bluuebunny/crossref_metadata_2025_split huggingface dataset:
A hybrid XGBoost-SMOTE model for optimization of operational air quality numerical model forecasts
Authors: Ke Huabing , Gong Sunling , He Jianjun , Zhang Lei , Mo Jingyue 
Published: September 2022

As a main technical tool, the air quality numerical model is widely used in the forecasts of atmospheric pollutants, and its development is of great significance to the atmospheric environment and human health. In this study, a hybrid XGBoost-SMOTE model has been developed and applied for the optimization of forecasted PM2.5 and O3 concentrations from the Chinese operational air quality forecasting model - CMA Unified Atmospheric Chemistry Environment model (CUACE), which automatically finds the optimal hyperparameters and features without human intervention. Supported by a knowledge base including the ground-observed, CUACE-forecasted pollutants and meteorological data as well as some auxiliary variables, and based on the evaluation analysis of 46 selected key national cities, it was found that the XGBoost-SMOTE model can achieve satisfactory optimization effects for the operational model, especially the significant improvement of the pollutant extreme values on high-pollution days. The results show that after optimization, the 5-day average correlation coefficient (R), mean error (ME) and root mean square error (RMSE) values can reach 0.87, 10.34 µg/m3 and 16.53 µg/m3 for PM25, and 0.89, 14.53 µg/m3 and 18.83 µg/m3 for O3, far better than those from original CUACE model and XGBoost model. Furthermore, the optimization of the spatial distribution of pollutants from the CUACE model and the impact analysis of the input features by the SHAP method were also explored. The developed hybrid model unveils a good application prospect in the field of environmental meteorology forecasts.
Fisheries as ecosystem services: A case study of the Cauvery river basin, India
Authors: Pownkumar V. , Ananthan P.S. , Ekka A. , Qureshi Neha W. , T Velumani 
Published: September 2022

Habitat alterations and fragmentation caused by anthropogenic modifications of the riverine landscape have affected fish biodiversity by reducing the number of fish species. Fish are a major element of the aquatic environment, and they play an important role in maintaining ecosystem resilience. However, an incomplete understanding of links between river ecosystem functions and processes with fisheries is one of the major reasons for the alarming rate of decline of fish species. Recognizing the ecosystem services generated by fish populations is essential and is one step toward comprehensive, ecosystem-based management of riverine fisheries. Therefore, this paper is motivated by the need to explore the dimensions of fisheries as an ecosystem service. The data was collected from primary field observations and checklist-based key informant interviews at the seventeen fishing sites selected across an 800 km river stretch of the river. In addition, two focused group discussions with fishers at two sampling sites were held to provide first-hand knowledge of ecosystem services generated by fisheries. At first, the role of fisheries in generating ecosystem services for riverine ecosystem functioning and human demands is outlined using the Millennium Ecosystem Assessment approach. Then, the findings of a survey carried out from the headwaters to the delta of the Cauvery river are presented detailing the fisheries provisioning services, livelihoods, and other ecosystem services. The findings showed that the provisioning and cultural services are highly represented among the four categories of ecosystem services identified by the Millennium Ecosystem Assessment. However, in the literature reviewed, supporting, and regulating services are not well-represented. Based on these findings, the applicability of the ecosystem service concept can be elaborated to inform researchers and policymakers to enhance conservation efforts for fisheries.
Application of RNA processing factors for predicting clinical outcomes in colon cancer
Authors: Hou Liujin , Huang Fan , Chen Guanghou , Qiu Jian , Liu Yuyao , Zhao Hongchuan , Wang Zhengguang 
Published: September 2022

