bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lactate exacerbates lung damage induced by nanomicroplastic through the gut microbiota–HIF1a/PTBP1 pathway
Authors: Xuan Lihui , Xu Zheng , Luo Jinhua , Wang Yin , Yan Yuhui , Qu Can , Xie Zuozhong , Skonieczna Magdalena , Zhou Ping-Kun , Huang Ruixue 
Published: December 2023

AbstractExposure to nanomicroplastics (nano-MPs) can induce lung damage. The gut microbiota is a critical modulator of the gut–lung axis. However, the mechanisms underlying these interactions have not been elucidated. This study explored the role of lactate, a key metabolite of the microbiota, in the development of lung damage induced by nano-MPs (LDMP). After 28 days of exposure to nano-MPs (50–100 nm), mice mainly exhibited damage to the lungs and intestinal mucosa and dysbiosis of the gut microbiota. Lactate accumulation was observed in the lungs, intestines and serum and was strongly associated with the imbalance in lactic acid bacteria in the gut. Furthermore, no lactate accumulation was observed in germ-free mice, while the depletion of the gut microbiota using a cocktail of antibiotics produced similar results, suggesting that lactate accumulation in the lungs may have been due to changes in the gut microbiota components. Mechanistically, elevated lactate triggers activation of the HIF1a/PTBP1 pathway, exacerbating nano-MP-induced lung damage through modulation of the epithelial–mesenchymal transition (EMT). Conversely, mice with conditional knockout of Ptbp1 in the lungs (Ptbp1flfl) and PTBP1-knockout (PTBP1-KO) human bronchial epithelial (HBE) cells showed reversal of the effects of lactate through modulation of the HIF1a/PTBP1 signaling pathway. These findings indicate that lactate is a potential target for preventing and treating LDMP.
Mesenchymal stem cell-derived apoptotic bodies alleviate alveolar bone destruction by regulating osteoclast differentiation and function
Authors: Li Xiaoyan , Jiang Yiyang , Liu Xu , Fu Jingfei , Du Juan , Luo Zhenhua , Xu Junji , Bhawal Ujjal Kumar , Liu Yi , Guo Lijia 
Published: December 2023

AbstractPeriodontitis is caused by overactive osteoclast activity that results in the loss of periodontal supporting tissue and mesenchymal stem cells (MSCs) are essential for periodontal regeneration. However, the hypoxic periodontal microenvironment during periodontitis induces the apoptosis of MSCs. Apoptotic bodies (ABs) are the major product of apoptotic cells and have been attracting increased attention as potential mediators for periodontitis treatment, thus we investigated the effects of ABs derived from MSCs on periodontitis. MSCs were derived from bone marrows of mice and were cultured under hypoxic conditions for 72 h, after which ABs were isolated from the culture supernatant using a multi-filtration system. The results demonstrate that ABs derived from MSCs inhibited osteoclast differentiation and alveolar bone resorption. miRNA array analysis showed that miR-223-3p is highly enriched in those ABs and is critical for their therapeutic effects. Targetscan and luciferase activity results confirmed that Itgb1 is targeted by miR-223-3p, which interferes with the function of osteoclasts. Additionally, DC-STAMP is a key regulator that mediates membrane infusion. ABs and pre-osteoclasts expressed high levels of DC-STAMP on their membranes, which mediates the engulfment of ABs by pre-osteoclasts. ABs with knock-down of DC-STAMP failed to be engulfed by pre-osteoclasts. Collectively, MSC-derived ABs are targeted to be engulfed by pre-osteoclasts via DC-STAMP, which rescued alveolar bone loss by transferring miR-223-3p to osteoclasts, which in turn led to the attenuation of their differentiation and bone resorption. These results suggest that MSC-derived ABs are promising therapeutic agents for the treatment of periodontitis.
AURKAIP1 actuates tumor progression through stabilizing DDX5 in triple negative breast cancer
Authors: Tian Wenwen , Tang Yuhui , Luo Yongzhou , Xie Jindong , Zheng Shaoquan , Zou Yutian , Huang Xiaojia , Wu Linyu , Zhang Junsheng , Sun Yuying , Tang Hailin , Du Wei , Li Xing , Xie Xiaoming 
Published: December 2023

