bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parthenolide inhibits proliferation of Kaposi's sarcoma-associated herpesvirus infected cells by suppression of the NF-κB signaling pathway
Authors: Li Ying , Xu Huiling , Tan Xiaohua , Cui Qinghua , Gu Wenyi , Pan Zemin , Yang Lei , Li Dongmei , Wu Shuyuan , Wang Xiaolu , Li Dongmei 
Published: May 2022

Abstract
The disease caused by Kaposi's sarcoma-associated herpesvirus (KSHV) is one of the major reasons for the death in AIDS. Development of anti-KSHV drugs is thus crucial. This study is to investigate the effect of Parthenolide (PTL) on the proliferation and NF-κB signaling pathway of KSHV-infected cells. iSLK.219 and KSHV infected SH-SY5Y cells (SK-RG) were treated with PTL. Taq-Man real-time quantitative PCR was used to detect the KSHV copy number. mRNA and protein expression of KSHV genes were detected by real-time PCR and immunocytochemistry. Cell viability test and colony formation assay was used to detect the proliferation. The flow cytometry was used to detect the cell cycle. Cyclin D1, CDK6, CDK4 and NF-κB-related proteins, including IKKβ, P-p65 and P-IKB-α were detected by Western blotting. Results showed PTL alerted the cell morphology. PTL reduced the KSHV copy number. PTL suppressed the mRNA expression of ORF50, K8.1, v-GPCR and protein expression of LANA, ORF50, and K8.1. PTL blocked the G1 phase in iSLK.219 cells and decreased Cyclin D1, CDK6 and CDK4. PTL also inhibited the levels of NF-κB signaling protein, including IKKβ, P-p65 and P-IKB-α. Overall, these results suggest that PTL is a candidate drug against KSHV pathogenicity through suppressing the proliferation and NF-κB signaling pathway in KSHV-infected cells.
Distribution of biocide resistance genes and association with clonal complex genotypes in Staphylococcus aureus isolated from school-age children in Guangzhou
Authors: zhang chao , Liang Bingshao , Xiong Zhile , Liang Zhuwei , Cai Hao , Zhong Huamin , Xie Yongqiang , Xie Yuanwei , Liu Xiaochun , Xie Shiying , Lan Fangjun , Zhou Zhenwen 
Published: May 2022

Abstract
Background: Disinfectant and antibiotics such as chlorhexidine and mupirocin are often prescribed to children in affected communities to prevent colonization and transmission of Staphylococcus aureus, but this has led to an increasing rate of biocide resistance. In this study, we aimed to determine the distribution of biocide resistance genes among S. aureus isolates from school-age children in Guangzhou, investigate chlorhexidine gluconate and mupirocin susceptibility and clonal complex (CC) genotypes in strains carrying biocide-resistance genes, and further explore the role of biofilms in this resistance.Methods: Antibiotic resistance and multilocus sequence genotyping were performed on 722 S. aureus isolates from 2375 nasal swabs from school-aged children in Guangzhou. The distribution of nine biocide genes (qacA/B, mupA, mepA, sepA, norA, lmrS, smr, mupB, qacG) was determined by PCR. Isolates carrying qacA/B or mupA genes were further tested for susceptibility to chlorhexidine gluconate (CHG) and mupirocin using broth microdilution and their biofilm formation abilities were evaluated by a microtiter plate test.Results: The most prevalent of the nine biocide resistance genes were mepA (95.57%), followed by norA (78.81%), lmrS (77.01%), and sepA (58.17%). The qacG gene was not detected. We found that junior school students possessed a significantly higher distribution of qacA/B and mupA and a lower distribution of mepA, norA and lmrS genes; distribution of sepA was significantly decreased in CC30 and CC45 genotypes, and presence of sepA was associated with resistance to antibiotics such as CLI, ERY, TCY, SXT, CIP, and LVX. In addition, 64 (94.1%, n=68) qacA/B+ isolates showed CHG resistance, 12 (100.0%, n=12) mupA+ isolates were mupirocin resistant, and 4 (80%, n=5) and 5 (100%, n=5) qacA/B+mupA+ isolates were CHG and mupirocin resistant, respectively. Of these 85 isolates, 98.8 % (n=84) had different degrees of biofilm-forming abilities, which were positively associated with CHG and mupirocin resistance.Conclusion: The distribution of biocide resistance genes was associated with special CCs. The qacA/B and mupA genes are associated with resistance to CHG and mupirocin, and biofilm formation was found to contribute to this biocide resistance.
Probable human origin of the SARS-CoV-2 polybasic furin cleavage site
Authors: Romeu Antonio R. 
Published: May 2022

