bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel long non-coding RNAs associated with inflammation and macrophage activation in human
Authors: Chini Avisankar , Guha Prarthana , Malladi Venkat S. , Guo Zibiao , Mandal Subhrangsu S. 
Published: March 2023

AbstractInflammation plays a central role in immune response and macrophage activation. Emerging studies demonstrate that along with proteins and genomic factors, noncoding RNA are potentially involved in regulation of immune response and inflammation. Our recent study demonstrated that lncRNA HOTAIR plays key roles in cytokine expression and inflammation in macrophages. The primary goal of this study is to discover novel lncRNAs that are crucial players in inflammation, macrophage activation, and immune response in humans. Towards this, we have stimulated THP1-derived macrophages (THP1-MΦ) with lipopolysaccharides (LPS) and performed the whole transcriptome RNA-seq analysis. Based on this analysis, we discovered that along with well-known marker for inflammation (such as cytokines), a series of long noncoding RNAs (lncRNAs) expression were highly induced upon LPS-stimulation of macrophages, suggesting their potential roles in inflammation and macrophage activation. We termed these family of lncRNAs as Long-noncoding Inflammation Associated RNA (LinfRNA). Dose and time dependent analysis demonstrated that many human LinfRNA (hLinfRNAs) expressions follow similar patterns as cytokine expressions. Inhibition of NF-κB suppressed the expression of most hLinfRNAs suggesting their potential regulation via NF-κB activation during inflammation and macrophage activation. Antisense-mediated knockdown of hLinfRNA1 suppressed the LPS-induced expression of cytokines and pro-inflammatory genes such as IL6, IL1β, and TNFα expression, suggesting potential functionality of the hLinfRNAs in cytokine regulation and inflammation. Overall, we discovered a series of novel hLinfRNAs that are potential regulators of inflammation and macrophage activation and may be linked to inflammatory and metabolic diseases.
The PaleoJump database for abrupt transitions in past climates
Authors: Bagniewski Witold , Rousseau Denis-Didier , Ghil Michael 
Published: March 2023

AbstractTipping points (TPs) in Earth’s climate system have been the subject of increasing interest and concern in recent years, given the risk that anthropogenic forcing could cause abrupt, potentially irreversible, climate transitions. Paleoclimate records are essential for identifying past TPs and for gaining a thorough understanding of the underlying nonlinearities and bifurcation mechanisms. However, the quality, resolution, and reliability of these records can vary, making it important to carefully select the ones that provide the most accurate representation of past climates. Moreover, as paleoclimate time series vary in their origin, time spans, and periodicities, an objective, automated methodology is crucial for identifying and comparing TPs. To address these challenges, we introduce the open-source PaleoJump database, which contains a collection of carefully selected, high-resolution records originating in ice cores, marine sediments, speleothems, terrestrial records, and lake sediments. These records describe climate variability on centennial, millennial and longer time scales and cover all the continents and ocean basins. We provide an overview of their spatial distribution and discuss the gaps in coverage. Our statistical methodology includes an augmented Kolmogorov–Smirnov test and Recurrence Quantification Analysis; it is applied here, for illustration purposes, to selected records in which abrupt transitions are automatically detected and the presence of potential tipping elements is investigated. These transitions are shown in the PaleoJump database along with other essential information about the records, including location, temporal scale and resolution, as well as temporal plots. This open-source database represents, therefore, a valuable resource for researchers investigating TPs in past climates.
The prognostic role of C-reactive protein to albumin ratio and anti-MDA5 antibody-positive in idiopathic inflammatory myopathy: a retrospective study
Authors: Zhou Pei , Shen Qinxue , Zhou Shiting , Ouyang Xiaoli , Guo Ting , Song Min , Guo Wei , Zhang Yi , Peng Hong 
Published: March 2023

