bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnesium Isotopes of Carbonate Reveal Seasonal Climate Variation in the Central East Asia During the Middle Eocene
Authors: Zhu Huaxi , Hu Rong , Li Weiqiang , Long Yinshuang , Lai Wen , Zhang Yang , Zhang Xia , Guo Yangrui , Ji Junfeng , Lu Huayu 
Published: May 2024

AbstractIt is debated whether there was strong climate seasonality during the Eocene, which provides a close geological analogy for near‐future scenarios of greenhouse gas emissions. Lithological data suggest the existence of a broad arid zone centered around 30°N paleo‐latitude, while a humid climate was supported by palaeobotanic assemblages in East Asia. Here, we report the occurrence of massive primary lacustrine dolomite and magnesite in the central East Asia during the middle Eocene. We provide a novel perspective from magnesium isotopes to link the formation of Mg‐carbonates to seasonal dry‐wet cycles. Rapid magnesium input during the rainy season and intense evaporation in the dry season likely caused the formation of magnesium carbonates in an enclosed lake. These findings provide insights into hydroclimatic seasonality during the Eocene, contributing to our understanding of the hydrological cycle response to a greenhouse climate.
Attention towards chemistry agnostic and explainable battery lifetime prediction
Authors: Rahmanian Fuzhan , Lee Robert M. , Linzner Dominik , Michel Kathrin , Merker Leon , Berkes Balazs B. , Nuss Leah , Stein Helge Sören 
Published: May 2024

AbstractPredicting and monitoring battery life early and across chemistries is a significant challenge due to the plethora of degradation paths, form factors, and electrochemical testing protocols. Existing models typically translate poorly across different electrode, electrolyte, and additive materials, mostly require a fixed number of cycles, and are limited to a single discharge protocol. Here, an attention-based recurrent algorithm for neural analysis (ARCANA) architecture is developed and trained on an ultra-large, proprietary dataset from BASF and a large Li-ion dataset gathered from literature across the globe. ARCANA generalizes well across this diverse set of chemistries, electrolyte formulations, battery designs, and cycling protocols and thus allows for an extraction of data-driven knowledge of the degradation mechanisms. The model’s adaptability is further demonstrated through fine-tuning on Na-ion batteries. ARCANA advances the frontier of large-scale time series models in analytical chemistry beyond textual data and holds the potential to significantly accelerate discovery-oriented battery research endeavors.
Growing strings in a chemical reaction space for searching retrosynthesis pathways
Authors: Zipoli Federico , Baldassari Carlo , Manica Matteo , Born Jannis , Laino Teodoro 
Published: May 2024

AbstractMachine learning algorithms have shown great accuracy in predicting chemical reaction outcomes and retrosyntheses. However, designing synthesis pathways remains challenging for existing machine learning models which are trained for single-step prediction. In this manuscript, we propose to recast the retrosynthesis problem as a string optimization problem in a data-driven fingerprint space, leveraging the similarity between chemical reactions and embedding vectors. Based on this premise, multi-step complex synthesis can be conceptualized as sequences that link multidimensional vectors (fingerprints) representing individual chemical reaction steps. We extracted an extensive corpus of chemical synthesis from patents and converted them into multidimensional strings. While optimizing the retrosynthetic path, we use the Euclidean metric to minimize the distance between the expanded trajectory of the growing retrosynthesis string and the corpus of extracted strings. By doing so, we promote the assembly of synthetic pathways that, in the chemical reaction space, will be more similar to existing retrosyntheses, thereby inheriting the strategic guidelines designed by human experts. We integrated this approach into the RXN platform (https://rxn.res.ibm.com/) and present the method’s application to complex synthesis as well as its ability to produce better synthetic strategies than current methodologies.
A maturity model for catalogues of semantic artefacts
Authors: Corcho Oscar , Ekaputra Fajar J. , Heibi Ivan , Jonquet Clement , Micsik Andras , Peroni Silvio , Storti Emanuele 
Published: May 2024

