bluuebunny/crossref_metadata_2025_split huggingface dataset:
FTO deficiency in older livers exacerbates ferroptosis during ischaemia/reperfusion injury by upregulating ACSL4 and TFRC
Authors: Li Rong , Yan Xijing , Xiao Cuicui , Wang Tingting , Li Xuejiao , Hu Zhongying , Liang Jinliang , Zhang Jiebin , Cai Jianye , Sui Xin , Liu Qiuli , Wu Manli , Xiao Jiaqi , Chen Haitian , Liu Yasong , Jiang Chenhao , Lv Guo , Chen Guihua , Zhang Yingcai , Yao Jia , Zheng Jun , Yang Yang 
Published: June 2024

AbstractOlder livers are more prone to hepatic ischaemia/reperfusion injury (HIRI), which severely limits their utilization in liver transplantation. The potential mechanism remains unclear. Here, we demonstrate older livers exhibit increased ferroptosis during HIRI. Inhibiting ferroptosis significantly attenuates older HIRI phenotypes. Mass spectrometry reveals that fat mass and obesity-associated gene (FTO) expression is downregulated in older livers, especially during HIRI. Overexpressing FTO improves older HIRI phenotypes by inhibiting ferroptosis. Mechanistically, acyl-CoA synthetase long chain family 4 (ACSL4) and transferrin receptor protein 1 (TFRC), two key positive contributors to ferroptosis, are FTO targets. For ameliorative effect, FTO requires the inhibition of Acsl4 and Tfrc mRNA stability in a m6A-dependent manner. Furthermore, we demonstrate nicotinamide mononucleotide can upregulate FTO demethylase activity, suppressing ferroptosis and decreasing older HIRI. Collectively, these findings reveal an FTO-ACSL4/TFRC regulatory pathway that contributes to the pathogenesis of older HIRI, providing insight into the clinical translation of strategies related to the demethylase activity of FTO to improve graft function after older donor liver transplantation.
Predicting polymerization reactions via transfer learning using chemical language models
Authors: Ferrari Brenda S. , Manica Matteo , Giro Ronaldo , Laino Teodoro , Steiner Mathias B. 
Published: June 2024

AbstractPolymers are candidate materials for a wide range of sustainability applications such as carbon capture and energy storage. However, computational polymer discovery lacks automated analysis of reaction pathways and stability assessment through retro-synthesis. Here, we report an extension of transformer-based language models to polymerization for both reaction and retrosynthesis tasks. To that end, we have curated a polymerization dataset for vinyl polymers covering reactions and retrosynthesis for representative homo-polymers and co-polymers. Overall, we obtain a forward model Top-4 accuracy of 80% and a backward model Top-4 accuracy of 60%. We further analyze the model performance with representative polymerization examples and evaluate its prediction quality from a materials science perspective. To enable validation and reuse, we have made our models and data available in public repositories.
Significantly enhanced performance for phenol compounds removal by MOF-5 nano-composite via its surface modification
Authors: Razavi Leila , Raissi Heidar , Hashemzehi Ozra , Farzad Farzaneh 
Published: June 2024

