bluuebunny/crossref_metadata_2025_split huggingface dataset:
CXCL4 synergizes with TLR8 for TBK1-IRF5 activation, epigenomic remodeling and inflammatory response in human monocytes
Authors: Yang Chao , Bachu Mahesh , Du Yong , Brauner Caroline , Yuan Ruoxi , Ah Kioon Marie Dominique , Chesi Giancarlo , Barrat Franck J. , Ivashkiv Lionel B. 
Published: June 2022

AbstractRegulation of endosomal Toll-like receptor (TLR) responses by the chemokine CXCL4 is implicated in inflammatory and fibrotic diseases, with CXCL4 proposed to potentiate TLR responses by binding to nucleic acid TLR ligands and facilitating their endosomal delivery. Here we report that in human monocytes/macrophages, CXCL4 initiates signaling cascades and downstream epigenomic reprogramming that change the profile of the TLR8 response by selectively amplifying inflammatory gene transcription and interleukin (IL)−1β production, while partially attenuating the interferon response. Mechanistically, costimulation by CXCL4 and TLR8 synergistically activates TBK1 and IKKε, repurposes these kinases towards an inflammatory response via coupling with IRF5, and activates the NLRP3 inflammasome. CXCL4 signaling, in a cooperative and synergistic manner with TLR8, induces chromatin remodeling and activates de novo enhancers associated with inflammatory genes. Our findings thus identify new regulatory mechanisms of TLR responses relevant for cytokine storm, and suggest targeting the TBK1-IKKε-IRF5 axis may be beneficial in inflammatory diseases.
Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks
Authors: Amato Katherine A. , Haddock Luis A. , Braun Katarina M. , Meliopoulos Victoria , Livingston Brandi , Honce Rebekah , Schaack Grace A. , Boehm Emma , Higgins Christina A. , Barry Gabrielle L. , Koelle Katia , Schultz-Cherry Stacey , Friedrich Thomas C. , Mehle Andrew 
Published: June 2022

AbstractTransmission of influenza A viruses (IAV) between hosts is subject to numerous physical and biological barriers that impose genetic bottlenecks, constraining viral diversity and adaptation. The bottlenecks within hosts and their potential impacts on evolutionary pathways taken during infection are poorly understood. To address this, we created highly diverse IAV libraries bearing molecular barcodes on two gene segments, enabling high-resolution tracking and quantification of unique virus lineages within hosts. Here we show that IAV infection in lungs is characterized by multiple within-host bottlenecks that result in “islands” of infection in lung lobes, each with genetically distinct populations. We perform site-specific inoculation of barcoded IAV in the upper respiratory tract of ferrets and track viral diversity as infection spreads to the trachea and lungs. We detect extensive compartmentalization of discrete populations within lung lobes. Bottleneck events and localized replication stochastically sample individual viruses from the upper respiratory tract or the trachea that become the dominant genotype in a particular lobe. These populations are shaped strongly by founder effects, with limited evidence for positive selection. The segregated sites of replication highlight the jackpot-style events that contribute to within-host influenza virus evolution and may account for low rates of intrahost adaptation.
Programmable probiotics modulate inflammation and gut microbiota for inflammatory bowel disease treatment after effective oral delivery
Authors: Zhou Jun , Li Maoyi , Chen Qiufang , Li Xinjie , Chen Linfu , Dong Ziliang , Zhu Wenjun , Yang Yang , Liu Zhuang , Chen Qian 
Published: June 2022

