bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstructing runoff components and glacier mass balance with climate change: Niyang river basin, southeastern Tibetan plateau
Authors: He Qiule , Kuang Xingxing , Ma Enze , Chen Jianxin , Feng Yuqing , Zheng Chunmiao 
Published: July 2023

The southeastern part of the Tibetan Plateau (TP), one of the regions with the largest glacier distribution on the plateau, has been experiencing a significant loss in glacier mass balance (GMB) in recent decades due to climate warming. In this study, we used the Spatial Processes in Hydrology (SPHY) model and satellite data from LANDSAT to reconstruct the runoff components and glacier mass balance in the Niyang River basin (NRB). The measured river discharge data in the basin during 2000–2008 were used for model calibration and validation. Then, the validated model was applied to reconstruct the runoff components and GMB in the Niyang River basin for the period 1969–2013. Results showed that rainfall runoff (67%) was the dominant contributor to total runoff, followed by snowmelt runoff (14%), glacier melt runoff (10%), and baseflow (9%). The NRB experienced a severe loss in GMB, with a mean value of −1.26 m w. e./a (corresponding to a cumulative glacier mass loss of −56.72 m w. e.) during 1969–2013. During periods Ⅰ (1969–1983), Ⅱ (1984–1998), and Ⅲ (1999–2013) glacier mass loss was simulated at rates of −1.27 m w. e./a, −1.18 m w. e./a, and −1.33 m w. e./a, respectively. The annual loss of glacier mass in the northern region of the NRB (−1.43 m w. e./a) was significantly greater than that of the southern region (−0.53 m w. e./a) from 1969 to 2013, largely due to temperature variations, especially in summer months. These findings enhance our understanding of how different hydrological processes respond to climate change and provide a potential method to study runoff components and GMB in other glacierized catchments worldwide.
Analysis of lactate metabolism-related genes and their association with immune infiltration in septic shock via bioinformatics method
Authors: Jiang Huimin , Ren Yun , Yu Jiale , Hu Sheng , Zhang Jihui 
Published: July 2023

Background: Lactate, as an essential clinical evaluation index of septic shock, is crucial in the incidence and progression of septic shock. This study aims to investigate the differential expression, regulatory relationship, clinical diagnostic efficacy, and immune infiltration of lactate metabolism-related genes (LMGs) in septic shock.Methods: Two sepsis shock datasets (GSE26440 and GSE131761) were screened from the GEO database, and the common differentially expressed genes (DEGs) of the two datasets were screened out. LMGs were selected from the GeneCards database, and lactate metabolism-related DEGs (LMDEGs) were determined by integrating DEGs and LMGs. Protein-protein interaction networks, mRNA-miRNA, mRNA-RBP, and mRNA-TF interaction networks were constructed using STRING, miRDB, ENCORI, and CHIPBase databases, respectively. Receiver operating characteristic (ROC) curves were constructed for each of the LMDEGs to evaluate the diagnostic efficacy of the expression changes in relation to septic shock. Finally, immune infiltration analysis was performed using ssGSEA and CIBERSORT.Results: This study identified 10 LMDEGs, including LDHB, STAT3, LDHA, GSR, FOXM1, PDP1, GCDH, GCKR, ABCC1, and CDKN3. Enrichment analysis revealed that DEGs were significantly enriched in pathways such as pyruvate metabolism, hypoxia pathway, and immune-inflammatory pathways. PPI networks based on LMDEGs, as well as 148 pairs of mRNA-miRNA interactions, 243 pairs of mRNA-RBP interactions, and 119 pairs of mRNA-TF interactions were established. ROC curves of eight LMDEGs (LDHA, GSR, STAT3, CDKN3, FOXM1, GCKR, PDP1, and LDHB) with consistent expression patterns in two datasets had an area under the curve (AUC) ranging from 0.662 to 0.889. The results of ssGSEA and CIBERSORT both showed significant differences in the infiltration of various immune cells, including CD8 T cells, T regulatory cells, and natural killer cells, and LMDEGs such as STAT3, LDHB, LDHA, PDP1, GSR, FOXM1, and CDKN3 were significantly associated with various immune cells.Conclusion: The LMDEGs are significantly associated with the immune-inflammatory response in septic shock and have a certain diagnostic accuracy for septic shock.
Immunomodulatory potential of mesenchymal stromal cell-derived extracellular vesicles in chondrocyte inflammation
Authors: Ossendorff Robert , Grad Sibylle , Tertel Tobias , Wirtz Dieter C. , Giebel Bernd , Börger Verena , Schildberg Frank A. 
Published: July 2023