AbstractThe present study is focused on the use of cubic metal-organic frameworks-5 (MOF-5) and its functionalized form in the removal of phenolic pollutants by molecular dynamics (MD) and Well-tempered metadynamics (WTMD) simulation methods. It was found that the adsorption mechanism of MOF-5s/phenolic compounds is mostly due to the van der Waals and π–π interactions. However, electrostatic and hydrogen bond (HB) interactions also play a significant role in removing phenolic pollutants by MOF-5 and its functionalized form. The results show that the fluorine functional group (F-MOF-5) increases the adsorption capacity of phenol compounds on the adsorbent surface. By functionalizing the MOF-5 with a methyl functional group (CH3-MOF-5), the adsorption strength decreases. The WTMD calculation confirmed that at the most stable state, the free energy (FE) value of system II (the most stable system in functionalized systems with –F functional group) is about −289.528 kJ mol−1. This value is ~5.781 and 35.514 kJ mol−1 more negative than the FE of the I and III systems (the most stable systems in the pristine and CH3-MOF-5/pollutant systems, respectively). Altogether, the results indicate that F-MOF-5 can be considered a more suitable adsorbent than MOF-5 and CH3-MOF-5 for phenolic pollutants removal from the environment for more assessment.
Cell shape sensing licenses dendritic cells for homeostatic migration to lymph nodes
Authors: Alraies Zahraa , Rivera Claudia A. , Delgado Maria-Graciela , Sanséau Doriane , Maurin Mathieu , Amadio Roberto , Maria Piperno Giulia , Dunsmore Garett , Yatim Aline , Lacerda Mariano Livia , Kniazeva Anna , Calmettes Vincent , Sáez Pablo J. , Williart Alice , Popard Henri , Gratia Matthieu , Lamiable Olivier , Moreau Aurélie , Fusilier Zoé , Crestey Lou , Albaud Benoit , Legoix Patricia , Dejean Anne S. , Le Dorze Anne-Louise , Nakano Hideki , Cook Donald N. , Lawrence Toby , Manel Nicolas , Benvenuti Federica , Ginhoux Florent , Moreau Hélène D. , P. F. Nader Guilherme , Piel Matthieu , Lennon-Duménil Ana-Maria 
Published: June 2024

AbstractImmune cells experience large cell shape changes during environmental patrolling because of the physical constraints that they encounter while migrating through tissues. These cells can adapt to such deformation events using dedicated shape-sensing pathways. However, how shape sensing affects immune cell function is mostly unknown. Here, we identify a shape-sensing mechanism that increases the expression of the chemokine receptor CCR7 and guides dendritic cell migration from peripheral tissues to lymph nodes at steady state. This mechanism relies on the lipid metabolism enzyme cPLA2, requires nuclear envelope tensioning and is finely tuned by the ARP2/3 actin nucleation complex. We also show that this shape-sensing axis reprograms dendritic cell transcription by activating an IKKβ–NF-κB-dependent pathway known to control their tolerogenic potential. These results indicate that cell shape changes experienced by immune cells can define their migratory behavior and immunoregulatory properties and reveal a contribution of the physical properties of tissues to adaptive immunity.
Cervical cancer screening using DNA methylation triage in a real-world population
Authors: Schreiberhuber Lena , Barrett James E. , Wang Jiangrong , Redl Elisa , Herzog Chiara , Vavourakis Charlotte D. , Sundström Karin , Dillner Joakim , Widschwendter Martin 
Published: June 2024

AbstractCervical cancer (CC) screening in women comprises human papillomavirus (HPV) testing followed by cytology triage of positive cases. Drawbacks, including cytology’s low reproducibility and requirement for short screening intervals, raise the need for alternative triage methods. Here we used an innovative triage technique, the WID-qCIN test, to assess the DNA methylation of human genes DPP6, RALYL and GSX1 in a real-life cohort of 28,017 women aged ≥30 years who attended CC screening in Stockholm between January and March 2017. In the analysis of all 2,377 HPV-positive samples, a combination of WID-qCIN (with a predefined threshold) and HPV16 and/or HPV18 (HPV16/18) detected 93.4% of cervical intraepithelial neoplasia grade 3 and 100% of invasive CCs. The WID-qCIN/HPV16/18 combination predicted 69.4% of incident cervical intraepithelial neoplasia grade 2 or worse compared with 18.2% predicted by cytology. Cytology or WID-qCIN/HPV16/18 triage would require 4.1 and 2.4 colposcopy referrals to detect one cervical intraepithelial neoplasia grade 2 or worse, respectively, during the 6 year period. These findings support the use of WID-qCIN/HPV16/18 as an improved triage strategy for HPV-positive women.
AgEvidence: a dataset to explore agro-ecological effects of conservation agriculture
Authors: Atwood Lesley , Gannett Maria , Wood Stephen A. 
Published: June 2024

