bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD147 contributes to SARS-CoV-2-induced pulmonary fibrosis
Authors: Wu Jiao , Chen Liang , Qin Chuan , Huo Fei , Liang Xue , Yang Xu , Zhang Kui , Lin Peng , Liu Jiangning , Feng Zhuan , Zhou Jiansheng , Pei Zhuo , Wang Yatao , Sun Xiu-Xuan , Wang Ke , Geng Jiejie , Zheng Zhaohui , Fu Xianghui , Liu Man , Wang Qingyi , Zhang Zheng , Bian Huijie , Zhu Ping , Chen Zhi-Nan 
Published: November 2022

AbstractCOVID‐19 patients can develop clinical and histopathological features associated with fibrosis, but the pathogenesis of fibrosis remains poorly understood. CD147 has been identified as a universal receptor for SARS-CoV-2 and its variants, which could initiate COVID-19-related cytokine storm. Here, we systemically analyzed lung pathogenesis in SARS-CoV-2- and its delta variant-infected humanized CD147 transgenic mice. Histopathology and Transmission Electron Microscopy revealed inflammation, fibroblast expansion and pronounced fibrotic remodeling in SARS-CoV-2-infected lungs. Consistently, RNA-sequencing identified a set of fibrosis signature genes. Furthermore, we identified CD147 as a crucial regulator for fibroblast activation induced by SARS-CoV-2. We found conditional knockout of CD147 in fibroblast suppressed activation of fibroblasts, decreasing susceptibility to bleomycin-induced pulmonary fibrosis. Meplazumab, a CD147 antibody, was able to inhibit the accumulation of activated fibroblasts and the production of ECM proteins, thus alleviating the progression of pulmonary fibrosis caused by SARS-CoV-2. In conclusion, we demonstrated that CD147 contributed to SARS-CoV-2-triggered progressive pulmonary fibrosis and identified CD147 as a potential therapeutic target for treating patients with post-COVID-19 pulmonary fibrosis.
MYC and MET cooperatively drive hepatocellular carcinoma with distinct molecular traits and vulnerabilities
Authors: Sequera Celia , Grattarola Margherita , Holczbauer Agnes , Dono Rosanna , Pizzimenti Stefania , Barrera Giuseppina , Wangensteen Kirk J. , Maina Flavio 
Published: November 2022

AbstractEnhanced activation of the transcription factor MYC and of the receptor tyrosine kinase MET are among the events frequently occurring in hepatocellular carcinoma (HCC). Both genes individually act as drivers of liver cancer initiation and progression. However, their concomitant alteration in HCC has not been explored, nor functionally documented. Here, we analysed databases of five independent human HCC cohorts and found a subset of patients with high levels of MYC and MET (MYChigh/METhigh) characterised by poor prognosis. This clinical observation drove us to explore the functionality of MYC and MET co-occurrence in vivo, combining hydrodynamic tail vein injection for MYC expression in the R26stopMet genetic setting, in which wild-type MET levels are enhanced following the genetic deletion of a stop cassette. Results showed that increased MYC and MET expression in hepatocytes is sufficient to induce liver tumorigenesis even in the absence of pre-existing injuries associated with a chronic disease state. Intriguingly, ectopic MYC in MET tumours increases expression of the Mki67 proliferation marker, and switches them into loss of Afp, Spp1, Gpc3, Epcam accompanied by an increase in Hgma1, Vim, and Hep-Par1 levels. We additionally found a switch in the expression of specific immune checkpoints, with an increase in the Ctla-4 and Lag3 lymphocyte co-inhibitory responses, and in the Icosl co-stimulatory responses of tumour cells. We provide in vitro evidence on the vulnerability of some human HCC cell lines to combined MYC and MET targeting, which are otherwise resistant to single inhibition. Mechanistically, combined blockage of MYC and MET converts a partial cytostatic effect, triggered by individual blockage of MYC or MET, into a cytotoxic effect. Together, these findings highlight a subgroup of HCC characterised by MYChigh/METhigh, and document functional cooperativity between MYC and MET in liver tumorigenesis. Thus, the MYC-R26Met model is a relevant setting for HCC biology, patient classification and treatment.
Naa10p promotes cell invasiveness of esophageal cancer by coordinating the c-Myc and PAI1 regulatory axis
Authors: Pan Ke-Fan , Liu Yu-Cheng , Hsiao Michael , Cheng Tsu-Yao , Hua Kuo-Tai 
Published: November 2022

