bluuebunny/crossref_metadata_2025_split huggingface dataset:
The unique ORF8 protein from SARS-CoV-2 binds to human dendritic cells and induces a hyper-inflammatory cytokine storm
Authors: Hamdorf Matthias , Imhof Thomas , Bailey-Elkin Ben , Betz Janina , Theobald Sebastian J , Simonis Alexander , Di Cristanziano Veronica , Gieselmann Lutz , Dewald Felix , Lehmann Clara , Augustin Max , Klein Florian , Alejandre Alcazar Miguel A , Rongisch Robert , Fabri Mario , Rybniker Jan , Goebel Heike , Stetefeld Jörg , Brachvogel Bent , Cursiefen Claus , Koch Manuel , Bock Felix 
Published: October 2023

Abstract
The novel coronavirus pandemic, first reported in December 2019, was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 infection leads to a strong immune response and activation of antigen-presenting cells, which can elicit acute respiratory distress syndrome (ARDS) characterized by the rapid onset of widespread inflammation, the so-called cytokine storm. In response to viral infections, monocytes are recruited into the lung and subsequently differentiate into dendritic cells (DCs). DCs are critical players in the development of acute lung inflammation that causes ARDS. Here, we focus on the interaction of a specific SARS-CoV-2 open reading frame protein, ORF8, with DCs. We show that ORF8 binds to DCs, causes pre-maturation of differentiating DCs, and induces the secretion of multiple proinflammatory cytokines by these cells. In addition, we identified DC-SIGN as a possible interaction partner of ORF8 on DCs. Blockade of ORF8 leads to reduced production of IL-1β, IL-6, IL-12p70, TNF-α, MCP-1 (also named CCL2), and IL-10 by DCs. Therefore, a neutralizing antibody blocking the ORF8-mediated cytokine and chemokine response could be an improved therapeutic strategy against SARS-CoV-2.
Feeding and reproductive parameters of adult female Ixodes scapularis (Acari: Ixodidae) and Amblyomma americanum parasitizing white-tailed deer (Odocoileus virginianus)
Authors: Baker Alec S , Persinger Kelly A , Olafson Pia U , Mulenga Albert O , Johnson Tammi L 
Published: October 2023

Abstract
White-tailed deer Odocoileus virginianus (Zimmermann) (Artiodactyla: Cervidae) are the main host for adult Ixodes scapularis Say (Acari: Ixodidae) (blacklegged tick) and all stages of Amblyomma americanum Linnaeus (Acari: Ixodidae) (lone star tick). However, literature describing the feeding and reproductive parameters of these tick species when feeding on this host is limited. We experimentally infested white-tailed deer with adult pairs of either I. scapularis or A. americanum to improve our understanding of these tick–host relationships. Our study used tick-naïve white-tailed deer and restricted host grooming throughout the infestation. For I. scapularis, the days to repletion (mean ± SE, 6.04 ± 0.07), engorgement weight of replete females (0.20 ± 0.0032 g), duration of oviposition (32 ± 0.45 d), egg mass weight (0.10 ± 0.0027 g), and number of eggs laid per tick (1,803.00 ± 49.00) were recorded. Data from A. americanum were also recorded, including days to repletion (11.00 ± 0.063), engorgement weight of replete females (0.63 ± 0.025 g), duration of oviposition (37.00 ± 1.30 d), egg mass weight (0.34 ± 0.017 g), and number of eggs laid per tick (5,873.00 ± 291.00). These biological parameter data could be used as variables in models (e.g., LYMESIM 2.0) to determine how white-tailed deer influence I. scapularis and A. americanum populations in nature, and to evaluate the protective efficacy of tick-antigen-based antitick vaccines.
A numerical investigation of microtube length effect on convective boiling
Authors: Hsu Hua-Yi , Lin Yu-Chen , Chen Zong-You , Wang Ying , Li Cheng-En , Pai Shong-Han , Lin Chia-Wei 
Published: October 2023