Abstract
The origin of the SARS-CoV-2 is still unclear. Simply said, its emergence is due to the acquisition of the polybasic furin cleavage site on the S protein in one of its closest relatives. The recent discovery in Laos of bat Rhinolophus coronaviruses that contain receptor binding domains almost identical to that of SARS-CoV-2, and despite not having the furin site, they can therefore infect human cells (1), is the cornerstone to identify the SARS-CoV-2 progenitor. However, it is not yet known where the insertion of the furin site at the S1/S2 junction in the S protein of the pandemic virus came from, nor the how and when of such acquisition. The most surprising was: (i) that the polybasic furin cleavage site is unique to SARS-CoV-2 among Sarbecovirus (2), and (ii) that the inserted four amino acid motif has a CGG-CGG encoded arginine dimer which is rare in coronaviruses (3). So, my question was if the SARS-CoV-2 insert in the S gene would match to human transcripts. Here, I address this issue by using NCBI and GISAID databases, the NCBI Human Genome Resources, sequence analysis tools and in-house developed bioinformatic tools. I found that the 12-nucleotide insert encoding SARS-CoV-2 furin site 100% match to several human transcripts. Taken together the presence of these human transcripts and the expression patterns of their genes; and further evidences such as the codon optimization of that arginine dimer and other PRRA-like insertions in the S protein, results provide insight into the SARS-CoV-2 furin cleavage site origin, in the framework of a human-virus recombination link, during undetected human-to-human virus transmission.
Population aging challenge future mitigation of deaths attributable to PM2.5 pollution in China
Authors: Xu Fangjin , Huang Qingxu , Yue Huanbi , Feng Xingyun , Xu Haoran , He Chunyang , Yin Peng , Bryan Brett 
Published: May 2022

Abstract
Estimating the health burden of air pollution in China against the background of population aging is of great significance for the well-being of elderly individuals and achieving the United Nations Sustainable Development Goals (SDGs). Since previous studies did not fully consider the differences on drivers of deaths attributable to PM2.5 pollution (DAPP) (i.e., socioeconomic factors, climate factors, and disease mortalities) among provinces in China, the impact of future population aging on DAPP cannot be comprehensively and objectively estimated. In this study, we estimated and verified the spatiotemporal changes of DAPP in China from 2005 to 2017 based on a risk assessment framework. Then, using the latest climate projections, we estimated the changes and drivers in DAPP under four scenarios in China from 2018 to 2035 based on decomposition analysis. The results show that from 2017 to 2035, DAPP in China will decrease between 31.9 (26.6–45.6) thousand and 178.8 (152.5-210.5) thousand across three scenarios (sustainable development (SSP1-2.6), business as usual (SSP2-4.5), and fossil fuel development (SSP5-8.5). We found that population aging will be the leading driver contributing to the increase in DAPP and offset the positive gains achieved by improvement in air pollution and healthcare. In the future, reducing the exposure to air pollution and improving healthcare of the elderly is necessary to mitigate the global health burden of air pollution and this requires mutual cooperation and long-term efforts among countries worldwide.
Plasma and Cerebrospinal Fluid Neurofilament Light Concentrations Reflect Neuronal Damage in Systemic Lupus Erythematosus
Authors: Zervides Kristoffer Alexander , Janelidze Shorena , Nystedt Jessika , Gullstrand Birgitta , Nilsson Petra , Sundgren Pia C , Bengtsson Anders A , Hansson Oskar , Jönsen Andreas 
Published: May 2022

