lung cancer risk (RR: 1.06; 95% CI: 1.03, 1.09). In conclusion, we found a significant positive association between coffee consumption and risk of lung cancer.
Electrical resistivity tomography combined with seismic data estimates heterogeneous distribution of near-seafloor concentrated gas hydrates within gas chimneys
Authors: Ishizu Keiichi , Oda Ayako , Goto Tada-nori , Kasaya Takafumi , Watanabe Toshiki , Machiyama Hideaki 
Published: July 2024

AbstractNear-seafloor concentrated gas hydrates (GHs) containing large amounts of methane have been identified at various gas chimney sites. Although understanding the spatial distribution of GHs is fundamental for assessing their dissociation impact on aggravating global warming and resource potential, the spatial distribution of GHs within gas chimneys remains unclear. Here, we estimate the subseafloor distribution of GHs at a gas chimney site in the Japan Sea using marine electrical resistivity tomography data. The resulting two-dimensional subseafloor resistivity structure shows high anomalies (10–100 Ωm) within seismically inferred gas chimneys. As the resistivity anomalies are aligned with high amplitude seismic reflections and core positions recovering GHs, we interpret the resistivity anomalies are near-seafloor concentrated GH deposits. We also detect various distribution patterns of the high resistivity anomalies including 100-m wide and 40-m thick anomaly near the seafloor and 500-m wide anomaly buried 50 m below the seafloor, suggesting that GHs are heterogeneously distributed. Therefore, considering such heterogeneous GH distribution within gas chimneys is critical for in-depth assessments of GH environmental impacts and energy resources.
China can enhance its carbon and nitrogen reduction potential by optimizing maize trade across provinces
Authors: Liu Dantong , Song Changchun , Xin Zhuohang , Fang Chong , Liu Zhihong 
Published: July 2024

AbstractInterregional grain trade affects the environment while balancing supply and demand. However, what relationship exist between national carbon emissions reduction and nitrogen losses reduction in each export region is unclear. Here we used maize as a case study to address this gap by combining life cycle assessment method with linear programming model. We found that interprovincial maize trade can reduce the country’s overall carbon emissions and nitrogen losses. However, the carbon and nitrogen reduction potential varied across exporting provinces. Northeast provinces have great potential to reduce the country’s overall carbon emissions and nitrogen losses via interprovincial maize trade. Northwest provinces increase the overall carbon emissions but reduce the overall nitrogen losses when transferring out maize. Optimizing interprovincial maize trade schemes can further enhance the country’s overall carbon and nitrogen reduction potential. The research results provide a theoretical reference for China to develop carbon neutral and nitrogen reduction trade schemes.
Techno-productive experiences for climate action in Argentina: Insights from renewable energy projects
Authors: Canafoglia Eliana Celeste 
Published: July 2024

AbstractThe main purpose of this research is to analyze techno-productive experiences within the framework of renewable energy projects based on the use and exploitation of solar energy in a region defined by favorable bioclimatic conditions. Following a primarily qualitative method, the research has been based on four case studies of working groups and their experiences. Stakeholders from diverse origin and background, interested in developing their technologies (processes, inputs, components, equipment) for the use of solar energy have managed to enhance the links among such developments, the productive sector and the communities in the territorial area where they carry out their activities. As a possible path of sociotechnical transition, these specific processes materialize energy transition with the progressive change of production and consumption patterns in favor of climate action.
The role of prepulse inhibition in predicting new-onset postpartum depression
Authors: Eriksson Allison , Björvang Richelle D. , Ancker Ebba , Papadopoulos Fotios C. , Poromaa Inger Sundström , Fransson Emma , Skalkidou Alkistis 
Published: July 2024