AbstractThis cohort study aimed to identify the characteristics and risk factors of adult idiopathic inflammatory myopathy-associated interstitial lung disease (IIM-ILD) and further explore the prognostic factors of IIM-ILD. We extracted data regarding 539 patients with laboratory-confirmed idiopathic inflammatory myopathy (IIM) with or without interstitial lung disease (ILD) from the Second Xiangya Hospital of Central South University between January 2016 and December 2021. The regression analysis was conducted to identify the possible risk factors for ILD as well as mortality. Of 539 IIM patients, 343 (64.6%) were diagnosed with IIM-ILD. The median (IQR) baseline neutrophil-to-lymphocyte ratio (NLR), C-reactive protein to albumin ratio (CAR) and ferritin were 4.1371 (2.6994–6.8143), 0.1685 (0.0641–0.5456) and 393.6 (210.6–532.2), respectively. Risk factors associated with IIM-ILD were older age (p = 0.002), arthralgia (p = 0.014), lung infection (p = 0.027), hemoglobin (p = 0.022), high CAR (p = 0.014), anti-aminoacyl-tRNA synthetase (anti-ARS) antibody-positive (p < 0.001), and anti-MDA5 antibody-positive (p < 0.001). The IIM-ILD patients whose age at diagnosis of disease ≥ 59.5 (HR = 2.673, 95% CI 1.588–4.499, p < 0.001), NLR ≥ 6.6109 (HR = 2.004, 95% CI 1.193–3.368, p = 0.009), CAR ≥ 0.2506 (HR = 1.864, 95% CI 1.041–3.339, p = 0.036), ferritin ≥ 397.68 (HR = 2.451, 95% CI 1.245–4.827, p = 0.009) and anti-MDA5 antibody-positive (HR = 1.928, 95% CI 1.123–3.309, p = 0.017) had a higher mortality rate. High CAR and anti-MDA5 antibody-positive are more likely to be associated with a high mortality rate of IIM-ILD, which can be used as serum biomarkers, especially the CAR, a simple, objective tool to assess the prognosis of IIM.
The role of position in consensus dynamics of polarizable networks
Authors: Giese Helge , Gaisbauer Felix , Gradwohl Nico , Strandburg-Peshkin Ariana 
Published: March 2023

AbstractCommunication constraints often complicate group decision-making. In this experiment, we investigate how the network position of opinionated group members determines both the speed and the outcome of group consensus in 7-member communication networks susceptible to polarization. To this end, we implemented an online version of a color coordination task within experimentally controlled communication networks. In 72 networks, one individual was incentivized to prefer one of two options. In 156 networks, two individuals were incentivized to prefer conflicting options. The network positions of incentivized individuals were varied. In networks with a single incentivized individual, network position played no significant role in either the speed or outcome of consensus decisions. For conflicts, the incentivized individual with more neighbors was more likely to sway the group to their preferred outcome. Furthermore, consensus emerged more slowly when the opponents had the same number of neighbors, but could not see each other’s votes directly. These results suggest that the visibility of an opinion is key to wielding group influence, and that specific structures are sufficient to run communication networks into polarization, hindering a speedy consensus.
Chemical-state distributions in charged LiCoO2 cathode particles visualized by soft X-ray spectromicroscopy
Authors: Zhang Wenxiong , Hosono Eiji , Asakura Daisuke , Yuzawa Hayato , Ohigashi Takuji , Kobayashi Masaki , Kiuchi Hisao , Harada Yoshihisa 
Published: March 2023

AbstractLithium-ion deintercalation/intercalation during charge/discharge processes is one of the essential reactions that occur in the layered cathodes of lithium-ion batteries, and the performance of the cathode can be expressed as the sum of the reactions that occur in the local area of the individual cathode particles. In this study, the spatial distributions of the chemical states present in prototypical layered LiCoO2cathode particles were determined at different charging conditions using scanning transmission X-ray microscopy (STXM) with a spatial resolution of approximately 100 nm. The CoL3- and OK-edge X-ray absorption spectroscopy (XAS) spectra, extracted from the same area of the corresponding STXM images, at the initial state as well as after charging to 4.5 V demonstrate the spatial distribution of the chemical state changes depending on individual particles. In addition to the CoL3-edge XAS spectra, the OK-edge XAS spectra of the initial and charged LiCoO2particles are different, indicating that both the Co and O sites participate in charge compensation during the charging process possibly through the hybridization between the Co 3dand O 2porbitals. Furthermore, the element maps of both the Co and O sites, derived from the STXM stack images, reveal the spatial distribution of the chemical states inside individual particles after charging to 4.5 V. The element mapping analysis suggests that inhomogeneous reactions occur on the active particles and confirm the existence of non-active particles. The results of this study demonstrate that an STXM-based spatially resolved electronic structural analysis method is useful for understanding the charging and discharging of battery materials.
Insight into pressure effect on optoelectronic, mechanical, and lattice vibrational properties of nanostructured GaxIn1 − xPySbzAs1 − y − z for the solar cells system
Authors: Elkenany E. B. , Alfrnwani O. A. , Sallah M. 
Published: March 2023

