bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reservoir properties and CO2 storage capacity of the Rose Run Sandstone (Lower Ordovician, Knox Group) in the Central Appalachian Basin, northeast Kentucky
Authors: Bowersox J. Richard , Greb Stephen F. , Harris David C. 
Published: September 2022

The Lower Ordovician Rose Run Sandstone is a potential CO2storage reservoir in the Central Appalachian Basin in northeast Kentucky where the Kentucky Geological Survey’s 1 Hanson Aggregates research well penetrated it at drill depths of 1,000–1,009.5 m. Average Rose Run porosity and permeability from core plugs are 9.1% and 44.6 mD, respectively.In situreservoir properties were determined by step-rate testing an 18.6-m interval bracketing the Rose Run. Pressure derivative analysis of wellbore falloff pressure suggests that the Rose Run shares properties of both dual-porosity and dual-permeability reservoirs, consistent with its mixed lithologies. The Rose Run pore pressure was 9.3 MPa/km, 1.1 MPa/km underpressured compared to the expected hydrostatic gradient of 10.4 MPa/km. Average porosity of the Rose Run, at the industry-standard 7% porosity cutoff for assessing CO2storage capacity, calculated from 27 wells in the surrounding region, was 11.6% and the average net reservoir thickness was 6.2 m. Geomechanical properties of the overlying Beekmantown Dolomite show that it would act as a reservoir confining interval during CO2injection. The estimated P50supercritical CO2storage volume is 77.2 kt/km2, yielding P50storage capacity of 165.7 Mt in the region. By itself, an average surface area of 12.9 km2would be required to store 1 Mt of supercritical CO2in the Rose Run, thus lacking the volume to act as a stand-alone CO2storage reservoir in this area. It could contribute to a stacked-reservoir storage project developed in the larger Knox section, however. CO2–brine relative permeability tests suggest that nearly half of any supercritical CO2injected into the Rose Run would be residually trapped, and another portion would be trapped by mineral precipitation. The Rose Run in the KGS 1 Hanson Aggregates well is very close to the subsurface CO2critical depth in the northeast Kentucky region and lacks an updip reservoir trap. How far and fast the mobile CO2migration might occur at this site remains for future research and reservoir modeling.
Two Typical Patterns of Regional PM2.5 Transport for Heavy Air Pollution Over Central China: Rapid Transit Transport and Stationary Accumulation Transport
Authors: Wang Ying , Bai Yongqing , Zhi Xiefei , Wu Kai , Zhao Tianliang , Zhou Yue , Xiong Jie , Zhu Shoupeng , Zhou Wen , Hu Weiyang , Zhang Ling , Meng Kai 
Published: September 2022

The regional transport of air pollutants has been identified as a critical factor that affects air quality over downwind receptor areas; however, the regional transport patterns for air pollution episodes remain poorly understood. In this study, we identified two distinct patterns of regional transport: rapid transit transport (RTT) and stationary accumulation transport (SAT), both of which induced severe PM2.5 pollution episodes in central China during 2015–2020. The differences and similarities between the two regional transport patterns of air pollution were characterized by their influencing meteorological factors. Similar meteorological conditions trigger the RTT and SAT, with a high-PM2.5 concentration air mass from the upstream regions transported to the Twain-Hu Basin (THB) by the strong northerly winds with a southward advance of cold air mass. The average rate of increase in the PM2.5 concentration of the RTT (12.5 μg/m3/h) is more than that of the SAT (5.7 μg/m3/h). However, meteorological conditions evolved differently in RTT and SAT. For RTT with the fast passage of cold air, the THB is located behind the strong cold front during the later stage, and these events rapidly ended owing to the northerly winds and wet scavenging of precipitation. For SAT with the slow cold air accumulation, the THB is mainly occupied by a weak high-pressure system with low wind speeds, strong descending airflow, and a low atmospheric boundary layer height, trapping the air pollutants accumulated in the THB and resulting in persistent heavy pollution incidents. This study provides new insights into the meteorological mechanism underlying the formation of severe air pollution episodes over a receptor region owing to the regional transport patterns of air pollutants.
Development of a Novel Immune-Related Gene Prognostic Index for Breast Cancer
Authors: Yao Yan , Kong Xinru , Liu Ruijuan , Xu Fei , Liu Gongxi , Sun Changgang 
Published: September 2022