IntroductionOsteoarthritis (OA) affects a large percentage of the population worldwide. Current surgical and nonsurgical concepts for treating OA only result in symptom-modifying effects. However, there is no disease-modifying therapy available. Extracellular vesicles released by mesenchymal stem/stromal cells (MSC-EV) are promising agents to positively influence joint homeostasis in the osteoarthritic surroundings. This pilot study aimed to investigate the effect of characterized MSC-EVs on chondrogenesis in a 3D chondrocyte inflammation model with the pro-inflammatory cytokine TNFα.MethodsBovine articular chondrocytes were expanded and transferred into pellet culture at passage 3. TNFα, human MSC-EV preparations (MSC-EV batches 41.5-EVi1 and 84-EVi), EVs from human platelet lysate (hPL4-EV), or the combination of TNFα and EVs were supplemented. To assess the effect of MSC-EVs in the chondrocyte inflammation model after 14 days, DNA, glycosaminoglycan (GAG), total collagen, IL-6, and NO release were quantified, and gene expression of anabolic (COL-II, aggrecan, COMP, and PRG-4), catabolic (MMP-3, MMP-13, ADAMTS-4 and ADAMTS-5), dedifferentiation (COL-I), hypertrophy (COL-X, VEGF), and inflammatory (IL-8) markers were analyzed; histological evaluation was performed using safranin O/Fast Green staining and immunohistochemistry of COL I and II. For statistical evaluation, nonparametric tests were chosen with a significance level of p &lt; 0.05.ResultsTNFα supplementation resulted in catabolic stimulation with increased levels of NO and IL-6, upregulation of catabolic gene expression, and downregulation of anabolic markers. These findings were supported by a decrease in matrix differentiation (COL-II). Supplementation of EVs resulted in an upregulation of the chondrogenic marker PRG-4. All MSC-EV preparations significantly increased GAG retention per pellet. In contrast, catabolic markers and IL-8 expression were upregulated by 41.5-EVi1. Regarding protein levels, IL-6 and NO release were increased by 41.5-EVi1. Histologic and immunohistochemical evaluations indicated a higher differentiation potential of chondrocytes treated with 84-EVi.DiscussionMSC-EVs can positively influence chondrocyte matrix production in pro-inflammatory surroundings, but can also stimulate inflammation. In this study MSC-EV 41.5-EVi1 supplementation increased chondrocyte inflammation, whereas MSC-84-EVi supplementation resulted a higher chondrogenic potential of chondrocytes in 3D pellet culture. In summary, the selected MSC-EVs exhibited promising chondrogenic effects indicating their significant potential for the treatment of OA; however, the functional heterogeneity in MSC-EV preparations has to be solved.
Transcriptomic profile of TNFhigh MAIT cells is linked to B cell response following SARS-CoV-2 vaccination
Authors: Marzano Paolo , Balin Simone , Terzoli Sara , Della Bella Silvia , Cazzetta Valentina , Piazza Rocco , Sandrock Inga , Ravens Sarina , Tan Likai , Prinz Immo , Calcaterra Francesca , Di Vito Clara , Cancellara Assunta , Calvi Michela , Carletti Anna , Franzese Sara , Frigo Alessandro , Darwish Ahmed , Voza Antonio , Mikulak Joanna , Mavilio Domenico 
Published: July 2023