AbstractReactive oxygen species (ROS) play vital roles in intestinal inflammation. Therefore, eliminating ROS in the inflammatory site by antioxidant enzymes such as catalase and superoxide dismutase may effectively curb inflammatory bowel disease (IBD). Here, Escherichia coli Nissle 1917 (ECN), a kind of oral probiotic, was genetically engineered to overexpress catalase and superoxide dismutase (ECN-pE) for the treatment of intestinal inflammation. To improve the bioavailability of ECN-pE in the gastrointestinal tract, chitosan and sodium alginate, effective biofilms, were used to coat ECN-pE via a layer-by-layer electrostatic self-assembly strategy. In a mouse IBD model induced by different chemical drugs, chitosan/sodium alginate coating ECN-pE (ECN-pE(C/A)2) effectively relieved inflammation and repaired epithelial barriers in the colon. Unexpectedly, such engineered EcN-pE(C/A)2 could also regulate the intestinal microbial communities and improve the abundance of Lachnospiraceae_NK4A136 and Odoribacter in the intestinal flora, which are important microbes to maintain intestinal homeostasis. Thus, this study lays a foundation for the development of living therapeutic proteins using probiotics to treat intestinal-related diseases.
Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas
Authors: Walzer Mathias , García-Seisdedos David , Prakash Ananth , Brack Paul , Crowther Peter , Graham Robert L. , George Nancy , Mohammed Suhaib , Moreno Pablo , Papatheodorou Irene , Hubbard Simon J. , Vizcaíno Juan Antonio 
Published: June 2022

AbstractThe number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets.
A global database for conducting systematic reviews and meta-analyses in innovation and quality management
Authors: Csizmadia Tibor , Katona Attila Imre 
Published: June 2022

AbstractInnovation and quality management are two fundamental business orientations that complement each other in improving performance and are important drivers of long-term economic growth. These themes have generated widespread attention in the literature; however, most of these studies mainly focused on a narrow area and only in a short term. No systematic effort has been made to build an extended bibliometric database regarding these research areas, which can be immediately used to conduct literature reviews. This study presents a complete (from 1975–2021), up-to-date, preprocessed and geocoded bibliometric database combining published articles of the two themes. The data collection was performed following the PRISMA methodology. The database consists of seven data tables, including one core dataset with 59,231 records and six citation network-related tables, including latitude and longitude values of the affiliations. These data will benefit researchers conducting comparative and in-depth analyses, such as gaining an overview of relevant existing studies, identifying relevant trends and gaining opportunities for a variety of geographic analyses.
Novel inorganic crystal structures predicted using autonomous simulation agents
Authors: Ye Weike , Lei Xiangyun , Aykol Muratahan , Montoya Joseph H. 
Published: June 2022

AbstractWe report a dataset of 96640 crystal structures discovered and computed using our previously published autonomous, density functional theory (DFT) based, active-learning workflow named CAMD (Computational Autonomy for Materials Discovery). Of these, 894 are within 1 meV/atom of the convex hull and 26826 are within 200 meV/atom of the convex hull. The dataset contains DFT-optimized pymatgen crystal structure objects, DFT-computed formation energies and phase stability calculations from the convex hull. It contains a variety of spacegroups and symmetries derived from crystal prototypes derived from known experimental compounds, and was generated from active learning campaigns of various chemical systems. This dataset can be used to benchmark future active-learning or generative efforts for structure prediction, to seed new efforts of experimental crystal structure discovery, or to construct new models of structure-property relationships.
A map of bat virus receptors derived from single-cell multiomics
Authors: Lv Tianhang , Wang Xiaoshan , Yu Chao , Wang Zhifeng , Xiang Rong , Li Linmiao , Yuan Yue , Wang Yuhang , Wei Xiaoyu , Yu Yeya , He Xiangyang , Zhang Libiao , Deng Qiuting , Wu Peiying , Hou Yong , Chen Jinping , Liu Chuanyu , Wong Gary , Liu Longqi 
Published: June 2022

AbstractBats are considered reservoirs of many lethal zoonotic viruses and have been implicated in several outbreaks of emerging infectious diseases, such as SARS-CoV, MERS-CoV, and SARS-CoV-2. It is necessary to systematically derive the expression patterns of bat virus receptors and their regulatory features for future research into bat-borne viruses and the prediction and prevention of pandemics. Here, we performed single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) of major organ samples collected from Chinese horseshoe bats (Rhinolophus affinis) and systematically checked the expression pattern of bat-related virus receptors and chromatin accessibility across organs and cell types, providing a valuable dataset for studying the nature of infection among bat-borne viruses.
The ERP and psychophysical changes related to facial emotion perception by expertise in Japanese hospitality, “OMOTENASHI”
Authors: Miki Kensaku , Takeshima Yasuyuki , Kida Tetsuo , Kakigi Ryusuke 
Published: June 2022