AbstractThis work presents a maturity model for assessing catalogues of semantic artefacts, one of the keystones that permit semantic interoperability of systems. We defined the dimensions and related features to include in the maturity model by analysing the current literature and existing catalogues of semantic artefacts provided by experts. In addition, we assessed 26 different catalogues to demonstrate the effectiveness of the maturity model, which includes 12 different dimensions (Metadata, Openness, Quality, Availability, Statistics, PID, Governance, Community, Sustainability, Technology, Transparency, and Assessment) and 43 related features (or sub-criteria) associated with these dimensions. Such a maturity model is one of the first attempts to provide recommendations for governance and processes for preserving and maintaining semantic artefacts and helps assess/address interoperability challenges.
A tree-based corpus annotated with Cyber-Syndrome, symptoms, and acupoints
Authors: Wang Wenxi , Zhao Zhan , Ning Huansheng 
Published: May 2024

AbstractProlonged and over-excessive interaction with cyberspace poses a threat to people’s health and leads to the occurrence of Cyber-Syndrome, which covers not only physiological but also psychological disorders. This paper aims to create a tree-shaped gold-standard corpus that annotates the Cyber-Syndrome, clinical manifestations, and acupoints that can alleviate their symptoms or signs, designating this corpus as CS-A. In the CS-A corpus, this paper defines six entities and relations subject to annotation. There are 448 texts to annotate in total manually. After three rounds of updating the annotation guidelines, the inter-annotator agreement (IAA) improved significantly, resulting in a higher IAA score of 86.05%. The purpose of constructing CS-A corpus is to increase the popularity of Cyber-Syndrome and draw attention to its subtle impact on people’s health. Meanwhile, annotated corpus promotes the development of natural language processing technology. Some model experiments can be implemented based on this corpus, such as optimizing and improving models for discontinuous entity recognition, nested entity recognition, etc. The CS-A corpus has been uploaded to figshare.
Metagenomic sequencing and reconstruction of 82 microbial genomes from barley seed communities
Authors: Tshisekedi Kalonji A. , De Maayer Pieter , Botes Angela 
Published: May 2024

AbstractBarley (Hordeum vulgare) is essential to global food systems and the brewing industry. Its physiological traits and microbial communities determine malt quality. Although microbes influence barley from seed health to fermentation, there is a gap in metagenomic insights during seed storage. Crucially, elucidating the changes in microbial composition associated with barley seeds is imperative for understanding how these fluctuations can impact seed health and ultimately, influence both agricultural yield and quality of barley-derived products. Whole metagenomes were sequenced from eight barley seed samples obtained at different storage time points from harvest to nine months. After binning, 82 metagenome-assembled genomes (MAGs) belonging to 26 distinct bacterial genera were assembled, with a substantial proportion of potential novel species. Most of our MAG dataset (61%) showed over 90% genome completeness. This pioneering barley seed microbial genome retrieval provides insights into species diversity and structure, laying the groundwork for understanding barley seed microbiome interactions at the genome level.
SAROS: A dataset for whole-body region and organ segmentation in CT imaging
Authors: Koitka Sven , Baldini Giulia , Kroll Lennard , van Landeghem Natalie , Pollok Olivia B. , Haubold Johannes , Pelka Obioma , Kim Moon , Kleesiek Jens , Nensa Felix , Hosch René 
Published: May 2024

AbstractThe Sparsely Annotated Region and Organ Segmentation (SAROS) dataset was created using data from The Cancer Imaging Archive (TCIA) to provide a large open-access CT dataset with high-quality annotations of body landmarks. In-house segmentation models were employed to generate annotation proposals on randomly selected cases from TCIA. The dataset includes 13 semantic body region labels (abdominal/thoracic cavity, bones, brain, breast implant, mediastinum, muscle, parotid/submandibular/thyroid glands, pericardium, spinal cord, subcutaneous tissue) and six body part labels (left/right arm/leg, head, torso). Case selection was based on the DICOM series description, gender, and imaging protocol, resulting in 882 patients (438 female) for a total of 900 CTs. Manual review and correction of proposals were conducted in a continuous quality control cycle. Only every fifth axial slice was annotated, yielding 20150 annotated slices from 28 data collections. For the reproducibility on downstream tasks, five cross-validation folds and a test set were pre-defined. The SAROS dataset serves as an open-access resource for training and evaluating novel segmentation models, covering various scanner vendors and diseases.
Peripheral blood transcriptomic profiling of molecular mechanisms commonly regulated by binge drinking and placebo effects
Authors: Shetty Amol Carl , Sivinski John , Cornell Jessica , McCracken Carrie , Sadzewicz Lisa , Mahurkar Anup , Wang Xing-Qun , Colloca Luana , Lin Weihong , Pilli Nageswara , Kane Maureen A. , Seneviratne Chamindi 
Published: May 2024