AbstractThe electronic, optical, and elastic characteristics of the GaxIn1 − xPySbzAs1 − y − z alloy lattice matched to the GaSb substrate using a pseudo-potential formalism (EPM) based on the virtual crystal approximation (VCA) are performed. The mechanical features, acoustic velocity, and phonon frequencies of the GaxIn1 − xPySbzAs1 − y − z/GaSb system are calculated. The sensitivity of these properties to pressure is considered. Our findings are reasonably consistent with the experimental evidence that is currently available. The studied properties of this alloy under the influence of pressure are a new achievement. Novel device applications would be made possible by the pentanary GaxIn1 − xPySbzAs1 − y − z alloy under high pressure.
Inactivation and spike protein denaturation of novel coronavirus variants by CuxO/TiO2 nano-photocatalysts
Authors: Tatsuma Tetsu , Nakakido Makoto , Ichinohe Takeshi , Kuroiwa Yoshinori , Tomioka Kengo , Liu Chang , Miyamae Nobuhiro , Onuki Tatsuya , Tsumoto Kouhei , Hashimoto Kazuhito , Wakihara Toru 
Published: March 2023

AbstractIn order to reduce infection risk of novel coronavirus (SARS-CoV-2), we developed nano-photocatalysts with nanoscale rutile TiO2 (4–8 nm) and CuxO (1–2 nm or less). Their extraordinarily small size leads to high dispersity and good optical transparency, besides large active surface area. Those photocatalysts can be applied to white and translucent latex paints. Although Cu2O clusters involved in the paint coating undergo gradual aerobic oxidation in the dark, the oxidized clusters are re-reduced under > 380 nm light. The paint coating inactivated the original and alpha variant of novel coronavirus under irradiation with fluorescent light for 3 h. The photocatalysts greatly suppressed binding ability of the receptor binding domain (RBD) of coronavirus (the original, alpha and delta variants) spike protein to the receptor of human cells. The coating also exhibited antivirus effects on influenza A virus, feline calicivirus, bacteriophage Qβ and bacteriophage M13. The photocatalysts would be applied to practical coatings and lower the risk of coronavirus infection via solid surfaces.
Early exploitation of Neapolitan pozzolan (pulvis puteolana) in the Roman theatre of Aquileia, Northern Italy
Authors: Dilaria Simone , Secco Michele , Ghiotto Andrea R. , Furlan Guido , Giovanardi Tommaso , Zorzi Federico , Bonetto Jacopo 
Published: March 2023

AbstractThe paper reports the results of the analyses on mortar-based materials from the Roman theatre of Aquileia (Friuli Venezia Giulia, Northern Italy), recently dated between the mid-1st Century BCE and the mid-1st Century CE. Samples were characterized by Polarized Light Microscopy on thin sections (PLM), Scanning Electron Microscopy with Energy Dispersive Spectroscopy (SEM–EDS) and Quantitative Phase Analysis by X-Ray Powder Diffraction (QPA-XRPD). Pyroclastic aggregates (mainly pumices and scattered tuffs), incompatible with the regional geology, were found in two samples from the preparation layers of the ground floor of the building. Their provenance was determined by means of QPA-XRPD, SEM–EDS, X-Ray Fluorescence (XRF) and Laser-Ablation Inductively-Coupled-Plasma Mass-Spectrometry (LA-ICP-MS). Mineralogical and geochemical analyses demonstrated their provenance from the Bay of Naples, thus recognizing them aspulvis puteolana, a type of pozzolanic aggregate outcropping around the modern town of Pozzuoli and prescribed by Vitruvius (De Architectura, 2.6.1) in mortar-based materials to strengthen masonries and produce hydraulic concrete for harbor piers. This evidence represents the oldest analytically-established case ofpulvis puteolanaexploitation in Northern Italy up to now, and an early use of the material out of Campania adapted for civil constructions in a non-strictly maritime-related environment. Indeed, the theatre was built in the low-lying Aquileia’s deltaic plain, prone to water infiltrations that are typical in lagoon-like environments. The data highlight the craftsmen’s resilience in adapting and reinterpreting the traditional use of the Neapolitan volcanic materials to deal with the geomorphological challenges of Aquileia’s lowland.
Oncogenic role and potential regulatory mechanism of fatty acid binding protein 5 based on a pan-cancer analysis
Authors: Wang Jinhua , Zhao Siqi , Sun Jian , Wang Xiaobo , Guan Mingze , Yin Jiajun , Tang Bo 
Published: March 2023