AbstractWe investigated the emotion perception process based on hospitality expertise. Forty subjects were divided into the OMOTENASHI group working at inns considered to represent the spirit of hospitality, OMOTENASHI in Japan, and CONTROL group without experience in the hospitality industry. We presented neutral, happy, and angry faces to investigate P100 and N170 by these faces, and psychophysical changes by the favor rating test to evaluate emotional perception. In the favor rating test, the score was significantly smaller (less favorable) in OMOTENASHI than in CONTROL. Regarding event-related potential components, the maximum amplitude of P100 was significantly larger for a neutral face at the right occipital electrode in OMOTENASHI than in CONTROL, and it was significantly larger for an angry face at both occipital electrodes in OMOTENASHI than in CONTROL. However, the peak latency and maximum amplitude of N170 were not significantly different between OMOTENASHI and CONTROL at both temporal electrodes for each emotion condition. Differences on the favor rating test and P100 in OMOTENASHI suggested that workers at inns may more quickly notice and be more sensitive to the facial emotion of guests due to hospitality training, and/or that hospitality expertise may increase attention to emotion by top-down and/or bottom-up processing.
Exogenous human α-Synuclein acts in vitro as a mild platelet antiaggregant inhibiting α-thrombin-induced platelet activation
Authors: Acquasaliente Laura , Pontarollo Giulia , Radu Claudia Maria , Peterle Daniele , Artusi Ilaria , Pagotto Anna , Uliana Federico , Negro Alessandro , Simioni Paolo , De Filippis Vincenzo 
Published: June 2022

Abstractα-Synuclein (αSyn) is a small disordered protein, highly conserved in vertebrates and involved in the pathogenesis of Parkinson’s disease (PD). Indeed, αSyn amyloid aggregates are present in the brain of patients with PD. Although the pathogenic role of αSyn is widely accepted, the physiological function of this protein remains elusive. Beyond the central nervous system, αSyn is expressed in hematopoietic tissue and blood, where platelets are a major cellular host of αSyn. Platelets play a key role in hemostasis and are potently activated by thrombin (αT) through the cleavage of protease-activated receptors. Furthermore, both αT and αSyn could be found in the same spatial environment, i.e. the platelet membrane, as αT binds to and activates platelets that can release αSyn from α-granules and microvesicles. Here, we investigated the possibility that exogenous αSyn could interfere with platelet activation induced by different agonists in vitro. Data obtained from distinct experimental techniques (i.e. multiple electrode aggregometry, rotational thromboelastometry, immunofluorescence microscopy, surface plasmon resonance, and steady-state fluorescence spectroscopy) on whole blood and platelet-rich plasma indicate that exogenous αSyn has mild platelet antiaggregating properties in vitro, acting as a negative regulator of αT-mediated platelet activation by preferentially inhibiting P-selectin expression on platelet surface. We have also shown that both exogenous and endogenous (i.e. cytoplasmic) αSyn preferentially bind to the outer surface of activated platelets. Starting from these findings, a coherent model of the antiplatelet function of αSyn is proposed.
Removal of chemical and microbial water pollutants by cold plasma combined with Ag/TiO2-rGO nanoparticles
Authors: Abdel-Wahed Mahmoud S. , Hefny Mohamed Mokhtar , Abd-Elmaksoud Sherif , El-Liethy Mohamed A. , Kamel Marwa A. , El-Kalliny Amer S. , Hamza Ibrahim Ahmed 
Published: June 2022