AbstractAurora-A kinase interacting protein 1 (AURKAIP1) has been proved to take an intermediary role in cancer by functioning as a negative regulator of Aurora-A kinase. However, it remains unclear whether and how AURKAIP1 itself would directly engage in regulating malignancies. The expression levels of AURKAIP1 were detected in triple negative breast cancer (TNBC) by immunohistochemistry and western blots. The CCK8, colony formation assays and nude mouse model were conducted to determine cell proliferation whereas transwell and wound healing assays were performed to observe cell migration. The interaction of AURKAIP1 and DEAD-box helicase 5 (DDX5) were verified through co-immunoprecipitation and successively western blots. From the results, we found that AURKAIP1 was explicitly upregulated in TNBC, which was positively associated with tumor size, lymph node metastases, pathological stage and unfavorable prognosis. AURKAIP1 silencing markedly inhibited TNBC cell proliferation and migration in vitro and in vivo. AURKAIP1 directly interacted with and stabilized DDX5 protein by preventing ubiquitination and degradation, and DDX5 overexpression successfully reversed proliferation inhibition induced by knockdown of AURKAIP1. Consequently, AURKAIP1 silencing suppressed the activity of Wnt/β-catenin signaling in a DDX5-dependent manner. Our study may primarily disclose the molecular mechanism by which AURKAIP1/DDX5/β-catenin axis modulated TNBC progression, indicating that AURKAIP1 might serve as a therapeutic target as well as a TNBC-specific biomarker for prognosis.
Neutralization of SARS-CoV-2 Omicron BQ.1, BQ.1.1 and XBB.1 variants following SARS-CoV-2 infection or vaccination in children
Authors: Bellusci Lorenza , Grubbs Gabrielle , Sait Shaimaa , Yonker Lael M. , Randolph Adrienne G. , Novak Tanya , Kobayashi Takuma ,   Overcoming COVID−19 Investigators, Khurana Surender 
Published: December 2023

AbstractEmergence of highly transmissible Omicron subvariants led to increased SARS-CoV-2 infection and disease in children. However, minimal knowledge exists regarding the neutralization capacity against circulating Omicron BA.4/BA.5, BA.2.75, BQ.1, BQ.1.1 and XBB.1 subvariants following SARS-CoV-2 vaccination in children versus during acute or convalescent COVID-19, or versus multisystem inflammatory syndrome (MIS-C). Here, we evaluate virus-neutralizing capacity against SARS-CoV-2 variants in 151 age-stratified children ( <5, 5–11, 12–21 years old) hospitalized with acute severe COVID-19 or MIS-C or convalescent mild (outpatient) infection compared with 62 age-stratified vaccinated children. An age-associated effect on neutralizing antibodies is observed against SARS-CoV-2 following acute COVID-19 or vaccination. The primary series BNT162b2 mRNA vaccinated adolescents show higher vaccine-homologous WA-1 neutralizing titers compared with <12 years vaccinated children. Post-infection antibodies did not neutralize BQ.1, BQ.1.1 and XBB.1 subvariants. In contrast, monovalent mRNA vaccination induces more cross-neutralizing antibodies in young children <5 years against BQ.1, BQ.1.1 and XBB.1 variants compared with ≥5 years old children. Our study demonstrates that in children, infection and monovalent vaccination-induced neutralization activity is low against BQ.1, BQ.1.1 and XBB.1 variants. These findings suggest a need for improved SARS-CoV-2 vaccines to induce durable, more cross-reactive neutralizing antibodies to provide effective protection against emerging variants in children.
Haplotype-based inference of recent effective population size in modern and ancient DNA samples
Authors: Fournier Romain , Tsangalidou Zoi , Reich David , Palamara Pier Francesco 
Published: December 2023

AbstractIndividuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2000 years in both modern and ancient DNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe shows improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We apply HapNe to several modern populations from the 1,000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups.
Spatial transcriptomics deconvolution at single-cell resolution using Redeconve
Authors: Zhou Zixiang , Zhong Yunshan , Zhang Zemin , Ren Xianwen 
Published: December 2023

AbstractComputational deconvolution with single-cell RNA sequencing data as reference is pivotal to interpreting spatial transcriptomics data, but the current methods are limited to cell-type resolution. Here we present Redeconve, an algorithm to deconvolute spatial transcriptomics data at single-cell resolution, enabling interpretation of spatial transcriptomics data with thousands of nuanced cell states. We benchmark Redeconve with the state-of-the-art algorithms on diverse spatial transcriptomics platforms and datasets and demonstrate the superiority of Redeconve in terms of accuracy, resolution, robustness, and speed. Application to a human pancreatic cancer dataset reveals cancer-clone-specific T cell infiltration, and application to lymph node samples identifies differential cytotoxic T cells between IgA+ and IgG+ spots, providing novel insights into tumor immunology and the regulatory mechanisms underlying antibody class switch.
Two-dimensional heavy fermion in a monoatomic-layer Kondo lattice YbCu2
Authors: Nakamura Takuto , Sugihara Hiroki , Chen Yitong , Yukawa Ryu , Ohtsubo Yoshiyuki , Tanaka Kiyohisa , Kitamura Miho , Kumigashira Hiroshi , Kimura Shin-ichi 
Published: December 2023

AbstractThe Kondo effect between localized f-electrons and conductive carriers leads to exotic physical phenomena. Among them, heavy-fermion (HF) systems, in which massive effective carriers appear due to the Kondo effect, have fascinated many researchers. Dimensionality is also an important characteristic of the HF system, especially because it is strongly related to quantum criticality. However, the realization of the perfect two-dimensional (2D) HF materials is still a challenging topic. Here, we report the surface electronic structure of the monoatomic-layer Kondo lattice YbCu2 on a Cu(111) surface observed by synchrotron-based angle-resolved photoemission spectroscopy. The 2D conducting band and the Yb 4f state, located very close to the Fermi level, are observed. These bands are hybridized at low-temperature, forming the 2D HF state, with an evaluated coherence temperature of about 30 K. The effective mass of the 2D state is enhanced by a factor of 100 by the development of the HF state. Furthermore, clear evidence of the hybridization gap formation in the temperature dependence of the Kondo-resonance peak has been observed below the coherence temperature. Our study provides a new candidate as an ideal 2D HF material for understanding the Kondo effect at low dimensions.
Early warning signals have limited applicability to empirical lake data
Authors: O’Brien Duncan A. , Deb Smita , Gal Gideon , Thackeray Stephen J. , Dutta Partha S. , Matsuzaki Shin-ichiro S. , May Linda , Clements Christopher F. 
Published: December 2023

AbstractResearch aimed at identifying indicators of persistent abrupt shifts in ecological communities, a.k.a regime shifts, has led to the development of a suite of early warning signals (EWSs). As these often perform inaccurately when applied to real-world observational data, it remains unclear whether critical transitions are the dominant mechanism of regime shifts and, if so, which EWS methods can predict them. Here, using multi-trophic planktonic data on multiple lakes from around the world, we classify both lake dynamics and the reliability of classic and second generation EWSs methods to predict whole-ecosystem change. We find few instances of critical transitions, with different trophic levels often expressing different forms of abrupt change. The ability to predict this change is highly processing dependant, with most indicators not performing better than chance, multivariate EWSs being weakly superior to univariate, and a recent machine learning model performing poorly. Our results suggest that predictive ecology should start to move away from the concept of critical transitions, developing methods suitable for predicting resilience loss not limited to the strict bounds of bifurcation theory.
Charge-4e superconductivity and chiral metal in 45°-twisted bilayer cuprates and related bilayers
Authors: Liu Yu-Bo , Zhou Jing , Wu Congjun , Yang Fan 
Published: December 2023

