bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asialoglycoprotein receptor 1 promotes SARS-CoV-2 infection of human normal hepatocytes
Authors: Yang Xinyi , Zheng Xu , Zhu Yuqi , Zhao Xiaying , Liu Jun , Xun Jiangna , Yuan Songhua , Chen Jun , Pan Hanyu , Yang Jinlong , Wang Jing , Liang Zhimin , Shen Xiaoting , Liang Yue , Lin Qinru , Liang Huitong , Li Min , Peng Fei , Lu Daru , Xu Jianqing , Lu Hongzhou , Jiang Shibo , Zhao Ping , Zhu Huanzhang 
Published: February 2024

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes multi-organ damage, which includes hepatic dysfunction, as observed in over 50% of COVID-19 patients. Angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 (ACE2) is the primary receptor for SARS-CoV-2 entry into host cells, and studies have shown the presence of intracellular virus particles in human hepatocytes that express ACE2, but at extremely low levels. Consequently, we asked if hepatocytes might express receptors other than ACE2 capable of promoting the entry of SARS-CoV-2 into cells. To address this question, we performed a genome-wide CRISPR-Cas9 activation library screening and found that Asialoglycoprotein receptor 1 (ASGR1) promoted SARS-CoV-2 pseudovirus infection of HeLa cells. In Huh-7 cells, simultaneous knockout ofACE2andASGR1prevented SARS-CoV-2 pseudovirus infection. In the immortalized THLE-2 hepatocyte cell line and primary hepatic parenchymal cells, both of which barely expressed ACE2, SARS-CoV-2 pseudovirus could successfully establish an infection. However, after treatment with ASGR1 antibody or siRNA targeting ASGR1, the infection rate significantly dropped, suggesting that SARS-CoV-2 pseudovirus infects hepatic parenchymal cells mainly through an ASGR1-dependent mechanism. We confirmed that ASGR1 could interact with Spike protein, which depends on receptor binding domain (RBD) and N-terminal domain (NTD). Finally, we also used Immunohistochemistry and electron microscopy to verify that SARS-CoV-2 could infect primary hepatic parenchymal cells. After inhibiting ASGR1 in primary hepatic parenchymal cells by siRNA, the infection efficiency of the live virus decreased significantly. Collectively, these findings indicate that ASGR1 is a candidate receptor for SARS-CoV-2 that promotes infection of hepatic parenchymal cells.
IGF2BP3 enhances lipid metabolism in cervical cancer by upregulating the expression of SCD
Authors: Han Chenying , Hu Chenchen , Liu Tianyue , Sun Yuanjie , Hu Feiming , He Yuanli , Zhang Jiaxing , Chen Jiaxi , Ding Jiaqi , Fan Jiangjiang , Zhang Xiyang , Wang Jing , Qiao Xupeng , Jiang Dongbo , Yang Kun , Yang Shuya 
Published: February 2024

AbstractCervical cancer (CC) is the most common gynecologic malignancy, which seriously threatens the health of women. Lipid metabolism is necessary for tumor proliferation and metastasis. However, the molecular mechanism of the relationship between CC and lipid metabolism remains poorly defined. We revealed the expression of IGF2BP3 in CC exceeded adjacent tissues, and was positively associated with tumor stage using human CC tissue microarrays. The Cell Counting Kit-8, colony formation assay, 5-ethynyl-2′-deoxyuridine assay, transwell assays, wound-healing assays, and flow cytometry assessed the role of IGF2BP3 in proliferation and metastasis of CC cells. Besides, exploring the molecular mechanism participating in IGF2BP3-driven lipid metabolism used RNA-seq, which determined SCD as the target of IGF2BP3. Further, lipid droplets, cellular triglyceride (TG) contents, and fatty acids were accessed to discover that IGF2BP3 can enhance lipid metabolism in CC. Moreover, RIP assay and methylated RNA immunoprecipitation experiments seeked the aimed-gene-binding specificity. Lastly, the IGF2BP3 knockdown restrained CC growth and lipid metabolism, after which SCD overexpression rescued the influence in vitro and in vivo using nude mouse tumor-bearing model. Mechanistically, IGF2BP3 regulated SCD mRNA m6A modifications via IGF2BP3-METTL14 complex, thereby enhanced CC proliferation, metastasis, and lipid metabolism. Our study highlights IGF2BP3 plays a crucial role in CC progression and represents a therapeutic latent strategy. It is a potential tactic that blocks the metabolic pathway relevant to IGF2BP3 with the purpose of treating CC.
Innate and adaptive immune cell interaction drives inflammasome activation and hepatocyte apoptosis in murine liver injury from immune checkpoint inhibitors
Authors: Shojaie Layla , Bogdanov Jacob M. , Alavifard Helia , Mohamed Mahmoud G. , Baktash Aria , Ali Myra , Mahov Simeon , Murray Sue , Kanel Gary C. , Liu Zhang-Xu , Ito Fumito , In Gino K. , Merchant Akil , Stohl William , Dara Lily 
Published: February 2024