AbstractThis study aimed to investigate the synergistic effect of the cold atmospheric plasma (CAP) and heterogeneous photocatalytic processes in an aqueous solution to enhance water purification efficacy and reduce the energy cost required by CAP. 0.1% Ag/TiO2-reduced graphene oxide (rGO) nanoparticles (NPs) photo-composite were prepared and fully characterized. Data showed that Ag nanoparticles and the rGO play an important role in increasing the efficiency of the whole treatment process and the photo-composite (0.1% Ag/TiO2-1% rGO at 400 °C) revealed the highest phenol removal rate with excellent reusability. Also, complete inactivation (~ 5log10 reduction) of both E. coli and S. aureus by NPs was observed without CAP exposure, whereas a minimal effect (0.1–0.5 log10) on viruses (Adenovirus (AdV), rotavirus, and ɸX174) was observed after 10 min incubation. Interestingly, the photocatalytic virus inactivation test was promising, as it resulted in > 4.7log10 reduction of AdV at 2 min treatment, whereas < 1log10 could be reduced using only CAP at the same treatment time. Accordingly, we believe that this work could provide new insights into how the synergy between CAP and 0.1% Ag/TiO2-1% rGO photo-composite in aqueous media imposes a great potential for environmental applications, such as water purification and microbial inactivation.
Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients: a pilot study
Authors: Ruiz-Rodriguez Alicia , Lusarreta-Parga Paula , de Steenhuijsen Piters Wouter A. A. , Koppensteiner Lilian , Balcazar-Lopez Carlos E. , Campbell Robyn , Dewar Rebecca , McHugh Martin P. , Dockrell David , Templeton Kate E. , Bogaert Debby 
Published: June 2022

AbstractCo-infections with bacterial or fungal pathogens could be associated with severity and outcome of disease in COVID-19 patients. We, therefore, used a 16S and ITS-based sequencing approach to assess the biomass and composition of the bacterial and fungal communities in endotracheal aspirates of intubated COVID-19 patients. Our method combines information on bacterial and fungal biomass with community profiling, anticipating the likelihood of a co-infection is higher with (1) a high bacterial and/or fungal biomass combined with (2) predominance of potentially pathogenic microorganisms. We tested our methods on 42 samples from 30 patients. We observed a clear association between microbial outgrowth (high biomass) and predominance of individual microbial species. Outgrowth of pathogens was in line with the selective pressure of antibiotics received by the patient. We conclude that our approach may help to monitor the presence and predominance of pathogens and therefore the likelihood of co-infections in ventilated patients, which ultimately, may help to guide treatment.
Molecular dynamics study of lithium intercalation into –OH functionalized carbon nanotube bundle
Authors: Zheng Bin , Dong Huaze , Zhu Jinmiao , Wang Yanping 
Published: June 2022

AbstractThe influence of hydroxyl group (–OH) on carbon nanotube (CNT) interacting with lithium (Li) ions has been investigated via ab initio molecular dynamic (MD) simulations. Compared with the pure CNT, a higher efficiency has been observed for lithium intercalating into CNT-OH bundle. At lower Li ion density and CNT bundle density, CNT-OH exhibits higher intercalation efficiency than the pristine and ammonium functionalized CNTs. As the increasing of Li ion densities and CNT bundle densities, Li ions tend to intercalate into the interlayer between CNT-OH tubes instead of the interior of CNT-OH tubes. We also observe the destruction of hydroxyl groups during the intercalation of Li ions into interlayer of CNT-OH bundle. It is therefore suggested that eliminating the intercalation of Li ions into interlayer between tubes is important for the design of Li ion batteries.
Continuous noninvasive blood gas estimation in critically ill pediatric patients with respiratory failure
Authors: Dong Junzi , Xu-Wilson Minnan , Conroy Bryan R. , Khemani Robinder G. , Newth Christopher J. L. 
Published: June 2022