AbstractPredictive measures for postpartum depression (PPD), which affects around 12% of childbearing women, would enable early, targeted support. Here we explore prepulse inhibition (PPI), a measure of sensorimotor processing, as a biological tool for prediction of women at risk for PPD. Using data from the longitudinal BASIC study in Uppsala, Sweden, we used PPI measures from late pregnancy and reports on depressive symptoms assessed 6 weeks postpartum with the Edinburgh Postnatal Depression Scale to determine the association between pregnancy PPI and PPD. Lower PPI was associated with PPD onset in women who were not depressed during pregnancy. Further studies are encouraged to validate these promising results suggesting PPI as a predictive marker of new-onset PPD.
Applications of artificial intelligence in the analysis of histopathology images of gliomas: a review
Authors: Redlich Jan-Philipp , Feuerhake Friedrich , Weis Joachim , Schaadt Nadine S. , Teuber-Hanselmann Sarah , Buck Christoph , Luttmann Sabine , Eberle Andrea , Nikolin Stefan , Appenzeller Arno , Portmann Andreas , Homeyer André 
Published: July 2024

AbstractIn recent years, the diagnosis of gliomas has become increasingly complex. Analysis of glioma histopathology images using artificial intelligence (AI) offers new opportunities to support diagnosis and outcome prediction. To give an overview of the current state of research, this review examines 83 publicly available research studies that have proposed AI-based methods for whole-slide histopathology images of human gliomas, covering the diagnostic tasks of subtyping (23/83), grading (27/83), molecular marker prediction (20/83), and survival prediction (29/83). All studies were reviewed with regard to methodological aspects as well as clinical applicability. It was found that the focus of current research is the assessment of hematoxylin and eosin-stained tissue sections of adult-type diffuse gliomas. The majority of studies (52/83) are based on the publicly available glioblastoma and low-grade glioma datasets from The Cancer Genome Atlas (TCGA) and only a few studies employed other datasets in isolation (16/83) or in addition to the TCGA datasets (15/83). Current approaches mostly rely on convolutional neural networks (63/83) for analyzing tissue at 20x magnification (35/83). A new field of research is the integration of clinical data, omics data, or magnetic resonance imaging (29/83). So far, AI-based methods have achieved promising results, but are not yet used in real clinical settings. Future work should focus on the independent validation of methods on larger, multi-site datasets with high-quality and up-to-date clinical and molecular pathology annotations to demonstrate routine applicability.
YTHDC1 m6A-dependent and m6A-independent functions converge to preserve the DNA damage response
Authors: Elvira-Blázquez Daniel , Fernández-Justel José Miguel , Arcas Aida , Statello Luisa , Goñi Enrique , González Jovanna , Ricci Benedetta , Zaccara Sara , Raimondi Ivan , Huarte Maite 
Published: July 2024

AbstractCells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding of its impact on a fully efficient DNA damage response remains limited. Here, through a targeted CRISPR-knockout screen, we identify RNA-binding proteins and modifiers that participate in the p53 response. Among the top hits, we find the m6A reader YTHDC1 as a master regulator of p53 expression. YTHDC1 binds to the transcription start sites of TP53 and other genes involved in the DNA damage response, promoting their transcriptional elongation. YTHDC1 deficiency also causes the retention of introns and therefore aberrant protein production of key DNA damage factors. While YTHDC1-mediated intron retention requires m6A, TP53 transcriptional pause-release is promoted by YTHDC1 independently of m6A. Depletion of YTHDC1 causes genomic instability and aberrant cancer cell proliferation mediated by genes regulated by YTHDC1. Our results uncover YTHDC1 as an orchestrator of the DNA damage response through distinct mechanisms of co-transcriptional mRNA regulation.
Structural basis for Mis18 complex assembly and its implications for centromere maintenance
Authors: Thamkachy Reshma , Medina-Pritchard Bethan , Park Sang Ho , Chiodi Carla G , Zou Juan , de la Torre-Barranco Maria , Shimanaka Kazuma , Abad Maria Alba , Gallego Páramo Cristina , Feederle Regina , Ruksenaite Emilija , Heun Patrick , Davies Owen R , Rappsilber Juri , Schneidman-Duhovny Dina , Cho Uhn-Soo , Jeyaprakash A Arockia 
Published: July 2024