AbstractImmune checkpoints (CTLA4 & PD-1) are inhibitory pathways that block aberrant immune activity and maintain self-tolerance. Tumors co-opt these checkpoints to avoid immune destruction. Immune checkpoint inhibitors (ICIs) activate immune cells and restore their tumoricidal potential, making them highly efficacious cancer therapies. However, immunotolerant organs such as the liver depend on these tolerogenic mechanisms, and their disruption with ICI use can trigger the unintended side effect of hepatotoxicity termed immune-mediated liver injury from ICIs (ILICI). Learning how to uncouple ILICI from ICI anti-tumor activity is of paramount clinical importance. We developed a murine model to recapitulate human ILICI using CTLA4+/- mice treated with either combined anti-CTLA4 + anti-PDL1 or IgG1 + IgG2. We tested two forms of antisense oligonucleotides to knockdown caspase-3 in a total liver (parenchymal and non-parenchymal cells) or in a hepatocyte-specific manner. We also employed imaging mass cytometry (IMC), a powerful multiplex modality for immunophenotyping and cell interaction analysis in our model. ICI-treated mice had significant evidence of liver injury. We detected cleaved caspase-3 (cC3), indicating apoptosis was occurring, as well as Nod-like receptor protein 3 (NLRP3) inflammasome activation, but no necroptosis. Total liver knockdown of caspase-3 worsened liver injury, and induced further inflammasome activation, and Gasdermin-D-mediated pyroptosis. Hepatocyte-specific knockdown of caspase-3 reduced liver injury and NLRP3 inflammasome activation. IMC-generated single-cell data for 77,692 cells was used to identify 22 unique phenotypic clusters. Spatial analysis revealed that cC3+ hepatocytes had significantly closer interactions with macrophages, Kupffer cells, and NLRP3hi myeloid cells than other cell types. We also observed zones of three-way interaction between cC3+ hepatocytes, CD8 + T-cells, and macrophages. Our work is the first to identify hepatocyte apoptosis and NLRP3 inflammasome activation as drivers of ILICI. Furthermore, we report that the interplay between adaptive and innate immune cells is critical to hepatocyte apoptosis and ILICI.
Cardiac cell senescence: molecular mechanisms, key proteins and therapeutic targets
Authors: Luan Yi , Zhu Xiaofan , Jiao Yuxue , Liu Hui , Huang Zhen , Pei Jinyan , Xu Yawei , Yang Yang , Ren Kaidi 
Published: February 2024

AbstractCardiac aging, particularly cardiac cell senescence, is a natural process that occurs as we age. Heart function gradually declines in old age, leading to continuous heart failure, even in people without a prior history of heart disease. To address this issue and improve cardiac cell function, it is crucial to investigate the molecular mechanisms underlying cardiac senescence. This review summarizes the main mechanisms and key proteins involved in cardiac cell senescence. This review further discusses the molecular modulators of cellular senescence in aging hearts. Furthermore, the discussion will encompass comprehensive descriptions of the key drugs, modes of action and potential targets for intervention in cardiac senescence. By offering a fresh perspective and comprehensive insights into the molecular mechanisms of cardiac senescence, this review seeks to provide a fresh perspective and important theoretical foundations for the development of drugs targeting this condition.
ROS/MMP-9 mediated CS degradation in BMSC inhibits citric acid metabolism participating in the dual regulation of bone remodelling
Authors: Da Wacili , Jiang Wen , Tao Lin 
Published: February 2024