IntroductionHigher frequencies of mucosal-associated invariant T (MAIT) cells were associated with an increased adaptive response to mRNA BNT162b2 SARS-CoV-2 vaccine, however, the mechanistic insights into this relationship are unknown. In the present study, we hypothesized that the TNF response of MAIT cells supports B cell activation following SARS-CoV-2 immunization.MethodsTo investigate the effects of repeated SARS-CoV-2 vaccinations on the peripheral blood mononuclear cells (PBMCs), we performed a longitudinal single cell (sc)RNA-seq and scTCR-seq analysis of SARS-CoV-2 vaccinated healthy adults with two doses of the Pfizer-BioNTech BNT162b2 mRNA vaccine. Collection of PBMCs was performed 1 day before, 3 and 17 days after prime vaccination, and 3 days and 3 months following vaccine boost. Based on scRNA/TCR-seq data related to regulatory signals induced by the vaccine, we used computational approaches for the functional pathway enrichment analysis (Reactome), dynamics of the effector cell-polarization (RNA Velocity and CellRank), and cell-cell communication (NicheNet).ResultsWe identified MAIT cells as an important source of TNF across circulating lymphocytes in response to repeated SARS-CoV-2 BNT162b2 vaccination. The TNFhigh signature of MAIT cells was induced by the second administration of the vaccine. Notably, the increased TNF expression was associated with MAIT cell proliferation and efficient anti-SARS-CoV-2 antibody production. Finally, by decoding the ligand-receptor interactions and incorporating intracellular signaling, we predicted TNFhigh MAIT cell interplay with different B cell subsets. In specific, predicted TNF-mediated activation was selectively directed to conventional switched memory B cells, which are deputed to high-affinity long-term memory.DiscussionOverall, our results indicate that SARS-CoV-2 BNT162b2 vaccination influences MAIT cell frequencies and their transcriptional effector profile with the potential to promote B cell activation. This research also provides a blueprint for the promising use of MAIT cells as cellular adjuvants in mRNA-based vaccines.
Multi-phasic gene profiling using candidate gene approach predict the capacity of specific antibody production and maintenance following COVID-19 vaccination in Japanese population
Authors: Takemoto Yuki , Tanimine Naoki , Yoshinaka Hisaaki , Tanaka Yuka , Takafuta Toshiro , Sugiyama Aya , Tanaka Junko , Ohdan Hideki 
Published: July 2023

BackgroundVaccination against severe acute respiratory syndrome coronavirus type 2 is highly effective in preventing infection and reducing the severity of coronavirus disease (COVID-19). However, acquired humoral immunity wanes within six months. Focusing on the different tempo of acquisition and attenuation of specific antibody titers in individuals, we investigated the impact of genetic polymorphisms on antibody production after COVID-19 vaccination.MethodsIn total 236 healthcare workers from a Japanese municipal hospital, who received two doses of the vaccine were recruited. We employed a candidate gene approach to identify the target genetic polymorphisms affecting antibody production after vaccination. DNA samples from the study populations were genotyped for 33 polymorphisms in 15 distinct candidate genes encoding proteins involved in antigen-presenting cell activation, T cell activation, T-B interaction, and B cell survival. We measured total anti-SARS-Cov2 spike IgG antibody titers and analyzed the association with genetic polymorphisms at several time points after vaccination using an unbiased statistical method, and stepwise logistic regression following multivariate regression.ResultsSignificant associations were observed between seven SNPs in NLRP3, OAS1, IL12B, CTLA4, and IL4, and antibody titers at 3 weeks after the first vaccination as an initial response. Six SNPs in NLRP3, TNF, OAS1, IL12B, and CTLA4 were associated with high responders with serum antibody titer &gt; 4000 BAU/ml as boosting effect at 3 weeks after the second vaccination. Analysis of long-term maintenance showed the significance of the three SNPs in IL12B, IL7R, and MIF for the maintenance of antibody titers and that in BAFF for attenuation of neutralizing antibodies. Finally, we proposed a predictive model composed of gene profiles to identify the individuals with rapid antibody attenuation by receiver operating characteristic (ROC) analysis (area under the curve (AUC)= 0.76, sensitivity = 82.5%, specificity=67.8%).ConclusionsThe candidate gene approach successfully showed shifting responsible gene profiles and initial and boosting effect mainly related to the priming phase into antibody maintenance including B cell survival, which traces the phase of immune reactions. These gene profiles provide valuable information for further investigation of humoral immunity against COVID-19 and for building a strategy for personalized vaccine schedules.
Cellular immune response of SARS-CoV-2 vaccination in kidney transplant recipients: a systematic review and meta-analysis
Authors: Udomkarnjananun Suwasin , Gatechompol Sivaporn , Leelahavanichkul Asada , Kerr Stephen J. 
Published: July 2023