Abstract
The microtube length significantly influences the convective boiling process and associated heat transfer characteristics. Other than high heat transfer, low pressure drop is also desired to improve the energy efficiency of the pumping system. This work numerically investigates the microtube length effect on heat transfer and pressure drops of convective boiling with the volume of fluid (VOF) method. The simulation results of vapor formation, heat transfer coefficient, and pressure drop are shown with different microtube lengths L = 2–20 mm. The onset of boiling is around 2 mm away from the mass flux inlet. The subcooled boiling regime can be observed between 2 and 10 mm. Three distinct regimes, liquid single-phase flow, bubbly flow, and plug flow, are shown in the longer microtubes (L = 15 mm and 20 mm). It is found that shorter microtubes can lead to less bubble formation with higher heat transfer and lower pressure drop. The average heat transfer coefficient can achieve 2432 W/(m2K) with a lower quasi-steady total pressure drop Δp|total of 32.8 Pa inside a 2-mm-long microtube. This work offers a detailed study of the impact of microtube length on convective boiling, along with pertinent physical insights. It may serve as an indicator for future microscale heat transfer application designs.
Homeostatic evidence of management-induced phosphorus decoupling from soil microbial carbon and nitrogen metabolism
Authors: Zhang Lihua , Jia Lizhi , He Liyuan , Lipson David A , Wang Yihui , Wang Shunzhong , Xu Xiaofeng 
Published: October 2023

Abstract
The theory of microbial stoichiometry can predict the proportional coupling of microbial assimilation of carbon (C), nitrogen (N), and phosphorus (P). The proportional coupling is quantified by the homeostasis value (H). Covariation of H values for C, N, and P indicates that microbial C, N, and P assimilation are coupled. Here, we used a global dataset to investigate the spatiotemporal dynamics of H values of microbial C, N, and P across biomes. We found that land use and management led to the decoupling of P from C and N metabolism over time and across space. Results from structural equation modeling revealed that edaphic factors dominate the microbial homeostasis of P, while soil elemental concentrations dominate the homeostasis of C and N. This result was further confirmed using the contrasting factors on microbial P vs. microbial C and N derived from a machine-learning algorithm. Overall, our study highlights the impacts of management on shifting microbial roles in nutrient cycling.
Styrax (Liquidambar orientalis Mill.) promotes mitochondrial function and reduces cardiac damage following myocardial ischemic injury: the role of the AMPK-PGC1α signaling pathway
Authors: Mu Fei , Zhao Jiaxin , Zhao Meina , Lin Rui , Liu Kedi , Zhao Shi , Tao Xingru , Li Weihong , Dai Qi , Xi Miaomiao , Tang Haifeng , Wang Jingwen 
Published: October 2023

Abstract

Objectives
To explore the effect of extract of Styrax (ES) on myocardial ischemic injury and its molecular mechanism, indirectly providing a theoretical basis for the development of ES.

Methods
In order to assess the impact of ES treatment on ischemic heart disease, both a left anterior descending ligation-induced myocardial infarction (MI) model and an ischemia/hypoxia (I/H)-induced H9c2 cell injury model have been constructed. Specifically, Sprague–Dawley rats were randomly assigned to the following groups (n = 8) and administered intragastrically once a day for seven consecutive days: Sham group, MI group, ES-L (0.2 g/kg) group, ES-M (0.4 g/kg) group, ES-H (0.8 g/kg) group, and trimetazidine (TMZ, 0.02 g/kg) group. The cardiac functions and biochemical assessment of rats were detected. Then, we validated experimentally the targets and mechanism of ES on these pathological processes in I/H-induced H9c2 cell injury model.

Key findings
These results showed that different doses of ES (0.2 g/kg, 0.4 g/kg, 0.8 g/kg, intragastric) significantly improved myocardial structure and function when compared to the MI group. The results of 2,3,5-triphenyltetrazolium chloride (TTC), hematoxylin-eosin, and masson staining indicated that ES could significantly reduce infarct size, inhibit myocardium apoptosis, and decrease myocardial fibrosis. Moreover, ES distinctly suppressed the serum levels of lactate dehydrogenase (LDH), cardiac troponin T (cTnT), and creatine kinase-MB (CK-MB), alleviated myocardial mitochondrial morphology, and stimulated adenosine triphosphate (ATP) production, increased the level of succinate dehydrogenase (SDH), complex I and complex V activity. Different doses of ES (5 μg/ml, 10 μg/ml, 20 μg/ml) also improved cardiomyocyte morphology and decreased the apoptosis rate in H9c2 cells that had been exposed to I/H. Furthermore, the results of western blotting and qRT-PCR indicated that ES promoted the expression of proteins and mRNA related to energy metabolism, including phosphorylated adenosine monophosphate activated protein kinase (p-AMPK), peroxisome proliferator activated receptor gamma coactivator 1 alpha (PCG-1α), nuclear respiratory factor 1, and mitochondrial transcription factor A (TFAM). Mechanically, after the administration of Compound C (dorsomorphin), an AMPK inhibitor, these effects of myocardial protection produced by ES were reversed.