Background: Colon cancer is the fifth most common cause of cancer-related death worldwide, and despite significant advances in related treatment, the prognosis of colon cancer patients remains poor.Objective: This study performs systematic bioinformatics analysis of prognostic-associated RNA processing factor genes in colon cancer using the Cancer Related Genome Atlas database to explore their role in colon carcinogenesis and prognosis and excavate potential therapeutic targets.Methods: Data sets of colon cancer patients were obtained from GEO and TCGA databases. Univariate cox analysis was performed on the GSE39582 training set to identify prognosis-associated RNA processing factor genes and constructed a muticox model. The predictive performance of the model was validated by Correlation curve analysis. Similar results were obtained for the test dataset. Functional analyses were performed to explore the underlying mechanisms of colon carcinogenesis and prognosis.Results: A constructed muticox model consisting of βi and prognosis-related RNA processing factor gene expression levels (Expi) was established to evaluate the risk score of each patient. The subgroup with a higher risk score had lower overall survival (OS), higher risk factor, and mortality. We found that the risk score, age, gender, and TNM Stage were strongly associated with OS, and the 13-gene signature as an independent prognostic factor for colon cancer. The model has good accuracy in predicting patient survival and is superior to traditional pathological staging.Conclusion: This study proposes 13 RNA processing factor genes as a prognostic factor for colon cancer patients, which can independently predict the clinical outcome by risk score. The gene expression profile in this model is closely related to the immune status and prognosis of colon cancer patients. The interaction of the 13 RNA processing factor genes with the immune system during colon carcinogenesis provides new ideas for the molecular mechanisms and targeted therapies for colon cancer.
Biomarker identification of chronic atrophic gastritis and its potential drug analysis
Authors: Song Biao , Cao Qinglin , Li Tingting , Liu Yun , Sun Qin , Fan Shanshan , Li Xuejun 
Published: September 2022

BackgroundChronic atrophic gastritis (CAG) is the first step of gastric precancerous lesions, and the study of the pathogenesis of CAG is helpful for the prevention and treatment of gastric cancer(GC). The purpose of this study is to explore the potential biomarkers and therapeutic drugs of CAG through bioinformatics analysis.MethodsThe GSE11632 dataset was downloaded from Gene Expression Omnibus (GEO) database and the differentially expressed genes (DEGs) were obtained by using GEO2R online tool. We searched GeneCard and DisGeNET databases for genes related to CAG and used the overlapping genes as final DEGs for further functional enrichment analysis and Protein-protein Interaction (PPI) network analysis. Tissue-specific expressed genes were identified by BioGPS database. Cytoscape software was used to identify key hub genes and validated them in GSE27411 data sets. The upstream miRNAs of hub gene was predicted by TargetScan, miRDB and miRWalk. Finally, run the Connectivity Map (CMap) to identify new potential drugs for the treatment of CAG.ResultsA total of 430 differentially expressed mRNA were identified in this study, including 315 up-regulated genes and 115 down-regulated genes. After intersecting with CAG-related genes in GeneCard and DisGeNET databases, 42 DEGs were obtained. 24 DEGs were identified as tissue-specific expressed genes, most of which were expressed in stomach. GO and KEGG pathway analysis showed that DGEs was mainly enriched in digestion, IL-1 production, gastric acid secretion and so on. A total of 6 hub genes were generated by cytoHubba plug-in, among which ATP4A, CFTR and EPCAM had high diagnostic value. A total of 13 overlapping miRNA were predicted by 6 hub genes.ConclusionATP4A, CFTR and EPCAM may be potential biomarkers of CAG. hsa-miR-185-5p-CFTR, hsa-miR-4644-CFTR and hsa-miR-4505-CFTR are potential RNA regulatory pathways to control the progression of CAG disease. Finally, amonafide, etoposide, mycophenolate-mofetil, cycloheximide and Emetine may be potential therapeutic drugs for CAG.
Phenotypic characterization of Ghanaian P. falciparum clinical isolates reveals a homogenous parasite population
Authors: Thiam Laty G. , Nyarko Prince B. , Ansah Felix , Niang Makhtar , Awandare Gordon A. , Aniweh Yaw 
Published: September 2022

BackgroundErythrocyte invasion by P. falciparum involves functionally overlapping interactions between the parasite’s ligands and the erythrocyte surface receptors. While some P. falciparum isolates necessarily engage the sialic acid (SA) moieties of the erythrocytes during the invasion, others use ligands whose binding is independent of SA for successful invasion. Deciphering the major pathway used by P. falciparum clinical isolates represent a key step toward developing an efficient blood stage malaria vaccine.MethodsWe collected a total of 156 malaria-infected samples from Ghanaian children aged 2 to 14 years and used a two-color flow cytometry-based invasion assay to assess the invasion phenotype diversity of Ghanaian P. falciparum clinical isolates. Anti-human CR1 antibodies were used to determine the relative contribution of the PfRh4-CR1 interaction in the parasites invasion phenotype and RT-qPCR was used to assess the expression levels of key invasion-related ligands.ResultsOur findings show no clear association between demographic or clinical data and existing reports on the malaria transmission intensity. The complete invasion data obtained for 156 isolates, showed the predominance of SA-independent pathways in Ghanaian clinical isolates. Isolates from Hohoe and Navrongo had the highest diversity in invasion profile. Our data also confirmed that the PfRh4-CR1 mediated alternative pathway is important in Ghanaian clinical isolates. Furthermore, the transcript levels of ten invasion-related genes obtained in the study showed little variations in gene expression profiles within and between parasite populations across sites.ConclusionOur data suggest a low level of phenotypic diversity in Ghanaian clinical isolates across areas of varying endemicity and further highlight its importance in the quest for new intervention strategies, such as the investigation of blood-stage vaccine targets, particularly those targeting specific pathways and able to trigger the stimulation of broadly neutralizing invasion antibodies.
Serum hepatitis B virus large and medium surface proteins as novel tools for predicting HBsAg clearance
Authors: Lin Xiao , Zheng Yanhong , Li Hong , Lu Junfeng , Ren Shan , Liu Yisi , Wang Xiaoxiao , Zheng Sujun , Ma Lina , Cao Zhenhuan , Chen Xinyue 
Published: September 2022