ObjectiveTo construct an immune-related gene prognostic index (IRGPI) for breast cancer (BC) and investigate its prognostic specificity and the molecular and immune characteristics.MethodsBC hub genes were identified from The Cancer Genome Atlas and immune-related databases using weighted gene co-expression network analysis (WGCNA). IRGPI was constructed using univariate, LASSO, and multivariate regression analyses, and was validated with GSE58812 and GSE97342 in the Gene Expression Omnibus database (GEO). At the same time, we evaluated the predictive ability of IRGPI for different BC subtypes. Subsequently, the molecular and immune characteristics, clinical relevance, and benefits of immune checkpoint inhibitor treatment were analyzed for different IRGPI subgroups.ResultsIRGPI consisted of six genes: SOCS3, TCF7L2, TSLP NPR3, ANO6, and HMGB3. The IRGPI 1-, 5-, and 10-years area under curve (AUC) values were 0.635, 0.752, and 0.753, respectively, indicating that IRGPI has good potential in predicting the long-term survival of BC patients, consistent with the results in the GEO cohort. IRGPI showed good predictive power in four different breast cancer subtypes: ER positive, PR positive, HER2 positive and triple-negative (P&lt;0.01). Compared with the low-IRGPI group, the high-IRGPI group had a worse prognosis and a lower degree of immune infiltrating cells (p &lt; 0.05). IRGPI showed specificity in distinguishing age, TNM stage, ER, and HER2 statuses, and our study found that the high-IRGPI group had low tumor immune dysfunction and exclusion (TIDE), microsatellite instability (MSI), and T cell dysfunction scores (p &lt; 0.05). In addition, compared with the TIDE and TIS models, showed that the AUCs of IRGPI were better during the 5-year follow-up.ConclusionIRGPI can be used as an independent prognostic indicator of breast cancer, providing a method for monitoring the long-term treatment of BC.
Coexistence of multiple anti-neuronal antibodies in autoimmune encephalitis in China: A multi-center study
Authors: Qiao Shan , Zhang Shan-Chao , Wang Zhi-Hao , Wang Lei , Zhang Ran-Ran , Li Hai-Yun , Jin Yang , Liu Ling-Ling , Wang Mei-Ling , Wang Ai-Hua , Liu Xue-Wu 
Published: September 2022

BackgroundGiven that the combination of multiple antibodies in autoimmune encephalitis (AE) is rare and its clinical significance is unclear, this study aimed to investigate the clinical characteristics and significance of overlapping multiple anti-neuronal antibodies in patients with AE.MethodsWe conducted a retrospective analysis of the clinical characteristics, treatment, and prognostic details of 22 patients with multiple coexisting antibodies from multiple clinical centers in China.ResultsAmong the 276 patients who were AE antibody-positive, 22 (7.97%) had two or more antibodies. Among the 22 patients with coexisting AE-related antibodies, 14 patients (63.63%) were combined of cell surface and intracellular antibody, and the remaining 8 patients (36.36%) were detected to be cell surface antibody positive only. The main symptoms of the 22 patients in this cohort included fever, seizures, memory impairment, cognitive decline, and sleep disorders. Five (22.73%) patients had tumors, among whom four had small-cell lung cancers, and one had mediastinal tumors. A total of 20 patients were treated with steroids and intravenous immunoglobulin, and 18 showed varying degrees of symptomatic improvement after first-line immunotherapy. Three patients died of tumor progression or chemotherapy complications.ConclusionThe coexistence of multiple anti-neuronal antibodies in patients with AE may cause a superimposition and diversification of clinical manifestations. Combined paraneoplastic antibody positivity may be suggestive of an underlying malignancy.
Cuproptosis-related modification patterns depict the tumor microenvironment, precision immunotherapy, and prognosis of kidney renal clear cell carcinoma
Authors: Cai Zhiyong , He You'e , Yu Zhengzheng , Hu Jiao , Xiao Zicheng , Zu Xiongbing , Li Zhenghao , Li Huihuang 
Published: September 2022