AbstractN-α-acetyltransferase 10 protein, Naa10p, is involved in various cellular functions impacting tumor progression. Due to its capacity to acetylate a large spectrum of proteins, both oncogenic and tumor-suppressive roles of Naa10p have been documented. Here, we report an oncogenic role of Naa10p in promoting metastasis of esophageal cancer.NAA10is more highly expressed in esophageal cancer tissues compared to normal tissues. HigherNAA10expression also correlates with poorer survival of esophageal cancer patients. We found thatNAA10expression was transcriptionally regulated by the critical oncogene c-Myc in esophageal cancer. Furthermore, activation of the c-Myc-Naa10p axis resulted in upregulated cell invasiveness of esophageal cancer. This increased cell invasiveness was also elucidated to depend on the enzymatic activity of Naa10p. Moreover, Naa10p cooperated with Naa15p to interact with the protease inhibitor, PAI1, and prevent its secretion. This inhibition of PAI1 secretion may derive from the N-terminal acetylation effect of the Naa10p/Naa15p complex. Our results establish the significance of Naa10p in driving metastasis in esophageal cancer by coordinating the c-Myc-PAI1 axis, with implications for its potential use as a prognostic biomarker and therapeutic target for esophageal cancer.
The prognostic implication of visual acuity at the time of uveal melanoma diagnosis
Authors: Asplund Elin , Fili Maria , Pansell Tony , Brautaset Rune , Nilsson Maria , Stålhammar Gustav 
Published: November 2022

Abstract
Background
Visual outcomes after primary tumour treatment of uveal melanoma (UM) have been investigated repeatedly. This study evaluates the correlation between best-corrected visual acuity (BCVA) before treatment with clinicopathological factors and patient survival.

Subjects/Methods
Pre-treatment BCVA was examined in relation to tumour dimensions and location, and survival in a retrospective cohort of 1809 patients who underwent plaque brachytherapy. BCVA was also correlated to tumour histological factors in a second cohort of 137 enucleated eyes.

Results
The mean BCVA of the tumour eye prior to plaque brachytherapy was LogMAR 0.42 (SD 0.46). Patients with low BCVA (LogMAR ≥ 1.00) did not differ in age (p = 0.19) and had similar frequency of ciliary body involvement (p = 0.99) but had tumours with greater apical thickness (p < 0.0001), greater diameter (p < 0.0001) and shorter distance to the optic disc and fovea (p < 0.0001). There were no significant relations between low BCVA and any of 13 examined tumour histological factors at a Bonferroni-corrected significance level (p > 0.004). Patients with low BCVA had greater incidence of UM-related mortality in competing risk analysis (p = 0.0019) and shorter overall survival (p < 0.0001). Low BCVA was also associated with increased hazard ratio (HR) for UM-related mortality in univariate analysis (HR 1.5, 95% confidence interval 1.2 to 1.9), but not in multivariate analysis with tumour size and location as covariates.

Conclusions
UM patients with low BCVA before primary tumour treatment have a worse prognosis, likely related to increased tumour dimensions. Future studies should examine the prognostic significance of BCVA in relation to macula-involving retinal detachment and genetic factors.
Restoring cellular magnesium balance through Cyclin M4 protects against acetaminophen-induced liver damage
Authors: González-Recio Irene , Simón Jorge , Goikoetxea-Usandizaga Naroa , Serrano-Maciá Marina , Mercado-Gómez Maria , Rodríguez-Agudo Rubén , Lachiondo-Ortega Sofía , Gil-Pitarch Clàudia , Fernández-Rodríguez Carmen , Castellana Donatello , Latasa Maria U. , Abecia Leticia , Anguita Juan , Delgado Teresa C. , Iruzubieta Paula , Crespo Javier , Hardy Serge , Petrov Petar D. , Jover Ramiro , Avila Matías A. , Martín César , Schaeper Ute , Tremblay Michel L. , Dear James W. , Masson Steven , McCain Misti Vanette , Reeves Helen L. , Andrade Raul J. , Lucena M. Isabel , Buccella Daniela , Martínez-Cruz Luis Alfonso , Martínez-Chantar Maria L 
Published: November 2022