AbstractConservation agriculture (CA) is a set of principles thought to be able to enhance crop productivity while minimizing impacts on the environment. The evidence base for CA can be challenging to synthesize because it encompasses many different practices and social and agroecological outcomes. To facilitate synthesis of CA evidence we have created a dataset organizing 218 response variables from five common categories of CA: cover crops, tillage management, pest management, nutrient management, and crop diversification. These data cover the Midwestern United States (U.S.) from 1980–2020. The dataset is also summarized and visualized on the AgEvidence website, which enables users to interactively explore, filter, and download data. We hope this dataset will help a wide variety of stakeholders, including researchers, policy makers, advocacy groups, and growers access the evidence needed to make informed and impactful decisions about how to produce food with less negative environmental impact.
Multiparametric MRI dataset for susceptibility-based radiomic feature extraction and analysis
Authors: Fiscone Cristiana , Sighinolfi Giovanni , Manners David Neil , Motta Lorenzo , Venturi Greta , Panzera Ivan , Zaccagna Fulvio , Rundo Leonardo , Lugaresi Alessandra , Lodi Raffaele , Tonon Caterina , Castelli Mauro 
Published: June 2024

AbstractMultiple sclerosis (MS) is a progressive demyelinating disease impacting the central nervous system. Conventional Magnetic Resonance Imaging (MRI) techniques (e.g., T2w images) help diagnose MS, although they sometimes reveal non-specific lesions. Quantitative MRI techniques are capable of quantifying imaging biomarkers in vivo, offering the potential to identify specific signs related to pre-clinical inflammation. Among those techniques, Quantitative Susceptibility Mapping (QSM) is particularly useful for studying processes that influence the magnetic properties of brain tissue, such as alterations in myelin concentration. Because of its intrinsic quantitative nature, it is particularly well-suited to be analyzed through radiomics, including techniques that extract a high number of complex and multi-dimensional features from radiological images. The dataset presented in this work provides information about normal-appearing white matter (NAWM) in a cohort of MS patients and healthy controls. It includes QSM-based radiomic features from NAWM and its tracts, and MR sequences necessary to implement the pipeline: T1w, T2w, QSM, DWI. The workflow is outlined in this article, along with an application showing feature reliability assessment.
A dataset describing chip parameters for rock breaking by chisel pick under deep-sea hydrostatic pressure
Authors: Liu Zenghui , Lv Rui , Chen Xinlei , Liu Kai , Wu Peng , Wei Changyun 
Published: June 2024

AbstractChip is a visual representation of rock breaking by cutter, and their related parameters are crucial for revealing the rock breaking mechanism in deep-sea mining. Based on sieving and three-dimensional size measurement methods widely used in mining engineering, this paper reports a dataset of chip parameters for rock breaking by chisel pick under deep-sea hydrostatic pressure. Specifically, we first designed an experimental setup that can accurately simulate deep-sea hydrostatic pressure, conducted rock breaking experiments and carefully collected chips. Subsequently, those chips were sieved, high-resolution images were collected, and the coarseness index (CI), chip size uniformity (n), absolute chip size (de), and fractal dimension (D) were measured. Finally, three-dimensional size (long, intermediate and short) was measured for 3064 chips with particle sizes greater than 4.75 mm. This dataset will be used by researchers to validate numerical simulations or optimize equipment structures related to deep-sea mining, including deep-sea rock mechanics, mining cutter and conveyor pipes.
Gap-free chromosome-level genomes of male and female spotted longbarbel catfish Hemibagrus guttatus
Authors: Yang Yexin , Liu Yi , Chen Fangcan , Wang Yuanyuan , Wu Yuli , He Zhichao , Liu Chao , Jiang Zhiyong , Mu Xidong , Bian Chao 
Published: June 2024

AbstractHemibagrus guttatus, also named as spotted longbarbel catfish, is an economical fish in China. However, their gender cannot be easily distinguished from their appearance, which largely impedes their artificial breeding. Therefore, we provided two gap-free chromosome-level genomes of male and female spotted longbarbel catfish by combining wtdbg2, LR_Gapcloser and TGS-GapCloser assembly approaches with Hi-C data and accurate Pacbio HiFi long-reads. We assembled 30 chromosomes without any gap. Their genome sizes are approximately 749.1 Mb and 747.8 Mb of male and female individuals. The completeness results of BUSCO evaluation show about 94.2% and 95.0%, representing a high-level of completeness of both genomes. We also obtained 35,277 and 34,571 protein-coding gene sets from male and female individuals. Both available gap-free chromosome-level genomes of H. guttatus will provide excellent references for resequencing of male and female individuals to identify accurate markers for distinguishing gender of this fish.
Experimental investigation on strengthening of Zea mays root fibres for biodegradable composite materials using potassium permanganate treatment
Authors: Kavitha S. Anne , Priya Retnam Krishna , Arunachalam Krishna Prakash , Avudaiappan Siva , Saavedra Flores Erick I. , Blanco David 
Published: June 2024