AbstractAs one member of fatty acid binding proteins (FABPs), FABP5 makes a contribution in the occurrence and development of several tumor types, but existing analysis about FABP5 and FABP5-related molecular mechanism remains limited. Meanwhile, some tumor patients showed limited response rates to current immunotherapy, and more potential targets need to be explored for the improvement of immunotherapy. In this study, we made a pan-cancer analysis of FABP5 based on the clinical data from The Cancer Genome Atlas database for the first time. FABP5 overexpression was observed in many tumor types, and was statistically associated with poor prognosis of several tumor types. Additionally, we further explored FABP5-related miRNAs and corresponding lncRNAs. Then, miR-577-FABP5 regulatory network in kidney renal clear cell carcinoma as well as CD27-AS1/GUSBP11/SNHG16/TTC28-AS1-miR-22-3p-FABP5 competing endogenous RNA regulatory network in liver hepatocellular carcinoma were constructed. Meanwhile, Western Blot and reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) analysis were used to verify miR-22-3p-FABP5 relationship in LIHC cell lines. Moreover, the potential relationships of FABP5 with immune infiltration and six immune checkpoints (CD274, CTLA4, HAVCR2, LAG3, PDCD1 and TIGIT) were discovered. Our work not only deepens the understanding of FABP5’s functions in multiple tumors and supplements existing FABP5-related mechanisms, but also provides more possibilities for immunotherapy.
Differentiating malignant and benign eyelid lesions using deep learning
Authors: Lee Min Joung , Yang Min Kyu , Khwarg Sang In , Oh Eun Kyu , Choi Youn Joo , Kim Namju , Choung Hokyung , Seo Chang Won , Ha Yun Jong , Cho Min Ho , Cho Bum-Joo 
Published: March 2023

AbstractArtificial intelligence as a screening tool for eyelid lesions will be helpful for early diagnosis of eyelid malignancies and proper decision-making. This study aimed to evaluate the performance of a deep learning model in differentiating eyelid lesions using clinical eyelid photographs in comparison with human ophthalmologists. We included 4954 photographs from 928 patients in this retrospective cross-sectional study. Images were classified into three categories: malignant lesion, benign lesion, and no lesion. Two pre-trained convolutional neural network (CNN) models, DenseNet-161 and EfficientNetV2-M architectures, were fine-tuned to classify images into three or two (malignant versus benign) categories. For a ternary classification, the mean diagnostic accuracies of the CNNs were 82.1% and 83.0% using DenseNet-161 and EfficientNetV2-M, respectively, which were inferior to those of the nine clinicians (87.0–89.5%). For the binary classification, the mean accuracies were 87.5% and 92.5% using DenseNet-161 and EfficientNetV2-M models, which was similar to that of the clinicians (85.8–90.0%). The mean AUC of the two CNN models was 0.908 and 0.950, respectively. Gradient-weighted class activation map successfully highlighted the eyelid tumors on clinical photographs. Deep learning models showed a promising performance in discriminating malignant versus benign eyelid lesions on clinical photographs, reaching the level of human observers.
Quantum computing reduces systemic risk in financial networks
Authors: Aboussalah Amine Mohamed , Chi Cheng , Lee Chi-Guhn 
Published: March 2023

AbstractIn highly connected financial networks, the failure of a single institution can cascade into additional bank failures. This systemic risk can be mitigated by adjusting the loans, holding shares, and other liabilities connecting institutions in a way that prevents cascading of failures. We are approaching the systemic risk problem by attempting to optimize the connections between the institutions. In order to provide a more realistic simulation environment, we have incorporated nonlinear/discontinuous losses in the value of the banks. To address scalability challenges, we have developed a two-stage algorithm where the networks are partitioned into modules of highly interconnected banks and then the modules are individually optimized. We developed a new algorithms for classical and quantum partitioning for directed and weighed graphs (first stage) and a new methodology for solving Mixed Integer Linear Programming problems with constraints for the systemic risk context (second stage). We compare classical and quantum algorithms for the partitioning problem. Experimental results demonstrate that our two-stage optimization with quantum partitioning is more resilient to financial shocks, delays the cascade failure phase transition, and reduces the total number of failures at convergence under systemic risks with reduced time complexity.
Cryo-EM structure of a catalytic amyloid fibril
Authors: Heerde Thomas , Bansal Akanksha , Schmidt Matthias , Fändrich Marcus 
Published: March 2023