AbstractAcetaminophen overdose is one of the leading causes of acute liver failure and liver transplantation in the Western world. Magnesium is essential in several cellular processess. The Cyclin M family is involved in magnesium transport across cell membranes. Herein, we identify that among all magnesium transporters, only Cyclin M4 expression is upregulated in the liver of patients with acetaminophen overdose, with disturbances in magnesium serum levels. In the liver, acetaminophen interferes with the mitochondrial magnesium reservoir via Cyclin M4, affecting ATP production and reactive oxygen species generation, further boosting endoplasmic reticulum stress. Importantly, Cyclin M4 mutant T495I, which impairs magnesium flux, shows no effect. Finally, an accumulation of Cyclin M4 in endoplasmic reticulum is shown under hepatoxicity. Based on our studies in mice, silencing hepatic Cyclin M4 within the window of 6 to 24 h following acetaminophen overdose ingestion may represent a therapeutic target for acetaminophen overdose induced liver injury.
Integration of single-cell transcriptomes and biological function reveals distinct behavioral patterns in bone marrow endothelium
Authors: Kim Young-Woong , Zara Greta , Kang HyunJun , Branciamore Sergio , O’Meally Denis , Feng Yuxin , Kuan Chia-Yi , Luo Yingjun , Nelson Michael S. , Brummer Alex B. , Rockne Russell , Chen Zhen Bouman , Zheng Yi , Cardoso Angelo A. , Carlesso Nadia 
Published: November 2022

AbstractHeterogeneity of endothelial cell (EC) populations reflects their diverse functions in maintaining tissue’s homeostasis. However, their phenotypic, molecular, and functional properties are not entirely mapped. We use the Tie2-CreERT2;Rosa26-tdTomato reporter mouse to trace, profile, and cultivate primary ECs from different organs. As paradigm platform, we use this strategy to study bone marrow endothelial cells (BMECs). Single-cell mRNA sequencing of primary BMECs reveals that their diversity and native molecular signatures is transitorily preserved in an ex vivo culture that conserves key cell-to-cell microenvironment interactions. Macrophages sustain BMEC cellular diversity and expansion and preserve sinusoidal-like BMECs ex vivo. Endomucin expression discriminates BMECs in populations exhibiting mutually exclusive properties and distinct sinusoidal/arterial and tip/stalk signatures. In contrast to arterial-like, sinusoidal-like BMECs are short-lived, form 2D-networks, contribute to in vivo angiogenesis, and support hematopoietic stem/progenitor cells in vitro. This platform can be extended to other organs’ ECs to decode mechanistic information and explore therapeutics.
Inference of hyperedges and overlapping communities in hypergraphs
Authors: Contisciani Martina , Battiston Federico , De Bacco Caterina 
Published: November 2022

AbstractHypergraphs, encoding structured interactions among any number of system units, have recently proven a successful tool to describe many real-world biological and social networks. Here we propose a framework based on statistical inference to characterize the structural organization of hypergraphs. The method allows to infer missing hyperedges of any size in a principled way, and to jointly detect overlapping communities in presence of higher-order interactions. Furthermore, our model has an efficient numerical implementation, and it runs faster than dyadic algorithms on pairwise records projected from higher-order data. We apply our method to a variety of real-world systems, showing strong performance in hyperedge prediction tasks, detecting communities well aligned with the information carried by interactions, and robustness against addition of noisy hyperedges. Our approach illustrates the fundamental advantages of a hypergraph probabilistic model when modeling relational systems with higher-order interactions.
Precise tuning of interlayer electronic coupling in layered conductive metal-organic frameworks
Authors: Lu Yang , Zhang Yingying , Yang Chi-Yuan , Revuelta Sergio , Qi Haoyuan , Huang Chuanhui , Jin Wenlong , Li Zichao , Vega-Mayoral Victor , Liu Yannan , Huang Xing , Pohl Darius , Položij Miroslav , Zhou Shengqiang , Cánovas Enrique , Heine Thomas , Fabiano Simone , Feng Xinliang , Dong Renhao 
Published: November 2022

AbstractTwo-dimensional conjugated metal-organic frameworks (2D c-MOFs) have attracted increasing interests for (opto)-electronics and spintronics. They generally consist of van der Waals stacked layers and exhibit layer-depended electronic properties. While considerable efforts have been made to regulate the charge transport within a layer, precise control of electronic coupling between layers has not yet been achieved. Herein, we report a strategy to precisely tune interlayer charge transport in 2D c-MOFs via side-chain induced control of the layer spacing. We design hexaiminotriindole ligands allowing programmed functionalization with tailored alkyl chains (HATI_CX, X = 1,3,4; X refers to the carbon numbers of the alkyl chains) for the synthesis of semiconducting Ni3(HATI_CX)2. The layer spacing of these MOFs can be precisely varied from 3.40 to 3.70 Å, leading to widened band gap, suppressed carrier mobilities, and significant improvement of the Seebeck coefficient. With this demonstration, we further achieve a record-high thermoelectric power factor of 68 ± 3 nW m−1 K−2 in Ni3(HATI_C3)2, superior to the reported holes-dominated MOFs.
U.S. winter wheat yield loss attributed to compound hot-dry-windy events
Authors: Zhao Haidong , Zhang Lina , Kirkham M. B. , Welch Stephen M. , Nielsen-Gammon John W. , Bai Guihua , Luo Jiebo , Andresen Daniel A. , Rice Charles W. , Wan Nenghan , Lollato Romulo P. , Zheng Dianfeng , Gowda Prasanna H. , Lin Xiaomao 
Published: November 2022