AbstractIt is necessary to figure out the abnormal energy metabolites at the cellular level of postmenopausal osteoporosis (PMOP) bone microenvironment. In this study, we constructed PMOP model by ovariectomy and identified 9 differential metabolites compared with control femur by energy metabolomic. The enrichment analysis of differential metabolites revealed that tricarboxylic acid cycle, glucagon pathway and purinergic signaling pathway were the main abnormal metabolic processes. Citric acid was identified as the key metabolite by constructing compound reaction–enzyme–gene network. The functional annotation of citric acid targets identified by network pharmacological tools indicated that matrix metalloproteinase 9 (MMP-9) may be involved in regulating citric acid metabolism in the osteogenic differentiation of bone marrow mesenchymal stem cell (BMSC). Molecular docking shows that the interaction forces between MMP-9 and citric acid synthase (CS) is −638, and there are multiple groups of residues used to form hydrogen bonds. Exogenous H2O2 promotes the expression of MMP-9 in BMSC to further degrade CS resulting in a decrease in mitochondrial citric acid synthesis, which leads to the disorder of bone remodeling by two underlying mechanisms ((1) the decreased histone acetylation inhibits the osteogenic differentiation potential of BMSC; (2) the decreased bone mineralization by citric acid deposition). MMP-9-specific inhibitor (MMP-9-IN-1) could significantly improve the amount of CS in BMSC to promote cellular citric acid synthesis, and further enhance bone remodeling. These findings suggest inhibiting the degradation of CS by MMP-9 to promote the net production of citric acid in osteogenic differentiation of BMSC may be a new direction of PMOP research.
Biporous silica nanostructure-induced nanovortex in microfluidics for nucleic acid enrichment, isolation, and PCR-free detection
Authors: Jeon Eunyoung , Koo Bonhan , Kim Suyeon , Kim Jieun , Yu Yeonuk , Jang Hyowon , Lee Minju , Kim Sung-Han , Kang Taejoon , Kim Sang Kyung , Kwak Rhokyun , Shin Yong , Lee Joonseok 
Published: February 2024

AbstractEfficient pathogen enrichment and nucleic acid isolation are critical for accurate and sensitive diagnosis of infectious diseases, especially those with low pathogen levels. Our study introduces a biporous silica nanofilms-embedded sample preparation chip for pathogen and nucleic acid enrichment/isolation. This chip features unique biporous nanostructures comprising large and small pore layers. Computational simulations confirm that these nanostructures enhance the surface area and promote the formation of nanovortex, resulting in improved capture efficiency. Notably, the chip demonstrates a 100-fold lower limit of detection compared to conventional methods used for nucleic acid detection. Clinical validations using patient samples corroborate the superior sensitivity of the chip when combined with the luminescence resonance energy transfer assay. The enhanced sample preparation efficiency of the chip, along with the facile and straightforward synthesis of the biporous nanostructures, offers a promising solution for polymer chain reaction-free detection of nucleic acids.
β-Variational autoencoders and transformers for reduced-order modelling of fluid flows
Authors: Solera-Rico Alberto , Sanmiguel Vila Carlos , Gómez-López Miguel , Wang Yuning , Almashjary Abdulrahman , Dawson Scott T. M. , Vinuesa Ricardo 
Published: February 2024

AbstractVariational autoencoder architectures have the potential to develop reduced-order models for chaotic fluid flows. We propose a method for learning compact and near-orthogonal reduced-order models using a combination of aβ-variational autoencoder and a transformer, tested on numerical data from a two-dimensional viscous flow in both periodic and chaotic regimes. Theβ-variational autoencoder is trained to learn a compact latent representation of the flow velocity, and the transformer is trained to predict the temporal dynamics in latent-space. Using theβ-variational autoencoder to learn disentangled representations in latent-space, we obtain a more interpretable flow model with features that resemble those observed in the proper orthogonal decomposition, but with a more efficient representation. Using Poincaré maps, the results show that our method can capture the underlying dynamics of the flow outperforming other prediction models. The proposed method has potential applications in other fields such as weather forecasting, structural dynamics or biomedical engineering.
Operando investigation of the synergistic effect of electric field treatment and copper for bacteria inactivation
Authors: Jarin Mourin , Wang Ting , Xie Xing 
Published: February 2024