Abstract
Background: Neuronal damage in systemic lupus erythematosus (SLE) is common, but the extent and mechanisms are unclear. Neurofilament light (NfL) concentrations rise in plasma and cerebrospinal fluid (CSF) during neuronal damage in various neurological disorders. In this cross-sectional study, plasma and CSF concentrations of NfL were explored as a marker of neuronal damage in SLE.Methods: 72 consecutive SLE out-patients and 26 healthy controls, all female, aged <55 years, underwent magnetic resonance imaging (MRI) and neurocognitive testing. NfL concentrations in plasma from all individuals and in CSF from 32 patients were measured with single-molecule array technology. Patients were assessed by a rheumatologist and neurologist to define neuropsychiatric involvement (NPSLE) according to three attribution models: SLICC A, SLICC B and ACR.Results: Plasma and CSF NfL concentrations correlated strongly (r=0.72, p<0.001). Both NPSLE and non-NPSLE patients in all attribution models had higher plasma NfL concentrations compared with healthy controls (log-NfL, pg/ml, mean (SD); healthy controls (0.71 (0.17)); SLICC A model: NPSLE (0.87 (0.13), p=0.003), non-NPSLE (0.83 (0.18), p=0.005); SLICC B model: NPSLE (0.87 (0.14), p=0.001), non-NPSLE (0.83 (0.18), p=0.008); ACR model: NPSLE (0.86 (0.16), p<0.001), non-NPSLE (0.81 (0.17), p=0.044)). Plasma and CSF NfL concentrations did not differ between NPSLE and non-NPSLE patients. Higher plasma NfL concentrations correlated with larger CSF volumes on MRI (r=0.34, p=0.005), and was associated with poorer cognitive performance in the domains of simple attention, psychomotor speed and verbal memory. SLICC/ACR-Damage Index ≥1 was independently associated with higher plasma NfL concentrations (β=0.074, p=0.038). Higher plasma creatinine concentrations, anti-dsDNA-positivity, low complement C3 levels, or a history of renal involvement were associated with higher plasma NfL concentrations (β=0.003, p=0.009; β=0.072, p=0.031; β=0.077, p=0.027; β=0.069, p=0.047, respectively). Conclusions: Higher plasma NfL concentrations in NPSLE and non-NPSLE patients may indicate a higher degree of neuronal damage in SLE in general, corresponding to cognitive impairment and organ damage development. Furthermore, our results may indicate a higher degree of neuronal breakdown in patients with active SLE, also without overt clinical symptoms. NfL may serve as an indicator of neuronal damage in SLE in further studies.
Significance of heat transfer for second-grade Fuzzy hybrid nanofluid flow past over a stretching/shrinking Riga wedge
Authors: Nadeem Muhammad , Siddique Imran , Bilal Muhammad , Ali Rifaqat 
Published: May 2022

Abstract
This investigation presents the fuzzy nanoparticle volume fraction on heat transfer of second-grade hybrid Al2O3+Cu/EO nanofluid over a stretching/shrinking Riga wedge under the contribution of heat source, stagnation point, and nonlinear thermal radiation. Also, this inquiry includes flow simulations using modified Hartmann number, boundary wall slip and heat convective boundary condition. Engine oil is used as the host fluid and two distinct nanomaterials (Cu and Al2O3) are used as nanoparticles. The associated nonlinear governing PDEs are intended to be reduced into ODEs using suitable transformations. After that 'bvp4c,' a MATLAB technique is used to compute the solution of said problem. For validation, the current findings are consistent with those previously published. The temperature of hybrid nanofluid rises significantly more quickly than the temperature of the second-grade fluid, for larger values of the wedge angle parameter, the volume percentage of nanomaterials. For improvements to the wedge angle and Hartmann parameter, the skin friction factor improves. Also, for the comparison of nanofluids and hybrid nanofluids through membership function (MF), the nanoparticle volume fraction is taken as a triangular fuzzy number (TFN) in this work. Membership function and sigma-cut are controlled TFN which ranges from 0 to 1. According to the fuzzy analysis, the hybrid nanofluid gives a more heat transfer rate as compared to nanofluids.
Immunocolorimetric assay based on amplified gold nanoparticles and magnetic separation beads for detection of sesame allergens in food
Authors: Linghu Xiaopan , Liu Wentao , Wang Shasha , Wang Rui , Lu Yang 
Published: May 2022