AbstractMolecular responses to alcohol consumption are dynamic, context-dependent, and arise from a complex interplay of biological and external factors. While many have studied genetic risk associated with drinking patterns, comprehensive studies identifying dynamic responses to pharmacologic and psychological/placebo effects underlying binge drinking are lacking. We investigated transcriptome-wide response to binge, medium, and placebo alcohol consumption by 17 healthy heavy social drinkers enrolled in a controlled, in-house, longitudinal study of up to 12 days. Using RNA-seq, we identified 251 and 13 differentially expressed genes (DEGs) in response to binge drinking and placebo, respectively. Eleven protein-coding DEGs had very large effect sizes in response to binge drinking (Cohen’s d > 1). Furthermore, binge dose significantly impacted the Cytokine-cytokine receptor interaction pathway (KEGG: hsa04060) across all experimental sequences. Placebo also impacted hsa04060, but only when administered following regular alcohol drinking sessions. Similarly, medium-dose and placebo commonly impacted KEGG pathways of Systemic lupus erythematosus, Neutrophil extracellular trap formation, and Alcoholism based on the sequence of drinking sessions. These findings together indicate the “dose-extending effects” of placebo at a molecular level. Furthermore, besides supporting alcohol dose-specific molecular changes, results suggest that the placebo effects may induce molecular responses within the same pathways regulated by alcohol.
Low-density lipoprotein particle profiles compared with standard lipids measurements in the association with asymptomatic intracranial artery stenosis
Authors: Vu Thien , Yano Yuichiro , Pham Huy Kien Tai , Mondal Rajib , Ohashi Mizuki , Kitaoka Kaori , Moniruzzaman Mohammad , Torii Sayuki , Shiino Akihiko , Tsuji Atsushi , Hisamatsu Takashi , Okamura Tomonori , Kondo Keiko , Kadota Aya , Watanabe Yoshiyuki , Nozaki Kazuhiko , Ueshima Hirotsugu , Miura Katsuyuki 
Published: May 2024

AbstractThe Shiga Epidemiological Study of Subclinical Atherosclerosis was conducted in Kusatsu City, Shiga, Japan, from 2006 to 2008. Participants were measured for LDL-p through nuclear magnetic resonance technology. 740 men participated in follow-up and underwent 1.5 T brain magnetic resonance angiography from 2012 to 2015. Participants were categorized as no-ICAS, and ICAS consisted of mild-ICAS (1 to < 50%) and severe-ICAS (≥ 50%) in any of the arteries examined. After exclusion criteria, 711 men left for analysis, we used multiple logistic regression to examine the association between lipid profiles and ICAS prevalence. Among the study participants, 205 individuals (28.8%) had ICAS, while 144 individuals (20.3%) demonstrated discordance between LDL-c and LDL-p levels. The discordance “low LDL-c–high LDL-p” group had the highest ICAS risk with an adjusted OR (95% CI) of 2.78 (1.55–5.00) in the reference of the concordance “low LDL-c–low LDL-p” group. This was followed by the concordance “high LDL-c–high LDL-p” group of 2.56 (1.69–3.85) and the discordance “high LDL-c–low LDL-p” group of 2.40 (1.29–4.46). These findings suggest that evaluating LDL-p levels alongside LDL-c may aid in identifying adults at a higher risk for ICAS.
Molecular characteristics and phylogenetic analysis of pigeon paramyxovirus type 1 isolates from pigeon meat farms in Shanghai (2009–2012)
Authors: Sheng Wenwei , Wang Kexuan , Gui Yaping , Qi Xinyong , Shen Liping , Zhang Yujie , Tang Congsheng , Li Xin , Tao Jun , Cao Chuangui , Qian Weidong , Liu Jian 
Published: May 2024