AbstractAs the overuse of chemicals in our disinfection processes becomes an ever-growing concern, alternative approaches to reduce and replace the usage of chemicals is warranted. Electric field treatment has shown promising potential to have synergistic effects with standard chemical-based methods as they both target the cell membrane specifically. In this study, we use a lab-on-a-chip device to understand, observe, and quantify the synergistic effect between electric field treatment and copper inactivation. Observations in situ, and at a single cell level, ensure us that the combined approach has an enhancement effect leading more bacteria to be weakened by electric field treatment and susceptible to inactivation by copper ion permeation. The synergistic effects of electric field treatment and copper can be visually concluded here, enabling the further study of this technology to optimally develop, mature, and scale for its various applications in the future.
Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography
Authors: Bauda Elda , Gallet Benoit , Moravcova Jana , Effantin Gregory , Chan Helena , Novacek Jiri , Jouneau Pierre-Henri , Rodrigues Christopher D. A. , Schoehn Guy , Moriscot Christine , Morlot Cecile 
Published: February 2024

AbstractBacterial spores owe their incredible resistance capacities to molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary structure of the chromosome and an extracellular shell made of proteinaceous layers (the coat), the assembly of which remains poorly understood. Here, in situ cryo-electron tomography on lamellae generated by cryo-focused ion beam micromachining provides insights into the ultrastructural organization of Bacillus subtilis sporangia. The reconstructed tomograms reveal that early during sporulation, the chromosome in the forespore adopts a toroidal structure harboring 5.5-nm thick fibers. At the same stage, coat proteins at the surface of the forespore form a stack of amorphous or structured layers with distinct electron density, dimensions and organization. By analyzing mutant strains using cryo-electron tomography and transmission electron microscopy on resin sections, we distinguish seven nascent coat regions with different molecular properties, and propose a model for the contribution of coat morphogenetic proteins.
Eliciting parental preferences and values for the return of additional findings from genomic sequencing
Authors: Goranitis Ilias , Meng Yan , Martyn Melissa , Best Stephanie , Bouffler Sophie , Bombard Yvonne , Gaff Clara , Stark Zornitza 
Published: February 2024

AbstractHealth economic evidence is needed to inform the design of high-value and cost-effective processes for returning genomic results from analyses for additional findings (AF). This study reports the results of a discrete-choice experiment designed to elicit preferences for the process of returning AF results from the perspective of parents of children with rare conditions and to estimate the value placed on AF analysis. Overall, 94 parents recruited within the Australian Genomics and Melbourne Genomics programmes participated in the survey, providing preferences in a total of 1128 choice scenarios. Statistically significant preferences were identified for the opportunity to change the choices made about AF; receiving positive AF in person from a genetic counsellor; timely access to a medical specialist and high-quality online resources; receiving automatic updates through a secure online portal if new information becomes available; and lower costs. For AF uptake rates ranging between 50–95%, the mean per person value from AF analysis was estimated at AU$450–$1700 (US$300–$1140). The findings enable the design of a value-maximising process of analysis for AF in rare-disease genomic sequencing.
Harmonic memory signals in the human cerebral cortex induced by semantic relatedness of words
Authors: Noguchi Yasuki 
Published: February 2024

AbstractWhen we memorize multiple words simultaneously, semantic relatedness among those words assists memory. For example, the information about “apple”, “banana,” and “orange” will be connected via a common concept of “fruits” and become easy to retain and recall. Neural mechanisms underlying this semantic integration in verbal working memory remain unclear. Here I used electroencephalography (EEG) and investigated neural signals when healthy human participants memorized five nouns semantically related (Sem trial) or not (NonSem trial). The regularity of oscillatory signals (8–30 Hz) during the retention period was found to be lower in NonSem than Sem trials, indicating that memorizing words unrelated to each other induced a non-harmonic (irregular) waveform in the temporal cortex. These results suggest that (i) semantic features of a word are retained as a set of neural oscillations at specific frequencies and (ii) memorizing words sharing a common semantic feature produces harmonic brain responses through a resonance or integration (sharing) of the oscillatory signals.
Operando film-electrochemical EPR spectroscopy tracks radical intermediates in surface-immobilized catalysts
Authors: Seif-Eddine Maryam , Cobb Samuel J. , Dang Yunfei , Abdiaziz Kaltum , Bajada Mark A. , Reisner Erwin , Roessler Maxie M. 
Published: February 2024