AbstractClimate extremes cause significant winter wheat yield loss and can cause much greater impacts than single extremes in isolation when multiple extremes occur simultaneously. Here we show that compound hot-dry-windy events (HDW) significantly increased in the U.S. Great Plains from 1982 to 2020. These HDW events were the most impactful drivers for wheat yield loss, accounting for a 4% yield reduction per 10 h of HDW during heading to maturity. Current HDW trends are associated with yield reduction rates of up to 0.09 t ha−1 per decade and HDW variations are atmospheric-bridged with the Pacific Decadal Oscillation. We quantify the “yield shock”, which is spatially distributed, with the losses in severely HDW-affected areas, presumably the same areas affected by the Dust Bowl of the 1930s. Our findings indicate that compound HDW, which traditional risk assessments overlooked, have significant implications for the U.S. winter wheat production and beyond.
Induction of cross-neutralizing antibodies by a permuted hepatitis C virus glycoprotein nanoparticle vaccine candidate
Authors: Sliepen Kwinten , Radić Laura , Capella-Pujol Joan , Watanabe Yasunori , Zon Ian , Chumbe Ana , Lee Wen-Hsin , de Gast Marlon , Koopsen Jelle , Koekkoek Sylvie , del Moral-Sánchez Iván , Brouwer Philip J. M. , Ravichandran Rashmi , Ozorowski Gabriel , King Neil P. , Ward Andrew B. , van Gils Marit J. , Crispin Max , Schinkel Janke , Sanders Rogier W. 
Published: November 2022

AbstractHepatitis C virus (HCV) infection affects approximately 58 million people and causes ~300,000 deaths yearly. The only target for HCV neutralizing antibodies is the highly sequence diverse E1E2 glycoprotein. Eliciting broadly neutralizing antibodies that recognize conserved cross-neutralizing epitopes is important for an effective HCV vaccine. However, most recombinant HCV glycoprotein vaccines, which usually include only E2, induce only weak neutralizing antibody responses. Here, we describe recombinant soluble E1E2 immunogens that were generated by permutation of the E1 and E2 subunits. We displayed the E2E1 immunogens on two-component nanoparticles and these nanoparticles induce significantly more potent neutralizing antibody responses than E2. Next, we generated mosaic nanoparticles co-displaying six different E2E1 immunogens. These mosaic E2E1 nanoparticles elicit significantly improved neutralization compared to monovalent E2E1 nanoparticles. These results provide a roadmap for the generation of an HCV vaccine that induces potent and broad neutralization.
A resource for automated search and collation of geochemical datasets from journal supplements
Authors: Martin Erin L. , Barrote Vitor R. , Cawood Peter A. 
Published: November 2022

AbstractThis article presents a resource for automated search, extraction and collation of geochemical and geochronological data from the Figshare repository using web scraping code. To answer fundamental questions about the Earth’s evolution, such as spatial and temporal evolution and interrelationships between the planet’s solid and surficial reservoirs, researchers must utilize global geochemical datasets. Due to the volume of data being published, these datasets become quickly outdated. We present a resource that allows researchers to rapidly curate and update their own databases from existing published data. We use open-source Python code to web scrape the Figshare repository for journal supplementary files using the application programming interface, allowing for the collection and download of hundreds of supplementary files and metadata in minutes. Use of this web scraping tool is demonstrated here by collation of a zircon geochronology and chemistry database of >150,000 analyses. The database is consistent in reproducing trends in other published zircon compilations. Providing a resource for automated collection of Figshare data files will encourage data sharing and reuse.
MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques
Authors: DeBarry Jeremy D. , Nural Mustafa V. , Pakala Suman B. , Nayak Vishal , Warrenfeltz Susanne , Humphrey Jay , Lapp Stacey A. , Cabrera-Mora Monica , Brito Cristiana F. A. , Jiang Jianlin , Saney Celia L. , Hankus Allison , Stealey Hannah M. , DeBarry Megan B. , Lackman Nicolas , Legall Noah , Lee Kevin , Tang Yan , Gupta Anuj , Trippe Elizabeth D. , Bridger Robert R. , Weatherly Daniel Brent , Peterson Mariko S. , Jiang Xuntian , Tran ViLinh , Uppal Karan , Fonseca Luis L. , Joyner Chester J. , Karpuzoglu Ebru , Cordy Regina J. , Meyer Esmeralda V. S. , Wells Lance L. , Ory Daniel S. , Lee F. Eun-Hyung , Tirouvanziam Rabindra , Gutiérrez Juan B. , Ibegbu Chris , Lamb Tracey J. , Pohl Jan , Pruett Sarah T. , Jones Dean P. , Styczynski Mark P. , Voit Eberhard O. , Moreno Alberto , Galinski Mary R. , Kissinger Jessica C. 
Published: November 2022