Abstract
We had developed a magnetic separation immunocolorimetric assay to detect sesame allergens. Sesame monoclonal antibody (Ab) was modified to gold nanoparticles (AuNPs) as signal probes (AuNPs-Ab). Sesame allergens (SA) were attached to the carboxyl-functional magnetic polystyrene microspheres (MPMs) as capture probes (MPMs-SA). Based on the competition format, the capture probes competed with the sesame allergens in the sample to bind the corresponding signal probes. When sesame allergens were in the sample, two immune complexes (AuNPs-Ab@MPMs-SA and AuNPs-Ab@SA) were formed. The immune complex AuNPs-Ab@SA was used to quantify the sesame allergens in the sample. This immunoassay had a detection linear from 50 to 800 µg L− 1 with a limit of detection (LOD) of 45.53 µg L− 1. Based on the optimized conditions, the recovery results of sesame allergens in bread, biscuits, almond beverage and energy bars were between 82.50% and 116.67%. The LODs for the bread, biscuit, almond beverage and energy bar samples were 0.36, 0.36, 0.27 and 0.55 mg kg− 1 respectively.
Cellular senescence affects energy metabolism, immune infiltration and immunotherapeutic response in Hepatocellular Carcinoma
Authors: Gao Biao , Lu Shichun 
Published: May 2022

Abstract
Background：Aging is an inevitable consequence of life, characterized by a progressive decline in tissue and organ function and an increased risk of death. There is growing evidence that aging is closely related to tumor development and immune regulation. However, in hepatocellular carcinoma, the relationship between cellular senescence and immune infiltration, energy metabolism, chemokines, and immunotherapeutic response is unclear and needs further study. Methods: We first analyzed 274 cellular senescence-associated genes by the NMF algorithm and identified two cellular senescence-associated clusters. Subsequently, we compared the differences between the two clusters, in terms of immune infiltration, energy metabolism, chemokines, and immunotherapeutic response to treatment. We further constructed risk models using cellular senescence-associated signature genes that could effectively identify the two subpopulations. Finally, we validated the validity and robustness of the risk model using an external dataset.Results: We found significant differences in survival prognosis between two cellular senescence-associated clusters. In addition, we found significant differences in immune cell infiltration, expression of energy metabolism-related genes, expression of chemokine-related genes, expression of immune checkpoint-related genes, Tumor Immune Dysfunction and Exclusion between the two clusters. Also, a scoring system associated with cellular senescence was developed and validated as an independent prognostic indicator.It was validated as an independent prognostic factor and immunotherapeutic predictor for HCC.It was validated as an independent prognostic factor and immunotherapeutic predictor for HCC. The cellular senescence-related scoring system was validated as an independent prognostic factor and immunotherapy predictor for HCC, and patients with low CSS were characterized by prolonged survival time. Conclusion: Our study confirmed the relationship between cellular senescence and immune cell infiltration, energy metabolism, chemokines, expression of immune checkpoint-related genes, and response to immunotherapy. This enhances our understanding of cellular senescence and tumor immune microenvironment, energy metabolism, chemokines, and provides new insights to improve immunotherapy outcomes in HCC patients. It provides new insights to improve the outcome of immunotherapy in HCC patients.
Selecting and refining suitable methods of developing digital elevation models for wetlands in data-scarce environments
Authors: Waal Bennie van der , Grenfell Suzanne , Huchzermeyer Nicholaus , Schlegel Pippa 
Published: May 2022

Abstract
Land surface topography plays an important role in water and sediment dispersal processes in wetlands. For wetland practitioners and researchers to engage with these processes in time and space, they require topographic data in order to derive wetland surface gradient, cross-sectional shape and area, surface and subsurface hydrological connectivity, and hydraulic characteristics. A range of data options, with varying spatial resolutions, are available, ranging from free national and global resources (e.g. contour data and global elevation models) to project-specific high-resolution surveys (e.g. Differential Global Positioning Systems (DGPS), Photogrammetry, Light Detection And Ranging (LiDAR)). Due to the scarcity of high-resolution and high accuracy data, especially in developing countries, data gathering and processing costs can be significant. This paper presents a commentary on a range of topographic data and processing options for a floodplain wetland in the Eastern Cape, South Africa. It critically reviews the usefulness and shortfalls of various wetland related applications ranging from gradient calculations to more detailed hydraulic modelling, and the data resolution required for each application. Free, low resolution, datasets have a limited representation of topography due to low resolution and large vertical error. Field-based surveys (using survey-grade equipment such as a DGPS) have the benefit of providing accurate terrain results in areas with dense vegetation and surface water, while Structure from Motion and LiDAR data are useful to represent the higher resolution morphology across the wetland, despite shortcomings with dense vegetation and surface water. However, combining DGPS data with LiDAR proves to yield the best model for detailed process modelling.
A "data-driven" computational method to model and predict the dynamic instabilities of a frictional system
Authors: Maaboudallah Farouk , Atalla Noureddine 
Published: May 2022