BackgroundThere is still lack of reliable predictors for hepatitis B surface antigen (HBsAg) clearance. Recent studies have shown that the levels of large (LHBs) and medium hepatitis B surface proteins (MHBs) are closely related to antiviral efficacy. This study aimed to investigate the possibility of LHB and MHB levels to predict HBsAg clearance.MethodsAn inactive HBsAg carriers (IHCs) cohort that had received pegylated interferon (Peg-IFN) treatment was divided into the HBsAg-cleared group (R group) and the HBsAg non-cleared group (NR group) based on whether HBsAg was cleared at 96 weeks. We detected the levels of LHBs and MHBs to evaluate the possibility of predicting HBsAg clearance.ResultsThere were 39 patients in the R group and 21 in the NR group. The total HBsAg, LHB, and MHB levels at baseline and at 12 weeks were significantly lower in the R group than in the NR group (all p&lt; 0.05). Multivariate logistic regression indicated that LHB and MHB levels at baseline and 12 weeks were independent predictors of HBsAg clearance (OR = 0.435, p = 0.016; OR = 0.136, p = 0.003; OR = 0.137, p = 0.033; OR = 0.049, p = 0.043). The area under the curve (AUC) for the baseline and 12-week LHB and MHB levels was 0.827-0.896, which were greater than that of the total HBsAg level at baseline and 12-week (AUC: 0.654-0.755). Compared with the prediction results of a single indicator, the combination of LHB and MHB levels had better value in predicting HBsAg clearance. The AUCs of combination factor 1, constructed from baseline LHB and MHB, and combination factor 2, constructed from 12-week LHB and MHB, were 0.922 and 0.939, respectively, and the sensitivity (82.05%-100.00%) and specificity (85.71%-100.00%) were both high. The combined indicators based on baseline LHBs ≤ 13.99 ng/mL and MHBs ≤ 7.95 ng/mL predicted HBsAg clearance rate of more than 90%.ConclusionBaseline and 12-week LHB and MHB levels can predict HBsAg clearance obtained by Peg-IFN therapy in IHCs, and the predictive value is higher than that of the total HBsAg levels.
GSDMD contributes to myocardial reperfusion injury by regulating pyroptosis
Authors: Ye Xiaomiao , Zhang Peng , Zhang Yuting , Luan Jingyun , Xu Caili , Wu Zhengyu , Ju Dianwen , Hu Wei 
Published: September 2022