Conclusions
Collectively, these results demonstrated that ES could improve myocardial mitochondrial function and reduce ischemic injury by activating AMPK/PCG-1α signaling pathway, while indicating its potential advantages as a dietary supplement.
A Forty-Year-Old Campaign: Anne Frank’s Diary and the Holocaust Deniers, 1958–1998
Authors: Porat Dina 
Published: October 2023

Abstract
On December 9, 1998, the Dutch court in Amsterdam ruled Anne Frank’s diary to be authentic, and that anyone who cast doubt on its authenticity was breaking the law and would be fined. This article examines the ongoing battle between those who view themselves as charged with the legacy of the diary and the Holocaust deniers; it also examines the methods used by the latter and their possible influence on society. The first half deals with the events leading to the writing of the diary, its publication, theatrical and cinematic adaptations, and examines how the Holocaust deniers came to use those events in their claims. The second half deals with the claims themselves and their development over the years, and the deniers’ attempts to reach the widest possible audience in an attempt to sully the image of one of the central symbols of the Holocaust period, Anne Frank, The Diary of a Young Girl.
Compact binary formation in open star clusters – I. High formation efficiency of Gaia BHs and their multiplicities
Authors: Tanikawa Ataru , Cary Savannah , Shikauchi Minori , Wang Long , Fujii Michiko S 
Published: October 2023

ABSTRACT
Gaia BHs, black hole (BH) binaries discovered from data base of an astrometric telescope Gaia, pose a question to the standard binary evolution model. We have assessed whether Gaia BHs can be formed through dynamical capture in open clusters rather than through isolated binary evolution. We have performed gravitational N-body simulations of 100 open clusters with $10^5 \, \mathrm{M}_\odot$ in total for each metallicity Z = 0.02, 0.01, and 0.005. We have discovered one Gaia BH-like binary escaping from an open cluster, and found that the formation efficiency of Gaia BHs in open clusters ($\sim 10^{-5} \, \mathrm{M}_\odot ^{-1}$) is larger than in isolated binaries ($\sim 10^{-8} \, \mathrm{M}_\odot ^{-1}$) by 3 orders of magnitude. The Gaia BH-like binary is the inner binary of a triple star system. Gaia BHs can have tertiary stars frequently, if they are formed in open clusters. Combining additional N-body simulations with 8000 open clusters with $8 \times 10^6 \, \mathrm{M}_\odot$, we have estimated the number of Gaia BHs in the Milky Way disc to 104–105 (depending on the definitions of Gaia BHs), large enough for the number of Gaia BHs discovered so far. Our results indicate that the discoveries of Gaia BHs do not request the reconstruction of the standard binary evolution model, and that Gaia BHs are a probe for the dynamics of open clusters already evaporated.
MACC: a visual interactive knowledgebase of metabolite-associated cell communications
Authors: Gao Jian , Mo Saifeng , Wang Jun , Zhang Mou , Shi Yao , Zhu Chuhan , Shang Yuxuan , Tang Xinyue , Zhang Shiyue , Wu Xinwen , Xu Xinyan , Wang Yiheng , Li Zihao , Zheng Genhui , Chen Zikun , Wang Qiming , Tang Kailin , Cao Zhiwei 
Published: October 2023

Abstract
Metabolite-associated cell communications play critical roles in maintaining the normal biological function of human through coordinating cells, organs and physiological systems. Though substantial information of MACCs has been continuously reported, no relevant database has become available so far. To address this gap, we here developed the first knowledgebase (MACC), to comprehensively describe human metabolite-associated cell communications through curation of experimental literatures. MACC currently contains: (a) 4206 carefully curated metabolite-associated cell communications pairs involving 244 human endogenous metabolites and reported biological effects in vivo and in vitro; (b) 226 comprehensive cell subtypes and 296 disease states, such as cancers, autoimmune diseases, and pathogenic infections; (c) 4508 metabolite-related enzymes and transporters, involving 542 pathways; (d) an interactive tool with user-friendly interface to visualize networks of multiple metabolite-cell interactions. (e) overall expression landscape of metabolite-associated gene sets derived from over 1500 single-cell expression profiles to infer metabolites variations across different cells in the sample. Also, MACC enables cross-links to well-known databases, such as HMDB, DrugBank, TTD and PubMed etc. In complement to ligand-receptor databases, MACC may give new perspectives of alternative communication between cells via metabolite secretion and adsorption, together with the resulting biological functions. MACC is publicly accessible at: http://macc.badd-cao.net/
CMAUP database update 2024: extended functional and association information of useful plants for biomedical research
Authors: Hou Dongyue , Lin Hanbo , Feng Yuhan , Zhou Kaicheng , Li Xingxiu , Yang Yuan , Wang Shuaiqi , Yang Xue , Wang Jiayu , Zhao Hui , Zhang Xuyao , Fan Jiajun , Lu SongLin , Wang Dan , Zhu Lyuhan , Ju Dianwen , Chen Yu Zong , Zeng Xian 
Published: October 2023