AbstractHumans are the only species who generate waste materials that cannot be broken down by natural processes. The ideal solution to this waste problem would be to employ only compostable materials. Biodegradable materials play a key role in creating a safer and greener world. Biodegradability is the gift that keeps on giving, in the sense of creating an Earth worth living. The future is thus best served by green energy, sustainability, and renewable resources. To realize such goals, waste should be considered as a valuable resource. In this context,Zea mays(Zm) root fibres, which are normally considered as agricultural waste, can be used as reinforcing substances in polymer matrices to produce structural composite materials. Before being used in composites, such fibres must be analysed for their physical properties. Chemical treatments can be employed to improve the structural quality of fibres, and the changes due to such modification can be analysed. Therefore, the current work examines the effect of permanganate treatment on the surface properties of Zm fibres. The raw and potassium permanganate-treated samples were assayed for various properties. Physical analysis of the fibre samples yielded details concerning the physical aspects of the fibres. The thermal conductivity and moisture absorption behaviour of the samples were analysed. Chemical analysis was employed to characterize the composition of both treated and untreated samples. p-XRD was employed to examine the crystalline nature of the Zm fibres. Numerous functional groups present in each sample were analysed by FTIR. Thermogravimetric analysis was used to determine the thermal stability of Zm fibres. Elemental analysis (CHNS and EDS) was used to determine the elemental concentrations of both raw and treated samples. The surface alterations of Zm fibres brought on by treatment were described using SEM analysis. The characteristics of Zm roots and the changes in quality due to treatment were reviewed, and there were noticeable effects due to the treatment. Both samples would have applications in various fields, and each could be used as a potential reinforcing material in the production of efficient bio-composites.
Probiotics relieve perioperative postoperative cognitive dysfunction induced by cardiopulmonary bypass through the kynurenine metabolic pathway
Authors: Zhang Xiaodong , Yang Yanzhang , Ma Xinyi , Cao Huijuan , Sun Yingjie 
Published: June 2024

AbstractPostoperative cognitive dysfunction (POCD) has become the popular critical post-operative consequences, especially cardiopulmonary bypass surgery, leading to an increased risk of mortality. However, no therapeutic effect about POCD. Probiotics are beneficial bacteria living in the gut and help to reduce the risk of POCD. However, the detailed mechanism is still not entirely known. Therefore, our research aims to uncover the effect and mechanism of probiotics in relieving POCD and to figure out the possible relationship between kynurenine metabolic pathway. 36 rats were grouped into three groups: sham operated group (S group, n = 12), Cardiopulmonary bypass group (CPB group, n = 12), and probiotics+CPB (P group, n = 12). After CPB model preparation, water maze test and Garcia score scale was performed to identify the neurological function. Immunofluorescence and Hematoxylin and eosin staining has been used for hippocampal neurons detection. Brain injury related proteins, oxidative stress factors, and inflammatory factors were detected using enzyme-linked immunosorbent assays (ELISA). Neuronal apoptosis was detected by TdT-mediated dUTP nick end-labeling (TUNEL) staining and western blot. High-performance liquid chromatography/mass spectrometry (HPLC/MS) was performed to detect the key factors of the kynurenine metabolic pathway. Our results demonstrated that probiotics improved neurological function of post-CPB rats. The administration of probiotics ameliorated memory and learning in spatial terms CPB rats (P < 0.05). Hematoxylin and eosin (H&E) staining data, S‐100β and neuron-specific enolase (NSE) data convinced that probiotics agonists reduced brain damage in CPB rats (P < 0.05). Moreover, probiotics regulated inflammatory factors, meanwhile attenuated hippocampal neuronal apoptosis. Probiotics alleviated POCD in rats with CPB through regulation of kynurenine metabolic signaling pathway.
A pre-Campanian Ignimbrite techno-cultural shift in the Aurignacian sequence of Grotta di Castelcivita, southern Italy
Authors: Falcucci Armando , Arrighi Simona , Spagnolo Vincenzo , Rossini Matteo , Higgins Owen Alexander , Muttillo Brunella , Martini Ivan , Crezzini Jacopo , Boschin Francesco , Ronchitelli Annamaria , Moroni Adriana 
Published: June 2024