AbstractThe centromere, defined by the enrichment of CENP-A (a Histone H3 variant) containing nucleosomes, is a specialised chromosomal locus that acts as a microtubule attachment site. To preserve centromere identity, CENP-A levels must be maintained through active CENP-A loading during the cell cycle. A central player mediating this process is the Mis18 complex (Mis18α, Mis18β and Mis18BP1), which recruits the CENP-A-specific chaperone HJURP to centromeres for CENP-A deposition. Here, using a multi-pronged approach, we characterise the structure of the Mis18 complex and show that multiple hetero- and homo-oligomeric interfaces facilitate the hetero-octameric Mis18 complex assembly composed of 4 Mis18α, 2 Mis18β and 2 Mis18BP1. Evaluation of structure-guided/separation-of-function mutants reveals structural determinants essential for cell cycle controlled Mis18 complex assembly and centromere maintenance. Our results provide new mechanistic insights on centromere maintenance, highlighting that while Mis18α can associate with centromeres and deposit CENP-A independently of Mis18β, the latter is indispensable for the optimal level of CENP-A loading required for preserving the centromere identity.
Differential changes in end organ immune cells and inflammation in salt-sensitive hypertension: effects of lowering blood pressure
Authors: Navaneethabalakrishnan Shobana , Goodlett Bethany L. , Smith Hannah L. , Cardenas Alyssa , Burns Asia , Mitchell Brett M. 
Published: July 2024

Abstract
We reported that salt-sensitive hypertension (SSHTN) is associated with increased pro-inflammatory immune cells, inflammation, and inflammation-associated lymphangiogenesis in the kidneys and gonads of male and female mice. However, it is unknown whether these adverse end organ effects result from increased blood pressure (BP), elevated levels of salt, or both. We hypothesized that pharmaceutically lowering BP would not fully alleviate the renal and gonadal immune cell accumulation, inflammation, and lymphangiogenesis associated with SSHTN. SSHTN was induced in male and female C57BL6/J mice by administering nitro-L-arginine methyl ester hydrochloride (L-NAME; 0.5 mg/ml) in their drinking water for 2 weeks, followed by a 2-week washout period. Subsequently, the mice received a 3-week 4% high salt diet (SSHTN). The treatment group underwent the same SSHTN induction protocol but received hydralazine (HYD; 250 mg/L) in their drinking water during the diet phase (SSHTN+HYD). Control mice received tap water and a standard diet for 7 weeks. In addition to decreasing systolic BP, HYD treatment generally decreased pro-inflammatory immune cells and inflammation in the kidneys and gonads of SSHTN mice. Furthermore, the decrease in BP partially alleviated elevated renal and gonadal lymphatics and improved renal and gonadal function in mice with SSHTN. These data demonstrate that high systemic pressure and salt differentially act on end organ immune cells, contributing to the broader understanding of how BP and salt intake collectively shape immune responses and highlight implications for targeted therapeutic interventions.
Analysis of protection blinding in active distribution grids
Authors: Patil Amit Dilip , Ghasemi Abdorasoul , de Meer Hermann 
Published: July 2024

AbstractProtection blinding is a challenging issue in renewables‐penetrated distribution grids and refers to a situation where a circuit breaker may not trip due to fault current contribution from distributed generation. This research addresses how the distributed generation location and capacity impact the operation of the circuit breaker in terms of the response time of the circuit breakers. The relative electrical distances of the faults and distributed generation to the circuit breakers are considered. The impact of distributed generation capacity considering the fault location is characterized using a new index called the heterogeneity index. The electrical distance between distributed generations and circuit breakers and the electrical distance between fault and circuit breaker is considered by a second new index called the electrical distance ratio. Data analysis on simulation results shows that these indices capture the phenomena of protection blinding caused by distributed generation. Results show that a higher distributed generation penetration and faults that are electrically further away from a circuit breaker show severe cases of protection blinding captured by the indices. Furthermore, it is demonstrated how these indices can identify the worst impacted locations in the distribution grid. A key result is that protection blinding does not necessarily occur solely due to the presence of distributed generation between a circuit breaker and a fault, but is dependent on factors such as distributed generation location in the distribution grid, fault level, fault level distribution across the generation units and fault location.