AbstractThe majority of pigeon paramyxovirus type 1 (PPMV-1) strains are generally non-pathogenic to chickens; however, they can induce severe illness and high mortality rates in pigeons, leading to substantial economic repercussions. The genomes of 11 PPMV-1 isolates from deceased pigeons on meat pigeon farms during passive monitoring from 2009 to 2012 were sequenced and analyzed using polymerase chain reaction and phylogenetic analysis. The complete genome lengths of 11 isolates were approximately 15,192 nucleotides, displaying a consistent gene order of 3′-NP-P-M-F-HN-L-5′. ALL isolates exhibited the characteristic motif of 112RRQKRF117 at the fusion protein cleavage site, which is characteristic of velogenic Newcastle disease virus. Moreover, multiple mutations have been identified within the functional domains of the F and HN proteins, encompassing the fusion peptide, heptad repeat region, transmembrane domains, and neutralizing epitopes. Phylogenetic analysis based on sequences of the F gene unveiled that all isolates clustered within genotype VI in class II. Further classification identified at least two distinct sub-genotypes, with seven isolates classified as sub-genotype VI.2.1.1.2.2, whereas the others were classified as sub-genotype VI.2.1.1.2.1. This study suggests that both sub-genotypes were implicated in severe disease manifestation among meat pigeons, with sub-genotype VI.2.1.1.2.2 displaying an increasing prevalence among Shanghai’s meat pigeon population since 2011. These results emphasize the value of developing pigeon-specific vaccines and molecular diagnostic tools for monitoring and proactively managing potential PPMV-1 outbreaks.
Enhancing Ethiopian power distribution with novel hybrid renewable energy systems for sustainable reliability and cost efficiency
Authors: Agajie Takele Ferede , Fopah-Lele Armand , Amoussou Isaac , Khan Baseem , Bajaj Mohit , Zaitsev Ievgen , Tanyi Emmanuel 
Published: May 2024

AbstractEconomic development relies on access to electrical energy, which is crucial for society’s growth. However, power shortages are challenging due to non-renewable energy depletion, unregulated use, and a lack of new energy sources. Ethiopia’s Debre Markos distribution network experiences over 800 h of power outages annually, causing financial losses and resource waste on diesel generators (DGs) for backup use. To tackle these concerns, the present study suggests a hybrid power generation system, which combines solar and biogas resources, and integrates Superconducting Magnetic Energy Storage (SMES) and Pumped Hydro Energy Storage (PHES) technologies into the system. The study also thoroughly analyzes the current and anticipated demand connected to the distribution network using a backward/forward sweep load flow analysis method. The results indicate that the total power loss has reached its absolute maximum, and the voltage profiles of the networks have dropped below the minimal numerical values recommended by the Institute of Electrical and Electronics Engineers (IEEE) standards (i.e., 0.95–1.025 p.u.). After reviewing the current distribution network’s operation, additional steps were taken to improve its effectiveness, using metaheuristic optimization techniques to account for various objective functions and constraints. In the results section, it is demonstrated that the whale optimization algorithm (WOA) outperforms other metaheuristic optimization techniques across three important objective functions: financial, reliability, and greenhouse gas (GHG) emissions. This comparison is based on the capability of the natural selection whale optimization algorithm (NSWOA) to achieve the best possible values for four significant metrics: Cost of Energy (COE), Net Present Cost (NPC), Loss of Power Supply Probability (LPSP), and GHG Emissions. The NSWOA achieved optimal values for these metrics, namely 0.0812 €/kWh, 3.0017 × 106 €, 0.00875, and 7.3679 × 106 kg reduced, respectively. This is attributable to their thorough economic, reliability, and environmental evaluation. Finally, the forward/backward sweep load flow analysis employed during the proposed system’s integration significantly reduced the impact of new energy resources on the distribution network. This was evident in the reduction of total power losses from 470.78 to 18.54 kW and voltage deviation from 6.95 to 0.35 p.u., as well as the voltage profile of the distribution system being swung between 1 and 1.0234 p.u., which now comply with the standards set by the IEEE. Besides, a comparison of the cost and GHG emission efficiency of the proposed hybrid system with existing (grid + DGs) and alternative (only DGs) scenarios was done. The findings showed that, among the scenarios examined, the proposed system is the most economical and produces the least amount of GHG emissions.
Integrated multi-omic approach reveals the effect of a Graminaceae-derived biostimulant and its lighter fraction on salt-stressed lettuce plants
Authors: Monterisi Sonia , Zhang Leilei , Garcia-Perez Pascual , Alzate Zuluaga Monica Yorlady , Ciriello Michele , El-Nakhel Christophe , Buffagni Valentina , Cardarelli Mariateresa , Colla Giuseppe , Rouphael Youssef , Cesco Stefano , Lucini Luigi , Pii Youry 
Published: May 2024