BackgroundGasdermin D (GSDMD) plays an essential role in the pathway of pyroptosis. However, whether GSDMD participates in myocardial ischaemia/reperfusion injury (MI/RI) remains poorly understood.MethodsSerum levels of GSDMD and IL-18 in ST-segment elevation myocardial infarction (STEMI) patients were measured by ELISA. The expression of GSDMD and GSDMD N-terminal (GSDMD-NT) in vivo and in vitro was assessed by western blot and immunofluorescence staining. GSDMD-/- mice and wild type (WT) mice were induced MI/RI, followed by cardiac ultrasound and histological analysis.ResultsClinically, patients suffering from STEMI after percutaneous coronary intervention (PCI) exhibited higher levels of GSDMD and IL-18 than that in the controls. In vitro, the cleavage of GSDMD was significantly upregulated in macrophages exposed to hypoxia/reoxygenation or H2O2. In vivo, the levels of GSDMD and GSDMD-NT increased notably after MI/RI, especially in macrophages infiltrating in the infarct area. Moreover, compared with WT mice, GSDMD-/- mice showed reduced infarct size (25.45 ± 3.07% versus 36.47 ± 3.72%), improved left ventricular ejection fraction (37.71 ± 1.81% versus 29.44 ± 2.28%) and left ventricular fractional shortening (18.01 ± 0.97% versus 13.62 ± 1.15%) as well as attenuated pathological damage after I/R injury, along with reduced levels of proinflammatory cytokines and decreased infiltration of neutrophils.ConclusionsOur study revealed that GSDMD deficiency significantly alleviated the inflammatory response by regulating pyroptosis, reduced the infarct size and preserved cardiac function after MI/RI, thus providing a potential strategy for the treatment of myocardial reperfusion injury.
Assessment of type I interferon signatures in undifferentiated inflammatory diseases: A Japanese multicenter experience
Authors: Miyamoto Takayuki , Honda Yoshitaka , Izawa Kazushi , Kanazawa Nobuo , Kadowaki Saori , Ohnishi Hidenori , Fujimoto Masakazu , Kambe Naotomo , Kase Naoya , Shiba Takeshi , Nakagishi Yasuo , Akizuki Shuji , Murakami Kosaku , Bamba Masahiro , Nishida Yutaka , Inui Ayano , Fujisawa Tomoo , Nishida Daisuke , Iwata Naomi , Otsubo Yoshikazu , Ishimori Shingo , Nishikori Momoko , Tanizawa Kiminobu , Nakamura Tomoyuki , Ueda Takeshi , Ohwada Yoko , Tsuyusaki Yu , Shimizu Masaki , Ebato Takasuke , Iwao Kousho , Kubo Akiharu , Kawai Toshinao , Matsubayashi Tadashi , Miyazaki Tatsuhiko , Kanayama Tomohiro , Nishitani-Isa Masahiko , Nihira Hiroshi , Abe Junya , Tanaka Takayuki , Hiejima Eitaro , Okada Satoshi , Ohara Osamu , Saito Megumu K. , Takita Junko , Nishikomori Ryuta , Yasumi Takahiro 
Published: September 2022

PurposeUpregulation of type I interferon (IFN) signaling has been increasingly detected in inflammatory diseases. Recently, upregulation of the IFN signature has been suggested as a potential biomarker of IFN-driven inflammatory diseases. Yet, it remains unclear to what extent type I IFN is involved in the pathogenesis of undifferentiated inflammatory diseases. This study aimed to quantify the type I IFN signature in clinically undiagnosed patients and assess clinical characteristics in those with a high IFN signature.MethodsThe type I IFN signature was measured in patients’ whole blood cells. Clinical and biological data were collected retrospectively, and an intensive genetic analysis was performed in undiagnosed patients with a high IFN signature.ResultsA total of 117 samples from 94 patients with inflammatory diseases, including 37 undiagnosed cases, were analyzed. Increased IFN signaling was observed in 19 undiagnosed patients, with 10 exhibiting clinical features commonly found in type I interferonopathies. Skin manifestations, observed in eight patients, were macroscopically and histologically similar to those found in proteasome-associated autoinflammatory syndrome. Genetic analysis identified novel mutations in the PSMB8 gene of one patient, and rare variants of unknown significance in genes linked to type I IFN signaling in four patients. A JAK inhibitor effectively treated the patient with the PSMB8 mutations. Patients with clinically quiescent idiopathic pulmonary hemosiderosis and A20 haploinsufficiency showed enhanced IFN signaling.ConclusionsHalf of the patients examined in this study, with undifferentiated inflammatory diseases, clinically quiescent A20 haploinsufficiency, or idiopathic pulmonary hemosiderosis, had an elevated type I IFN signature.
Kinetics of vaccine-induced neutralizing antibody titers and estimated protective immunity against wild-type SARS-CoV-2 and the Delta variant: A prospective nationwide cohort study comparing three COVID-19 vaccination protocols in South Korea
Authors: Nham Eliel , Ko Jae-Hoon , Song Kyoung-Ho , Choi Ju-Yeon , Kim Eu Suk , Kim Hye-Jin , Kim Byoungguk , Lim Hee-Young , Kim Kyung-Chang , Jang Hee-Chang , Lee Kyoung Hwa , Song Young Goo , Baek Yae Jee , Ahn Jin Young , Choi Jun Yong , Kim Yong Chan , Park Yoon Soo , Choi Won Suk , Bae Seongman , Kim Sung-Han , Kang Eun-Suk , Jeong Hye Won , Kim Shin-Woo , Kwon Ki Tae , Kim Sung Soon , Peck Kyong Ran 
Published: September 2022