AbstractThe material realization of charge-4e/6e superconductivity (SC) is a big challenge. Here, we propose to realize charge-4e SC in maximally-twisted homobilayers, such as 45∘-twisted bilayer cuprates and 30∘-twisted bilayer graphene, referred to as twist-bilayer quasicrystals (TB-QC). When each monolayer hosts a pairing state with the largest pairing angular momentum, previous studies have found that the second-order interlayer Josephson coupling would drive chiral topological SC (TSC) in the TB-QC. Here we propose that, above the Tc of the chiral TSC, either charge-4e SC or chiral metal can arise as vestigial phases, depending on the ordering of the total- and relative-pairing-phase fields of the two layers. Based on a thorough symmetry analysis to get the low-energy effective Hamiltonian, we conduct a combined renormalization-group and Monte-Carlo study and obtain the phase diagram, which includes the charge-4e SC and chiral metal phases.
Vertical tearing of subducting plates controlled by geometry and rheology of oceanic plates
Authors: Chen Yaguang , Chen Hanlin , Liu Mingqi , Gerya Taras 
Published: December 2023

AbstractLateral non-uniform subduction is impacted by continuous plate segmentation owing to vertical tearing of the subducting plate. However, the dynamics and physical controls of vertical tearing remain controversial. Here, we employed 3D numerical models to investigate the effects of trench geometry (offset by a transform boundary) and plate rheology (plate age and the magnitude of brittle/plastic strain weakening) on the evolution of shear stress-controlled vertical tearing within a homogenous subducting oceanic plate. Numerical results suggest that the trench offset geometry could result in self-sustained vertical tearing as a narrow shear zone within the intact subducting oceanic plate, and that this process of tearing could operate throughout the entire subduction process. Further, the critical trench offset length for the maturation of vertical tearing is impacted by plate rheology. Comparison between numerical modelling results and natural observations suggests that vertical tearing attributed to trench offset geometry is broadly developed in modern subduction and collision systems worldwide.
Genetic diversity modulates the physical and transcriptomic response of skeletal muscle to simulated microgravity in male mice
Authors: Zeineddine Yasmina , Friedman Michael A. , Buettmann Evan G. , Abraham Lovell B. , Hoppock Gabriel A. , Donahue Henry J. 
Published: December 2023

AbstractDevelopments in long-term space exploration necessitate advancements in countermeasures against microgravity-induced skeletal muscle loss. Astronaut data shows considerable variation in muscle loss in response to microgravity. Previous experiments suggest that genetic background influences the skeletal muscle response to unloading, but no in-depth analysis of genetic expression has been performed. Here, we placed eight, male, inbred founder strains of the diversity outbred mice (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/ShiLtJ, NZO/HILtJ, PWK/PhJ, and WSB/EiJ) in simulated microgravity (SM) via hindlimb unloading for three weeks. Body weight, muscle morphology, muscle strength, protein synthesis marker expression, and RNA expression were collected. A/J and CAST/EiJ mice were most susceptible to SM-induced muscle loss, whereas NOD/ShiLtJ mice were the most protected. In response to SM, A/J and CAST/EiJ mice experienced reductions in body weight, muscle mass, muscle volume, and muscle cross-sectional area. A/J mice had the highest number of differentially expressed genes (68) and associated gene ontologies (328). Downregulation of immunological gene ontologies and genes encoding anabolic immune factors suggest that immune dysregulation contributes to the response of A/J mice to SM. Several muscle properties showed significant interactions between SM and mouse strain and a high degree of heritability. These data imply that genetic background plays a role in the degree of muscle loss in SM and that more individualized programs should be developed for astronauts to protect their skeletal muscles against microgravity on long-term missions.
Cluster-assembled superatomic crystals for chirality-dependent charge-to-spin conversion
Authors: Zhao Yanyan , Zhao Jijun , Guo Yu , Zhou Si 
Published: December 2023