BackgroundEvidence has demonstrated inferior humoral immune responses after SARS-CoV-2 vaccination in kidney transplant recipients compared to the general population. However, data on cellular immune responses in this population have not been established.MethodsWe searched the MEDLINE, Scopus, and Cochrane databases and included studies reporting cellular immune response rates in kidney transplant recipients after receiving SARS-CoV-2 vaccines. Studies that reported factors associated with cellular immune responders or non-responders were also included (PROSPERO: CRD42022375544).ResultsFrom a total of 1,494 articles searched, 53 articles were included in the meta-analysis. In all, 21 studies assessed cellular immune response by interferon-γ enzyme-linked immunosorbent spot (IFN-γ ELISPOT), 22 studies used interferon-γ release assay (IGRA), and 10 studies used flow cytometric analysis. The pooled response rate after two doses (standard regimen) and three doses of vaccination was 47.5% (95%CI 38.4-56.7%) and 69.1% (95%CI 56.3-80.6%) from IFN-γ ELISPOT, 25.8% (95%CI 19.7-32.4%) and 14.7% (95%CI 8.5-22.2%) from IGRA, and 73.7% (95%CI 55.2-88.8%) and 86.5% (95%CI 75.3-94.9%) from flow cytometry, respectively. Recipients with seroconversion were associated with a higher chance of having cellular immune response (OR 2.58; 95%CI 1.89-3.54). Cellular immune response in kidney transplant recipients was lower than in dialysis patients (OR 0.24; 95%CI 0.16-0.34) and the general population (OR 0.10; 95%CI 0.07-0.14). Age and immunosuppressants containing tacrolimus or corticosteroid were associated with inferior cellular immune response.ConclusionCellular immune response after SARS-CoV-2 vaccination in kidney transplant recipients was lower than in dialysis patients and the general population. Age, tacrolimus, and corticosteroid were associated with poor response. Cellular immune response should also be prioritized in vaccination studies.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier CRD42022375544.
Cool skin effect and warm skin phenomenon observed by shipboard radiometer in the Northwest Pacific
Authors: Yang Minglun , Guan Lei , Qu Liqin , Zhang Kailin 
Published: July 2023

Sea surface temperature (SST) is an important variable in the study of ocean boundary layers and heat exchange. The accurate simulation and measurement of skin effects are vital to air–sea model processing and satellite SST retrieval. Shipboard measurements from eleven cruises in the Northwest Pacific between August 2015 and October 2018 were used to estimate the cool skin effect and compare model results. The temperature difference ΔT between the sea surface skin temperature (SSTskin), as measured by an infrared radiometer, and the sea surface depth temperature (SSTdepth) at around 4 meters showed a mean difference and a standard deviation of the same 0.2 K, with a total of 5-min 39909 measurements. Both daytime and nighttime ΔT values were compared to physical model simulations and were found to have relatively larger mean values. A set of new coefficients for an exponential parameterization of the cool skin effect was derived in the research area, which performed well in comparison to previous empirical models. In nighttime observations from two summer cruises, the reverse process of heat flux transfer from the air to the sea in the form of a warm skin was distinguished. There were 667 positive ΔT values out of the 1917 nighttime observations, with magnitudes ranging from around 0 to 0.3 K. A high proportion of the cases of the warm skin phenomenon occurred when the air was very humid and much warmer than the sea surface.
Clinical, radiological, and pathological features of minute pulmonary meningothelial-like nodules and diffuse pulmonary meningotheliomatosis
Authors: Li Naijian , Quan Sicui , Liu Qin , Xie Zhiling , Wang Qiong , Wang Nian , Wang Jinlin 
Published: July 2023