AbstractPlasmodium cynomolgi causes zoonotic malarial infections in Southeast Asia and this parasite species is important as a model for Plasmodium vivax and Plasmodium ovale. Each of these species produces hypnozoites in the liver, which can cause relapsing infections in the blood. Here we present methods and data generated from iterative longitudinal systems biology infection experiments designed and performed by the Malaria Host-Pathogen Interaction Center (MaHPIC) to delve deeper into the biology, pathogenesis, and immune responses of P. cynomolgi in the Macaca mulatta host. Infections were initiated by sporozoite inoculation. Blood and bone marrow samples were collected at defined timepoints for biological and computational experiments and integrative analyses revolving around primary illness, relapse illness, and subsequent disease and immune response patterns. Parasitological, clinical, haematological, immune response, and -omic datasets (transcriptomics, proteomics, metabolomics, and lipidomics) including metadata and computational results have been deposited in public repositories. The scope and depth of these datasets are unprecedented in studies of malaria, and they are projected to be a F.A.I.R., reliable data resource for decades.
Field test study on the evaluation of the microvibration controlling capacity of a mass concrete layer
Authors: Zheng Ming , Zhuang Liangdong , Fan Jiansheng , Liu Yufei , Ren Jinlong , Rong Muning , Zhai Wei 
Published: November 2022

AbstractMicrovibration induced by natural disturbance and human activities has an adverse effect on the operation of the large-scale and ultraprecise facilities in the world. Under such circumstances, a passive vibration control method is generally deployed for such vibration-sensitive facilities, taking the High Energy Photo Source (HEPS) in Beijing as an example, a 3 m-thick mass concrete layer forming a ring foundation was cast at the facility, where a 1 m-thick reinforced concrete slab (RC slab) lies. Since microvibration control plays a crucial role in the operation of such large-scale scientific and ultraprecise facilities and few studies have been reported for large-scale concrete layer as antimicrovibration devices, this paper presents four field tests in Beijing, China, to evaluate the vibration control capacity of a mass concrete layer. Based on a large number of field tests, the effect of applying the concrete layer is discussed, and a reference is provided for the construction of similar facilities. The vibration signals, generated by shock excitation and ambient excitation, are measured through a highly sensitive and high-accuracy vibration acquisition system. It is concluded that the existence of the 1 m-thick RC slab has little influence on the microvibration signal frequency distribution in the vertical direction and that the signals from the concrete layer and subsoil differ by approximately 10 Hz in the vertical direction while differing by approximately 5 Hz in the horizontal direction. The microvibration control ability of the concrete layer is favorable in a higher frequency band over 20 ~ 30 Hz and more than 50% attenuation can be gained through the concrete layer; however, the microvibration control ability is not significant below 20 ~ 30 Hz. The vibration levels across different heights of the concrete layer section are the same. To prevent adverse vibration disturbance below 20 ~ 30 Hz, it is suggested that the traffic and road surface conditions should be taken into consideration when choosing the construction location. In addition, a long-term monitoring shows that 75% vibration energy at the site is firmly related to the construction activities which are approximately 1.4 km from the site.
Manipulations of Libet clock parameters affect intention timing awareness
Authors: Ivanof Bianca E. , Terhune D. B. , Coyle D. , Moore J. W. 
Published: November 2022

AbstractW judgments are a widely used intention timing awareness estimate. These judgments are typically obtained by using the classic Libet-style paradigm whereby participants are asked to estimate the time they become aware of their intention to act by using the location of a rotating object on a clock face. There is an inconsistency in the Libet clock parameters used in previous studies, and it is unclear whether this variability impacts W judgments and other outcome measures, with implications for the construct validity of this measure and the generalisability of results across studies. Here, we present a four-experiment study that systematically manipulated the Libet clock speed, number of clock markings, length of the clock hand and type of clock radius in order to examine whether these parameter manipulations affect intention timing awareness estimates. Our results demonstrate W judgments can be significantly influenced by the clock speed and number of clock markings. The meaning and implications of these results are discussed.