AbstractIn chiral materials, spins and chirality are coupled via spin-orbit interaction, provoking a fast-growing field of chiral spintronics. Compared with the widely explored chiral molecules, exploration of chirality-dependent spin effects in crystals and supramolecules remain limited. Here we assemble chiral superatomic crystals MXTe4 (M = transition metal; X = Ga or Ge) using telluride tetrahedra clusters as building blocks. Distinct from atomic crystals, these assembled monolayers have tunable symmetries and electronic characteristics by tilting the tetrahedral units through the variation of inter-cluster interaction. Dresselhaus-type spin textures and anisotropic spin Hall effect with inversed sign of spin current under opposite geometrical handedness are demonstrated in these chiral monolayers by symmetry analysis and verified by ab initio calculations. These results provide an innovative paradigm for assembling superatomic crystals with designated symmetry and hierarchical structures to access the chirality-driven quantum effects.
Global and local drivers of Echinococcus multilocularis infection in the western Balkan region
Authors: Moloi Sibusiso , Tari Tamás , Halász Tibor , Gallai Bence , Nagy Gábor , Csivincsik Ágnes 
Published: December 2023

AbstractThe cestode, Echinococcus multilocularis, is one of the most threatening parasitic challenges in the European Union. Despite the warming climate, the parasite intensively spread in Europe's colder and warmer regions. Little is known about the expansion of E. multilocularis in the Balkan region. Ordinary least squares, geographically weighted and multi-scale geographically weighted regressions were used to detect global and local drivers that influenced the prevalence in red foxes and golden jackals in the southwestern part of Hungary. Based on the study of 391 animals, the overall prevalence exceeded 18% (in fox 15.2%, in jackal 21.1%). The regression models revealed that the wetland had a global effect (β = 0.391, p = 0.006). In contrast, on the local scale, the mean annual precipitation (β = 0.285, p = 0.008) and the precipitation seasonality (β = − 0.211, p = 0.014) had statistically significant effects on the infection level. The geospatial models suggested that microclimatic effects might compensate for the disadvantages of a warmer Mediterranean climate. This study calls attention to fine-scale analysis and locally acting environmental factors, which can delay the expected epidemic fade-out. The findings of our study are suggested to consider in surveillance strategies.
A survey on performance evaluation of artificial intelligence algorithms for improving IoT security systems
Authors: Meziane Hind , Ouerdi Noura 
Published: December 2023

AbstractSecurity is an important field in the Internet of Things (IoT) systems. The IoT and security are topical domains. Because it was obtained 35,077 document results from the Scopus database. Hence, the AI (Artificial Intelligence) has proven its efficiency in several domains including security, digital marketing, healthcare, big data, industry, education, robotic, and entertainment. Thus, the contribution of AI to the security of IoT systems has become a huge breakthrough. This contribution adopts the artificial intelligence (AI) as a base solution for the IoT security systems. Two different subsets of AI algorithms were considered: Machine Learning (ML) and Deep Learning (DL) methods. Nevertheless, it is difficult to determine which AI method and IoT dataset are best (more suitable) for classifying and/or detecting intrusions and attacks in the IoT domain. The large number of existing publications on this phenomenon explains the need for the current state of research that covers publications on IoT security using AI methods. Thus, this study compares the results regarding AI algorithms that have been mentioned in the related works. The goal of this paper is to compare the performance assessment of the existing AI algorithms in order to choose the best algorithm as well as whether the chosen algorithm can be used for classifying or/and detecting intrusions and attacks in order to improve security in the IoT domain. This study compares these methods in term of accuracy rate. Evaluating the current state of IoT security, AI and IoT datasets is the main aim for considering our future work. After that, this paper proposes, as result, a new and general taxonomy of AI techniques for IoT security (classification and detection techniques). Finally, the obtained results from this assessment survey that was dedicated to research conducted between 2018 and 2023 were satisfactory. This paper provides a good reference for researchers and readers in the IoT domain.