IntroductionDespite vaccine development, the COVID-19 pandemic is ongoing due to immunity-escaping variants of concern (VOCs). Estimations of vaccine-induced protective immunity against VOCs are essential for setting proper COVID-19 vaccination policy.MethodsWe performed plaque-reduction neutralizing tests (PRNTs) using sera from healthcare workers (HCWs) collected from baseline to six months after COVID-19 vaccination and from convalescent COVID-19 patients. The 20.2% of the mean PRNT titer of convalescent sera was used as 50% protective value, and the percentage of HCWs with protective immunity for each week (percent-week) was compared among vaccination groups. A correlation equation was deduced between a PRNT 50% neutralizing dose (ND50) against wild type (WT) SARS-CoV-2 and that of the Delta variant.ResultsWe conducted PRNTs on 1,287 serum samples from 297 HCWs (99 HCWs who received homologous ChAdOx1 vaccination (ChAd), 99 from HCWs who received homologous BNT162b2 (BNT), and 99 from HCWs who received heterologous ChAd followed by BNT (ChAd-BNT)). Using 365 serum samples from 116 convalescent COVID-19 patients, PRNT ND50 of 118.25 was derived as 50% protective value. The 6-month cumulative percentage of HCWs with protective immunity against WT SARS-CoV-2 was highest in the BNT group (2297.0 percent-week), followed by the ChAd-BNT (1576.8) and ChAd (1403.0) groups. In the inter-group comparison, protective percentage of the BNT group (median 96.0%, IQR 91.2–99.2%) was comparable to the ChAd-BNT group (median 85.4%, IQR 15.7–100%; P =0.117) and significantly higher than the ChAd group (median 60.1%, IQR 20.0–87.1%; P &lt;0.001). When Delta PRNT was estimated using the correlation equation, protective immunity at the 6-month waning point was markedly decreased (28.3% for ChAd group, 52.5% for BNT, and 66.7% for ChAd-BNT).ConclusionDecreased vaccine-induced protective immunity at the 6-month waning point and lesser response against the Delta variant may explain the Delta-dominated outbreak of late 2021. Follow-up studies for newly-emerging VOCs would also be needed.
Investigation of the efficacy and safety of cryoablation and intra-arterial PD-1 inhibitor in patients with advanced disease not responding to checkpoint inhibitors: An exploratory study
Authors: Wei Fuqun , Guo Rui , Yan Yuan , Lin Ruixiang , Chen Jin , Lin Zhengyu 
Published: September 2022

ObjectiveTo explore the effectiveness of cryoablation combined with arterial perfusion with programmed cell death protein 1 inhibitors in overcoming immune resistance in advanced solid cancers.MethodsIn this pilot retrospective study, nine patients with solid cancers were treated with tumour cryoablation and arterial perfusion with programmed cell death protein 1 inhibitors, which had previously proven ineffective. The CIBERSORT software was used to estimate the levels of tumour-infiltrating immune cells in the challenged tumour. Changes in the levels of circulating T cells were assessed using flow cytometry. The primary endpoints were disease control and objective response rates, and the secondary endpoint was safety.ResultsThe nine patients with advanced solid tumours received cryoablation combined with arterial perfusion with programmed cell death protein 1 inhibitors between June and December 2021. The median follow-up time was 5.8 months. We recorded an objective response rate in two patients (22.22%). The best overall responses were partial responses in two patients (22.22%) and one case (11.11%) of stable disease, while six patients (66.67%) presented progressive disease. However, the median overall survival time was not reached. The median progression-free survival was 2.4 months. Treatment-related severe adverse events included one case of abdominal infection and one case of upper gastrointestinal bleeding, which were cured after the intervention. The CIBERSORT software confirmed the importance of cryoablation in regulating tumour-infiltrating immune cells. Thus, macrophage polarisation from the M2 to the M1 phenotype in the challenged tumour and a gradual increase in the levels of circulating CD4+ T cells were observed after administration of the combination therapy.ConclusionCryoablation combined with arterial perfusion with programmed cell death protein 1 inhibitors has the potential efficacy and safety to overcome immune resistance in patients with advanced solid cancers. The combination therapy leads to macrophage polarisation from the M2 to the M1 phenotype in the challenged tumour to enhance antitumour immunity.