AbstractPatients supported by mechanical ventilation require frequent invasive blood gas samples to monitor and adjust the level of support. We developed a transparent and novel blood gas estimation model to provide continuous monitoring of blood pH and arterial CO2 in between gaps of blood draws, using only readily available noninvasive data sources in ventilated patients. The model was trained on a derivation dataset (1,883 patients, 12,344 samples) from a tertiary pediatric intensive care center, and tested on a validation dataset (286 patients, 4030 samples) from the same center obtained at a later time. The model uses pairwise non-linear interactions between predictors and provides point-estimates of blood gas pH and arterial CO2 along with a range of prediction uncertainty. The model predicted within Clinical Laboratory Improvement Amendments of 1988 (CLIA) acceptable blood gas machine equivalent in 74% of pH samples and 80% of PCO2 samples. Prediction uncertainty from the model improved estimation accuracy by 15% by identifying and abstaining on a minority of high-uncertainty samples. The proposed model estimates blood gas pH and CO2 accurately in a large percentage of samples. The model’s abstention recommendation coupled with ranked display of top predictors for each estimation lends itself to real-time monitoring of gaps between blood draws, and the model may help users determine when a new blood draw is required and delay blood draws when not needed.
Development and validation of a prognostic prediction model including the minor lymphatic pathway for distant metastases in cervical cancer patients
Authors: Thephamongkhol Kullathorn , Korpraphong Pornpim , Muangsomboon Kobkun , Sitathanee Chomporn , Lertkhachonsuk Arb-aroon , Phongkitkarun Sith , Srirattanapong Saowanee , Prapruttam Duangkamon , Bridhikitti Jidapa , Dendumrongsup Thaworn , Alisanant Petch , Amornwichet Napapat , Khorprasert Chonlakiet , Sasiwimonphan Kewalee , Tanprasertkul Chamnan , Dhanachai Mantana , Patumanond Jayanton , Setakornnukul Jiraporn 
Published: June 2022

AbstractTo develop and validate a prognostic model, including the minor lymphatic pathway (internal iliac and presacral nodes). Study design: Retrospective cohort. Participants: Locally advanced cervical cancer underwent concurrent chemoradiotherapy. Sample size: 397 and 384 patients in the development and validation data set. Predictors: Our new nodal staging system with the minor lymphatic pathway. Outcome: Distant metastases. Statistical analysis: Cox regression; net reclassification improvement (NRI) and decision curve analysis (DCA). Our new nodal system was the strongest predictor. The predictors in the final model were new nodal system, tumor stage, adenocarcinoma, initial hemoglobin, tumor size and age. The nodal system and the pretreatment model had concordance indices of 0.661 and 0.708, respectively, with good calibration curves. Compared to the OUTBACK eligibility criteria, the nodal system showed NRI for both cases (22%) and controls (16%). The pretreatment model showed NRI for cases (31%) and controls (18%). DCA in both models showed threshold probability of 15% and 12%, respectively, when compared with 24% in OUTBACK eligibility criteria. Our new nodal staging system and the pretreatment model could differentiate between high-risk and low-risk patients, thus facilitating decisions to provide more aggressive treatment to prevent distant metastases.
Spontaneous recovery from overexpectation in an insect
Authors: Terao Kanta , Matsumoto Yukihisa , Álvarez Beatriz , Mizunami Makoto 
Published: June 2022

AbstractIn associative learning in mammals, it is widely accepted that learning is determined by the prediction error, i.e., the error between the actual reward and the reward predicted by the animal. However, it is unclear whether error-based learning theories are applicable to the learning occurring in other non-mammalian species. Here, we examined whether overexpectation, a phenomenon that supports error-based learning theories, occurs in crickets. Crickets were independently trained with two different conditioned stimuli (CSs), an odour and a visual pattern, that were followed by an appetitive unconditioned stimulus (US). Then the two CSs were presented simultaneously as a compound, followed by the same US. This treatment resulted in a reduced conditioned response to the odour CS when tested immediately after training. However, the response to the CS was partially recovered after 1 day. These results are the first to show overexpectation and its spontaneous recovery in an invertebrate species. While the results showing overexpectation are in agreement with the prediction by the Rescorla-Wagner model, a major form of error-based learning theories, the ones showing spontaneous recovery are not. Our results suggest that conventional error-based learning models account for some, but not for all essential features of Pavlovian conditioning in crickets.