AbstractThe Aurignacian is the first European technocomplex assigned toHomo sapiensrecognized across a wide geographic extent. Although archaeologists have identified marked chrono-cultural shifts within the Aurignacian mostly by examining the techno-typological variations of stone and osseous tools, unraveling the underlying processes driving these changes remains a significant scientific challenge. Scholars have, for instance, hypothesized that the Campanian Ignimbrite (CI) super-eruption and the climatic deterioration associated with the onset of Heinrich Event 4 had a substantial impact on European foraging groups. The technological shift from the Protoaurignacian to the Early Aurignacian is regarded as an archaeological manifestation of adaptation to changing environments. However, some of the most crucial regions and stratigraphic sequences for testing these scenarios have been overlooked. In this study, we delve into the high-resolution stratigraphic sequence of Grotta di Castelcivita in southern Italy. Here, the Uluzzian is followed by three Aurignacian layers, sealed by the eruptive units of the CI. Employing a comprehensive range of quantitative methods—encompassing attribute analysis, 3D model analysis, and geometric morphometrics—we demonstrate that the key technological feature commonly associated with the Early Aurignacian developed well before the deposition of the CI tephra. Our study provides thus the first direct evidence that the volcanic super-eruption played no role in this cultural process. Furthermore, we show that local paleo-environmental proxies do not correlate with the identified patterns of cultural continuity and discontinuity. Consequently, we propose alternative research paths to explore the role of demography and regional trajectories in the development of the Upper Paleolithic.
Using organ-on-a-chip technology to study haemorrhagic activities of snake venoms on endothelial tubules
Authors: Bittenbinder Mátyás A. , Bonanini Flavio , Kurek Dorota , Vulto Paul , Kool Jeroen , Vonk Freek J. 
Published: June 2024

AbstractSnakebite envenomation is a major public health issue which causes severe morbidity and mortality, affecting millions of people annually. Of a diverse range of clinical manifestations, local and systemic haemorrhage are of particular relevance, as this may result in ischemia, organ failure and even cardiovascular shock. Thus far, in vitro studies have failed to recapitulate the haemorrhagic effects observed in vivo. Here, we present an organ-on-a-chip approach to investigate the effects of four different snake venoms on a perfused microfluidic blood vessel model. We assess the effect of the venoms of four snake species on epithelial barrier function, cell viability, and contraction/delamination. Our findings reveal two different mechanisms by which the microvasculature is being affected, either by disruption of the endothelial cell membrane or by delamination of the endothelial cell monolayer from its matrix. The use of our blood vessel model may shed light on the key mechanisms by which tissue-damaging venoms exert their effects on the capillary vessels, which could be helpful for the development of effective treatments against snakebites.
Revealing short-term dynamics of tropical cyclone wind speeds from satellite synthetic aperture radar
Authors: Avenas Arthur , Chapron Bertrand , Mouche Alexis , Platzer Paul , Vinour Léo 
Published: June 2024

AbstractBoth unresolved physics in numerical models and limited theoretical understanding of the small-scale diffusion processes occurring near the ocean surface hamper predictability of tropical cyclone (TC) wind changes. An analytical model is here developed to diagnose the short-term evolution of the TC wind profile. An effective frictional parameter is introduced to control the unknown diffusion effects. When this frictional parameter is adjusted to match the TC intensity change, solutions are consistent with observed high-resolution ocean surface wind speeds from satellite synthetic aperture radar (SAR). The initial high-resolution estimate of the near-core wind structure is then found to strongly modulate the wind profile evolution. The frictional parameter can, unfortunately, not efficiently be calibrated using outer-core wind speed changes. Low-resolution observations or standard numerical weather predictions may thus not be directly used to reinterpret and anticipate short-term TC wind changes. The expected accumulation of orbiting SAR sensors as well as improved measurements of the ocean-atmosphere boundary layer characteristics shall then become essential to more precisely monitor TC dynamics.