BackgroundMinute pulmonary meningothelial-like nodules (MPMNs) and diffuse pulmonary meningotheliomatosis (DPM) are both rare lung diseases that involve the proliferation of cells of meningothelial origin in the lungs. However, few studies have focused on the clinical, pathological, and radiological features of MPMNs and DPMs.MethodsThe clinicopathological data of 167 cases diagnosed as MPMNs and 13 cases diagnosed as DPM in the China National Center for Respiratory Medicine were examined. Based on clinical data, CT images, and morphological features, this study analyzed the similarities and differences between MPMNs and DPM.ResultsThe detection rates of MPMNs and DPM were 1.9 and 0.15%, respectively. Compared to MPMNs, DPM patients were all women (100% vs. 79.4%, P = 0.066), had a younger age (51.4 ± 7.7 vs. 57.9 ± 8.5, P &lt; 0.01), and had higher pulmonary function (P &lt; 0.01 or P &lt; 0.05). The chest CT of DPM patients showed diffuse ground-glass opacity nodules measuring 2.0–8.0 mm in diameter, with the number of nodules ranging from 40 to &gt;600 per lung. There were no significant differences in nodule volume [28.0 (12.1, 65.1) mm3 vs. 28.7 (17.1, 48.9) mm3, P = 0.451] and CT values [−646.8 (−732.5, −514.5) Hu vs. −588 (−674, −480) Hu, P = 0.215] between MPMNs and DPM. MPMNs are characterized by reactive hyperplasia pulmonary nodules, which can be solitary or multiple.ConclusionThis study suggests that there are many different characteristics between patients with MPMNs and DPM. The limited findings challenge the notion that DPM is a rare subtype of MPMNS.
Prediction of the occurrence of leprosy reactions based on Bayesian networks
Authors: de Andrade Rodrigues Rafael Saraiva , Heise Eduardo Ferreira José , Hartmann Luis Felipe , Rocha Guilherme Eduardo , Olandoski Marcia , de Araújo Stefani Mariane Martins , Latini Ana Carla Pereira , Soares Cleverson Teixeira , Belone Andrea , Rosa Patrícia Sammarco , de Andrade Pontes Maria Araci , de Sá Gonçalves Heitor , Cruz Rossilene , Penna Maria Lúcia Fernandes , Carvalho Deborah Ribeiro , Fava Vinicius Medeiros , Bührer-Sékula Samira , Penna Gerson Oliveira , Moro Claudia Maria Cabral , Nievola Julio Cesar , Mira Marcelo Távora 
Published: July 2023

IntroductionLeprosy reactions (LR) are severe episodes of intense activation of the host inflammatory response of uncertain etiology, today the leading cause of permanent nerve damage in leprosy patients. Several genetic and non-genetic risk factors for LR have been described; however, there are limited attempts to combine this information to estimate the risk of a leprosy patient developing LR. Here we present an artificial intelligence (AI)-based system that can assess LR risk using clinical, demographic, and genetic data.MethodsThe study includes four datasets from different regions of Brazil, totalizing 1,450 leprosy patients followed prospectively for at least 2 years to assess the occurrence of LR. Data mining using WEKA software was performed following a two-step protocol to select the variables included in the AI system, based on Bayesian Networks, and developed using the NETICA software.ResultsAnalysis of the complete database resulted in a system able to estimate LR risk with 82.7% accuracy, 79.3% sensitivity, and 86.2% specificity. When using only databases for which host genetic information associated with LR was included, the performance increased to 87.7% accuracy, 85.7% sensitivity, and 89.4% specificity.ConclusionWe produced an easy-to-use, online, free-access system that identifies leprosy patients at risk of developing LR. Risk assessment of LR for individual patients may detect candidates for close monitoring, with a potentially positive impact on the prevention of permanent disabilities, the quality of life of the patients, and upon leprosy control programs.
The first rare case of Candida palmioleophila infection reported in China and its genomic evolution in a human host environment
Authors: Wu Na , Wu Yusheng , Chu Yunzhuo , Ren Zhihui , Li Hailong , Rong Chen , Yang Min , Jiang Ning , Jiang Yanyan , Chen Jingjing , Zhang Jingping , Tian Sufei 
Published: July 2023