Abstract
Most of the recently developed methods for predicting the dynamic instabilities of frictional systems couple stochastic algorithms with the finite element method (FEM). They use random variables to model theuncertainty of input parameters through standard probability laws. Regardless of the fact that advanced numerical schemes are available nowadays, a systematic and accurate method to describe finely the uncertainties upstream the model, and thus predict its response is still missing. In this contribution, we present a data-driven stochastic finite element scheme to predict the dynamic behavior of a rubbing system. The proposed framework relies on data-driven approach and uses four steps. In the first, the measured data are integrated directly, for the uncertainty quantification, by means of the random balance design (RBD). In the second step, the generated stochastic data are evaluated in an iterative way to solve friction-inducedvibration problem. In the third step, the resulted data are reordered in such a way that the corresponding values of each measured input parameters are ranked in ascending order. Finally, the Fourier spectrum is introduced on the reordered results to compute the sensitivity indices. Thus, instead of Monte Carlo-based formalism or Fourier Amplitude Sensitivity Test (FAST), the computational cost of the proposed method is kept down to O(N) with N the number of samples. We investigate the efficiency of the suggested solver on a reduced brake system. Altogether, the suggested procedure achieves excellent accuracy at a much reduced computational time compared to the methods available in the literature.
A spatial multi-omics atlas of the human lung reveals a novel gland-associated immune niche
Authors: Meyer Kerstin , Madissoon Elo , Oliver Amanda , Kleshchevnikov Vitalii , Wilbrey-Clark Anna , Polański Krzysztof , Richoz Nathan , Orsi Ana Elisa Ribeiro , Mamanova Lira , Bolt Liam , Elmentaite Rasa , Pett Jan , Huang Ni , Xu Chuan , He Peng , Dabrowska Monika , Pritchard Sophie , Tuck Elizabeth , Prigmore Elena , Perera Shani , Knights Andrew , Oszlanczi Agnes , Hunter Adam , Vieira Sara Filipa , Patel Minal , Yoshida Masahiro , Worlock Kaylee , Lindeboom Rik , Nikolic Marko , Georgakopoulos Nikitas , Mahbubani Krishna , Saeb-Parsy Kourosh , Bayraktar Omer Ali , Clatworthy Menna , Stegle Oliver , Kumasaka Natsuhiko , Teichmann Sarah 
Published: May 2022

Abstract
To (re)define tissue architecture of the lung and airways at the cellular and molecular level, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and Visium Spatial Transcriptomics. Using computational data integration and analysis, we extend beyond the suspension cell paradigm of lung atlases to date, to define and discover macro and micro-anatomical tissue compartments. We describe novel cell types and states in vascular, stromal and nerve bundle microenvironments. From our spatial transcriptomics, we discover and validate a novel survival niche for IgA plasma cells in the airway submucosal glands (SMG). In this niche we define a supporting role for SMG epithelial cells in mucosal immunity through recruitment and maintenance of IgA plasma, B and CD4 T cells locally at the airway SMG. We identify an immune-supporting role for SMG duct and serous cells with distinct signalling circuits to recruit B cells and IgA plasma cells, promoting longevity and antibody secretion through expression of CCL28, APRIL and IL6. We find high expression of MHC-II in SMG duct and serous cells, which are localised closely with memory CD4 T cells, suggesting local modulation of antigen specific immune responses locally at the glands. This new tissue microenvironment, which we term the “gland-associated immune niche” (GAIN) has major implications for respiratory immunity and infection response. Our single cell and spatial data is available for download and query at lungcellatlas.org.