AbstractCatalytic amyloid fibrils are novel types of bioinspired, functional materials that combine the chemical and mechanical robustness of amyloids with the ability to catalyze a certain chemical reaction. In this study we used cryo-electron microcopy to analyze the amyloid fibril structure and the catalytic center of amyloid fibrils that hydrolyze ester bonds. Our findings show that catalytic amyloid fibrils are polymorphic and consist of similarly structured, zipper-like building blocks that consist of mated cross-β sheets. These building blocks define the fibril core, which is decorated by a peripheral leaflet of peptide molecules. The observed structural arrangement differs from previously described catalytic amyloid fibrils and yielded a new model of the catalytic center.
A high-resolution melt curve toolkit to identify lineage-defining SARS-CoV-2 mutations
Authors: Fraser Alice J. , Greenland-Bews Caitlin , Kelly Daniel , Williams Christopher T. ,   LSTM Diagnostics Group, Bengey Daisy , Buist Kate , Clerkin Karina , Finch Lorna S , Gould Susan , Kontogianni Konstantina , Savage Helen R , Thompson Caitlin R , Wardale Jahanara , Watkins Rachel L , Wooding Dominic ,   CONDOR Steering Group, Allen A. Joy , Body Richard , Braybrook Julian , Buckle Peter , Clark Eloïse , Dark Paul , Davis Kerrie , Gordon Adam , Hayward Gail , Halstead Anna , Harden Charlotte , Inkson Colette , Jones Naoko , Jones William , Lasserson Dan , Lee Joseph , Lendrem Clare , Lewington Andrew , Logan Mary , Micocci Massimo , Nicholson Brian , Perera-Salazar Rafael , Prestwich Graham , Price Ashley , Reynard Charles , Riley Beverley , Simpson A. J. , Tate Valerie , Turner Philip , Wilcox Mark , Zhifang Melody , Body Richard , Adams Emily R. , Atienzar Ana Cubas , Edwards Thomas , Allen David J. 
Published: March 2023

AbstractThe emergence of severe acute respiratory syndrome 2 (SARS-CoV-2) variants of concern (VOCs), with mutations linked to increased transmissibility, vaccine escape and virulence, has necessitated the widespread genomic surveillance of SARS-CoV-2. This has placed a strain on global sequencing capacity, especially in areas lacking the resources for large scale sequencing activities. Here we have developed three separate multiplex high-resolution melting assays to enable the identification of Alpha, Beta, Delta and Omicron VOCs. The assays were evaluated against whole genome sequencing on upper-respiratory swab samples collected during the Alpha, Delta and Omicron [BA.1] waves of the UK pandemic. The sensitivities of the eight individual primer sets were all 100%, and specificity ranged from 94.6 to 100%. The multiplex HRM assays have potential as a tool for high throughput surveillance of SARS-CoV-2 VOCs, particularly in areas with limited genomics facilities.
Occupant privacy perception, awareness, and preferences in smart office environments
Authors: Li Beatrice , Tavakoli Arash , Heydarian Arsalan 
Published: March 2023

AbstractBuilding management systems tout numerous benefits, such as energy efficiency and occupant comfort but rely on vast amounts of data from various sensors. Advancements in machine learning algorithms make it possible to extract personal information about occupants and their activities beyond the intended design of a non-intrusive sensor. However, occupants are not informed of data collection and possess different privacy preferences and thresholds for privacy loss. While privacy perceptions and preferences are most understood in smart homes, limited studies have evaluated these factors in smart office buildings, where there are more users and different privacy risks. To better understand occupants’ perceptions and privacy preferences, we conducted twenty-four semi-structured interviews between April 2022 and May 2022 on occupants of a smart office building. We found that data modality features and personal features contribute to people’s privacy preferences. The features of the collected modality define data modality features – spatial, security, and temporal context. In contrast, personal features consist of one’s awareness of data modality features and data inferences, definitions of privacy and security, and the available rewards and utility. Our proposed model of people’s privacy preferences in smart office buildings helps design more effective measures to improve people’s privacy.