Abstract
Knowledge of the collective activities of individual plants together with the derived clinical effects and targeted disease associations is useful for plant-based biomedical research. To provide the information in complement to the established databases, we introduced a major update of CMAUP database, previously featured in NAR. This update includes (i) human transcriptomic changes overlapping with 1152 targets of 5765 individual plants, covering 74 diseases from 20 027 patient samples; (ii) clinical information for 185 individual plants in 691 clinical trials; (iii) drug development information for 4694 drug-producing plants with metabolites developed into approved or clinical trial drugs; (iv) plant and human disease associations (428 737 associations by target, 220 935 reversion of transcriptomic changes, 764 and 154121 associations by clinical trials of individual plants and plant ingredients); (v) the location of individual plants in the phylogenetic tree for navigating taxonomic neighbors, (vi) DNA barcodes of 3949 plants, (vii) predicted human oral bioavailability of plant ingredients by the established SwissADME and HobPre algorithm, (viii) 21–107% increase of CMAUP data over the previous version to cover 60 222 chemical ingredients, 7865 plants, 758 targets, 1399 diseases, 238 KEGG human pathways, 3013 gene ontologies and 1203 disease ontologies. CMAUP update version is freely accessible at https://bidd.group/CMAUP/index.html.
AnimalMetaOmics: a multi-omics data resources for exploring animal microbial genomes and microbiomes
Authors: Hu Ruirui , Li Fulin , Chen Yifan , Liu Chuyang , Li Jiawei , Ma Zhongchen , Wang Yue , Cui Chaowen , Luo Chengfang , Zhou Ping , Ni Wei , Yang Qing-Yong , Hu Shengwei 
Published: October 2023

Abstract
The Animal Meta-omics landscape database (AnimalMetaOmics, https://yanglab.hzau.edu.cn/animalmetaomics#/) is a comprehensive and freely available resource that includes metagenomic, metatranscriptomic, and metaproteomic data from various non-human animal species and provides abundant information on animal microbiomes, including cluster analysis of microbial cognate genes, functional gene annotations, active microbiota composition, gene expression abundance, and microbial protein identification. In this work, 55 898 microbial genomes were annotated from 581 animal species, including 42 924 bacterial genomes, 12 336 virus genomes, 496 archaea genomes and 142 fungi genomes. Moreover, 321 metatranscriptomic datasets were analyzed from 31 animal species and 326 metaproteomic datasets from four animal species, as well as the pan-genomic dynamics and compositional characteristics of 679 bacterial species and 13 archaea species from animal hosts. Researchers can efficiently access and acquire the information of cross-host microbiota through a user-friendly interface, such as species, genomes, activity levels, expressed protein sequences and functions, and pan-genome composition. These valuable resources provide an important reference for better exploring the classification, functional diversity, biological process diversity and functional genes of animal microbiota.
Mutual promotion of co-condensation of KRAS G-quadruplex and a well-folded protein HMGB1
Authors: Wang Yu , Cao Kaiming , Zong Mingxi , Yuan Siming , Zhang Na , Liu Yangzhong 
Published: October 2023

Abstract
Liquid−liquid phase separation (LLPS) of G-quadruplex (GQ) is involved in many crucial cellular processes, while the quadruplex-folding and their functions are typically modulated by specific DNA-binding proteins. However, the regulatory mechanism of binding proteins, particularly the well-folded proteins, on the LLPS of GQs is largely unknown. Here, we investigated the effect of HMGB1 on the condensation of a G-quadruplex of KRAS promoter (GQKRAS). The results show that these two rigid macro-biomolecules undergo co-condensation through a mutual promotion manner, while neither of them can form LLPS alone. Fluidity measurements confirm that the liquid-like droplets are highly dynamic. HMGB1 facilitates and stabilizes the quadruplex folding of GQKRAS, and this process enhances their co-condensation. The KRAS promoter DNA retains quadruplex folding in the droplets; interference with the GQ-folding disrupts the co-condensation of GQKRAS/HMGB1. Mechanistic studies reveal that electrostatic interaction is a key driving force of the interaction and co-condensation of GQKRAS/HMGB1; meanwhile, the recognition of two macro-biomolecules plays a crucial role in this process. This result indicates that the phase separation of GQs can be modulated by DNA binding proteins, and this process could also be an efficient way to recruit specific DNA binding proteins.
Human HELQ regulates DNA end resection at DNA double-strand breaks and stalled replication forks
Authors: Zhao Yuqin , Hou Kaiping , Li Youhang , Hao Shuailin , Liu Yu , Na Yinan , Li Chao , Cui Jian , Xu Xingzhi , Wu Xiaohua , Wang Hailong 
Published: October 2023