AbstractPlant biostimulants are widely applied in agriculture for their ability to improve plant fitness. In the present work, the impact of Graminaceae-derived protein hydrolysate (P) and its lighter molecular fraction F3 (< 1 kDa) on lettuce plants, subjected to either no salt or high salt conditions, was investigated through the combination of metabolomics and transcriptomics. The results showed that both treatments significantly modulated the transcriptome and metabolome of plants under salinity stress, highlighting an induction of the hormonal response. Nevertheless, P and F3 also displayed several peculiarities. F3 specifically modulated the response to ethylene and MAPK signaling pathway, whereas P treatment induced a down-accumulation of secondary metabolites, albeit genes controlling the biosynthesis of osmoprotectants and antioxidants were up-regulated. Moreover, according with the auxin response modulation, P promoted cell wall biogenesis and plasticity in salt-stressed plants. Notably, our data also outlined an epigenetic control of gene expression induced by P treatment. Contrarily, experimental data are just partially in agreement when not stressed plants, treated with P or F3, were considered. Indeed, the reduced accumulation of secondary metabolites and the analyses of hormone pathways modulation would suggest a preferential allocation of resources towards growth, that is not coherent with the down-regulation of the photosynthetic machinery, the CO2 assimilation rate and leaves biomass. In conclusion, our data demonstrate that, although they might activate different mechanisms, both the P and F3 can result in similar benefits, as far as the accumulation of protective osmolytes and the enhanced tolerance to oxidative stress are concerned. Notably, the F3 fraction exhibits slightly greater growth promotion effects under high salt conditions. Most importantly, this research further corroborates that biostimulants’ mode of action is dependent on plants’ physiological status and their composition, underscoring the importance of investigating the bioactivity of the different molecular components to design tailored applications for the agricultural practice.
Metabolic network analysis of pre-ASD newborns and 5-year-old children with autism spectrum disorder
Authors: Lingampelly Sai Sachin , Naviaux Jane C. , Heuer Luke S. , Monk Jonathan M. , Li Kefeng , Wang Lin , Haapanen Lori , Kelland Chelsea A. , Van de Water Judy , Naviaux Robert K. 
Published: May 2024

AbstractClassical metabolomic and new metabolic network methods were used to study the developmental features of autism spectrum disorder (ASD) in newborns (n = 205) and 5-year-old children (n = 53). Eighty percent of the metabolic impact in ASD was caused by 14 shared biochemical pathways that led to decreased anti-inflammatory and antioxidant defenses, and to increased physiologic stress molecules like lactate, glycerol, cholesterol, and ceramides. CIRCOS plots and a new metabolic network parameter, $$\dot{{{\boldsymbol{V}}}}\!$$

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net, revealed differences in both the kind and degree of network connectivity. Of 50 biochemical pathways and 450 polar and lipid metabolites examined, the developmental regulation of the purine network was most changed. Purine network hub analysis revealed a 17-fold reversal in typically developing children. This purine network reversal did not occur in ASD. These results revealed previously unknown metabolic phenotypes, identified new developmental states of the metabolic correlation network, and underscored the role of mitochondrial functional changes, purine metabolism, and purinergic signaling in autism spectrum disorder.
Fluorescence imaging sheds light on the immune evasion mechanisms of hepatic stellate cells mediated by superoxide anion
Authors: Mao Yuantao , Wu Chuanchen , Wang Xin , Zhang Fanghui , Qi Xinru , Li Xia , Li Ping , Tang Bo 
Published: May 2024

AbstractWhether and how the reactive oxygen species generated by hepatic stellate cells (HSCs) promote immune evasion of hepatocellular carcinoma (HCC) remains mysterious. Therefore, investigating the function of superoxide anion (O2•−), the firstly generated reactive oxygen species, during the immune evasion become necessary. In this work, we establish a novel in situ imaging method for visualization of O2•− changes in HSCs based on a new two-photon fluorescence probe TPH. TPH comprises recognition group for O2•− and HSCs targeting peptides. We observe that O2•− in HSCs gradually rose, impairing the infiltration of CD8+ T cells in HCC mice. Further studies reveal that the cyclin-dependent kinase 4 is deactivated by O2•−, and then cause the up-regulation of PD-L1. Our work provides molecular insights into HSC-mediated immune evasion of HCC, which may represent potential targets for HCC immunotherapy.