IntroductionCandida palmioleophila is a rare human pathogenic fungus, which has been poorly characterized at the genome level. In this study, we reported the first fatal case of C. palmioleophila infection in China and investigate the microevolution of C. palmioleophila in the human host environment.MethodsA series of C. palmioleophila stains were collected from the patient at different time points for routine microbial and drug sensitivity testing. The first C. palmioleophila isolate 07202534 was identified by de novo whole genome sequencing. The in vitro and in vivo genetic evolutionary characteristics of C. palmioleophila were discussed based on the analysis of bioinformatics data.ResultsThe six C. palmioleophila isolates displayed dose-dependent sensitivity to fluconazole. The C. palmioleophila genome contained homologous genes such as CDR1 and MDR1, which were recognized to be related to azole resistance. In addition, amino acid variation was detected at F105L and other important sites of ERG11. In addition, the mean divergence time between C. palmioleophila and Scheffersomyces stipites CBS 6054 was 406.04 million years, indicating that C. palmioleophila originated earlier than its closest relative. In addition, the six strains of C. palmioleophila isolated form the patient had higher homology and fewer mutation sites, which indicated the stability in C. palmioleophila genome. We also found that C. palmioleophila had a wide natural niche and may evolve slowly.DiscussionWe believe that this study will contribute to improve our understanding of the genetic evolution, pathogenicity, and drug resistance of C. palmioleophila and will aid in the prevention and control of its spread.
Identification of two novel papillomaviruses in belugas
Authors: Li Youyou , Xiao Meifang , Zhang Yun , Li Zihan , Bai Shijie , Su Haoxiang , Peng Ruoyan , Wang Gaoyu , Hu Xiaoyuan , Song Xinran , Li Xin , Tang Chuanning , Lu Gang , Yin Feifei , Zhang Peijun , Du Jiang 
Published: July 2023

IntroductionPapillomaviruses (PVs) can cause hyperplasia in the skin and mucous membranes of humans, mammals, and non-mammalian animals, and are a significant risk factor for cervical and genital cancers.MethodsUsing next-generation sequencing (NGS), we identified two novel strains of papillomavirus, PV-HMU-1 and PV-HMU-2, in swabs taken from belugas (Delphinapterus leucas) at Polar Ocean Parks in Qingdao and Dalian.ResultsWe amplified the complete genomes of both strains and screened ten belugas and one false killer whale (Pseudorca crassidens) for the late gene (L1) to determine the infection rate. In Qingdao, 50% of the two sampled belugas were infected with PV-HMU-1, while the false killer whale was negative. In Dalian, 71% of the eight sampled belugas were infected with PV-HMU-2. In their L1 genes, PV-HMU-1 and PV-HMU-2 showed 64.99 and 68.12% amino acid identity, respectively, with other members of Papillomaviridae. Phylogenetic analysis of combinatorial amino acid sequences revealed that PV-HMU-1 and PV-HMU-2 clustered with other known dolphin PVs but formed distinct branches. PVs carried by belugas were proposed as novel species under Firstpapillomavirinae.ConclusionThe discovery of these two novel PVs enhances our understanding of the genetic diversity of papillomaviruses and their impact on the beluga population.