Abstract
Following a DNA double strand break (DSB), several nucleases and helicases coordinate to generate single-stranded DNA (ssDNA) with 3′ free ends, facilitating precise DNA repair by homologous recombination (HR). The same nucleases can act on stalled replication forks, promoting nascent DNA degradation and fork instability. Interestingly, some HR factors, such as CtIP and BRCA1, have opposite regulatory effects on the two processes, promoting end resection at DSB but inhibiting the degradation of nascent DNA on stalled forks. However, the reason why nuclease actions are regulated by different mechanisms in two DNA metabolism is poorly understood. We show that human HELQ acts as a DNA end resection regulator, with opposing activities on DNA end resection at DSBs and on stalled forks as seen for other regulators. Mechanistically, HELQ helicase activity is required for EXO1-mediated DSB end resection, while ssDNA-binding capacity of HELQ is required for its recruitment to stalled forks, facilitating fork protection and preventing chromosome aberrations caused by replication stress. Here, HELQ synergizes with CtIP but not BRCA1 or BRCA2 to protect stalled forks. These findings reveal an unanticipated role of HELQ in regulating DNA end resection at DSB and stalled forks, which is important for maintaining genome stability.
A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms
Authors: Badaczewska-Dawid Aleksandra E , Kuriata Aleksander , Pintado-Grima Carlos , Garcia-Pardo Javier , Burdukiewicz Michał , Iglesias Valentín , Kmiecik Sebastian , Ventura Salvador 
Published: October 2023

Abstract
Protein aggregation has been associated with aging and different pathologies and represents a bottleneck in the industrial production of biotherapeutics. Numerous past studies performed in Escherichia coli and other model organisms have allowed to dissect the biophysical principles underlying this process. This knowledge fuelled the development of computational tools, such as Aggrescan 3D (A3D) to forecast and re-design protein aggregation. Here, we present the A3D Model Organism Database (A3D-MODB) http://biocomp.chem.uw.edu.pl/A3D2/MODB, a comprehensive resource for the study of structural protein aggregation in the proteomes of 12 key model species spanning distant biological clades. In addition to A3D predictions, this resource incorporates information useful for contextualizing protein aggregation, including membrane protein topology and structural model confidence, as an indirect reporter of protein disorder. The database is openly accessible without any need for registration. We foresee A3D-MOBD evolving into a central hub for conducting comprehensive, multi-species analyses of protein aggregation, fostering the development of protein-based solutions for medical, biotechnological, agricultural and industrial applications.
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
Authors: Schmidt Thomas S B , Fullam Anthony , Ferretti Pamela , Orakov Askarbek , Maistrenko Oleksandr M , Ruscheweyh Hans-Joachim , Letunic Ivica , Duan Yiqian , Van Rossum Thea , Sunagawa Shinichi , Mende Daniel R , Finn Robert D , Kuhn Michael , Pedro Coelho Luis , Bork Peer 
Published: October 2023

Abstract
Meta’omic data on microbial diversity and function accrue exponentially in public repositories, but derived information is often siloed according to data type, study or sampled microbial environment. Here we present SPIRE, a Searchable Planetary-scale mIcrobiome REsource that integrates various consistently processed metagenome-derived microbial data modalities across habitats, geography and phylogeny. SPIRE encompasses 99 146 metagenomic samples from 739 studies covering a wide array of microbial environments and augmented with manually-curated contextual data. Across a total metagenomic assembly of 16 Tbp, SPIRE comprises 35 billion predicted protein sequences and 1.16 million newly constructed metagenome-assembled genomes (MAGs) of medium or high quality. Beyond mapping to the high-quality genome reference provided by proGenomes3 (http://progenomes.embl.de), these novel MAGs form 92 134 novel species-level clusters, the majority of which are unclassified at species level using current tools. SPIRE enables taxonomic profiling of these species clusters via an updated, custom mOTUs database (https://motu-tool.org/) and includes several layers of functional annotation, as well as crosslinks to several (micro-)biological databases. The resource is accessible, searchable and browsable via http://spire.embl.de.