AbstractThe development of surface-immobilized molecular redox catalysts is an emerging research field with promising applications in sustainable chemistry. In electrocatalysis, paramagnetic species are often key intermediates in the mechanistic cycle but are inherently difficult to detect and follow by conventional in situ techniques. We report a new method, operando film-electrochemical electron paramagnetic resonance spectroscopy (FE-EPR), which enables mechanistic studies of surface-immobilized electrocatalysts. This technique enables radicals formed during redox reactions to be followed in real time under flow conditions, at room temperature and in aqueous solution. Detailed insight into surface-immobilized catalysts, as exemplified here through alcohol oxidation catalysis by a surface-immobilized nitroxide, is possible by detecting active-site paramagnetic species sensitively and quantitatively operando, thereby enabling resolution of the reaction kinetics. Our finding that the surface electron-transfer rate, which is of the same order of magnitude as the rate of catalysis (accessible from operando FE-EPR), limits catalytic efficiency has implications for the future design of better surface-immobilized catalysts.
Harmonizing government responses to the COVID-19 pandemic
Authors: Cheng Cindy , Messerschmidt Luca , Bravo Isaac , Waldbauer Marco , Bhavikatti Rohan , Schenk Caress , Grujic Vanja , Model Tim , Kubinec Robert , Barceló Joan 
Published: February 2024

AbstractPublic health and safety measures (PHSM) made in response to the COVID-19 pandemic have been singular, rapid, and profuse compared to the content, speed, and volume of normal policy-making. Not only can they have a profound effect on the spread of the disease, but they may also have multitudinous secondary effects, in both the social and natural worlds. Unfortunately, despite the best efforts by numerous research groups, existing data on COVID-19 PHSM only partially captures their full geographical scale and policy scope for any significant duration of time. This paper introduces our effort to harmonize data from the eight largest such efforts for policies made before September 21, 2021 into the taxonomy developed by the CoronaNet Research Project in order to respond to the need for comprehensive, high quality COVID-19 data. In doing so, we present a comprehensive comparative analysis of existing data from different COVID-19 PHSM datasets, introduce our novel methodology for harmonizing COVID-19 PHSM data, and provide a clear-eyed assessment of the pros and cons of our efforts.
ShetlandsUAVmetry: unmanned aerial vehicle-based photogrammetric dataset for Antarctic environmental research
Authors: Román Alejandro , Navarro Gabriel , Tovar-Sánchez Antonio , Zarandona Pedro , Roque-Atienza David , Barbero Luis 
Published: February 2024

AbstractThe study of the functioning and responses of Antarctica to the current climate change scenario is a priority and a challenge for the scientific community aiming to predict and mitigate impacts at a regional and global scale. Due to the difficulty of obtaining aerial data in such extreme, remote, and difficult-to-reach region of the planet, the development of remote sensing techniques with Unmanned Aerial Vehicles (UAVs) has revolutionized polar research. ShetlandsUAVmetry comprises original datasets collected by UAVs during the Spanish Antarctic Campaign 2021–2022 (January to March 2022), along with the photogrammetric products resulting from their processing. It includes data recorded during twenty-eight distinct UAV flights at various study sites on Deception and Livingston islands (South Shetland Islands, Antarctica) and consists of a total of 15,691 high-resolution optical RGB captures. In addition, this dataset is accompanied by additional associated files that facilitate its use and accessibility. It is publicly accessible and can be downloaded from the figshare data repository.
Pollen viability and longevity in Juniperus taxa native to Slovakia
Authors: Galgóci Martin , Kormuťák Andrej , Klobučník Miroslav , Gömöry Dušan , Lukáčik Ivan , Boleček Peter 
Published: February 2024

AbstractPollen viability, dispersion ability and longevity during deep-freezer storage were studied in three Juniperus taxa distributed in Slovakia. All these characteristics of pollen are closely related to the pollination and/or fertilization success of the junipers in nature. Pollen viability varied considerably between the three populations of J. communis and one population of each, J. sibirica and J. communis var. intermedia. Pollen germination rate ranged between 40.75% and 75.06%, and pollen tube length between 30.32 and 40.41 µm. A clear tendency indicates a higher germination rate of J. communis pollen from lower altitudes and reduced germination of J. sibirica and J. communis var. intermedia pollen from higher altitudes. The dispersion potential of the J. communis pollen during its shedding seems relatively low. In 2021, pollen cloud density was diluted at 68.1% at the 4 m distance from the test shrub, in 2022 of 52.1% at the 17 m distance from the pollen source. A deep-freezer storage of juniper pollen in a double-walled polyethylene bag with silica gel was not efficient enough, as indicated by the drop of pollen germination rate of 31.2% in J. communis and of 79.4% in J. sibirica during a 1-year storage period at − 81 °C.