BackgroundDue to the different infiltration abundance of immune cells in tumor, the efficacy of immunotherapy varies widely among individuals. Recently, growing evidence suggested that cuproptosis has impact on cancer immunity profoundly. However, the comprehensive roles of cuproptosis-related genes in tumor microenvironment (TME) and in response to immunotherapy are still unclear.MethodsBased on 43 cuproptosis-related genes, we employed unsupervised clustering to identify cuproptosis-related patterns and single-sample gene set enrichment analysis algorithm to build a cuproptosis signature for individual patient’s immune cell infiltration and efficacy of immune checkpoint blockade (ICB) evaluation. Then, the cuproptosis-related genes were narrowed down using univariate Cox regression model and least absolute shrinkage and selection operator algorithm. Finally, a cuproptosis risk score was built by random survival forest based on these narrowed-down genes.ResultsTwo distinct cuproptosis-related patterns were developed, with cuproptosis cluster 1 showing better prognosis and higher enrichment of immune-related pathways and infiltration of immune cells. For individual evaluation, the cuproptosis signature that we built could be used not only for predicting immune cell infiltration in TME but also for evaluating an individual’s sensitivity to ICBs. Patients with higher cuproptosis signature scores exhibited more activated cancer immune processes, higher immune cell infiltration, and better curative efficacy of ICBs. Furthermore, a robust cuproptosis risk score indicated that patients with higher risk scores showed worse survival outcomes, which could be validated in internal and external validation cohorts. Ultimately, a nomogram which combined the risk score with the prognostic clinical factors was developed, and it showed excellent prediction accuracy for survival outcomes.ConclusionDistinct cuproptosis-related patterns have significant differences on prognosis and immune cell infiltration in kidney renal clear cell carcinoma (KIRC). Cuproptosis signature and risk score are able to provide guidance for precision therapy and accurate prognosis prediction for patients with KIRC.
A novel T-cell proliferation-associated regulator signature pre-operatively predicted the prognostic of bladder cancer
Authors: Hou Jian , Wen Xiangyang , Lu Zhenquan , Wu Guoqing , Yang Guang , Tang Cheng , Qu Genyi , Xu Yong 
Published: September 2022

BackgroundBladder cancer (BCa) is a remarkably malignant and heterogeneous neoplastic disease, and its prognosis prediction is still challenging. Even with the mounting researches on the mechanisms of tumor immunotherapy, the prognostic value of T-cell proliferation regulators in bladder cancer remains elusive.MethodsHerein, we collected mRNA expression profiles and relevant clinical information of bladder cancer sufferers from a publicly available data base. Then, the LASSO Cox regression model was utilized to establish a multi-gene signature for the TCGA cohort to predict the prognosis and staging of bladder cancer. Eventually, the predictive power of the model was validated by randomized grouping.ResultsThe outcomes revealed that most genes related to T-cell proliferation in the TCGA cohort exhibited different expressions between BCa cells and neighboring healthy tissues. Univariable Cox regressive analyses showed that four DEGs were related to OS in bladder cancer patients (p&lt;0.05). We constructed a histogram containing four clinical characteristics and separated sufferers into high- and low-risk groups. High-risk sufferers had remarkably lower OS compared with low-risk sufferers (P&lt;0.001). Eventually, the predictive power of the signature was verified by ROC curve analyses, and similar results were obtained in the validation cohort. Functional analyses were also completed, which showed the enrichment of immune-related pathways and different immune status in the two groups. Moreover, by single-cell sequencing, our team verified that CXCL12, a T-lymphocyte proliferation regulator, influenced bladder oncogenesis and progression by depleting T-lymphocyte proliferation in the tumor microenvironment, thus promoting tumor immune evasion.ConclusionThis study establishes a novel T cell proliferation-associated regulator signature which can be used for the prognostic prediction of bladder cancer. The outcomes herein facilitate the studies on T-cell proliferation and its immune micro-environment to ameliorate prognoses and immunotherapeutic responses.
(NZW × BXSB) F1 male mice: An unusual, severe and fatal mouse model of lupus erythematosus
Authors: Almizraq Ruqayyah J. , Frias Boligan Kayluz , Loriamini Melika , McKerlie Colin , Branch Donald R. 
Published: September 2022

BackgroundSystemic lupus erythematosus (SLE) is a chronic autoimmune/inflammatory disease. The heterogeneity and complexity of clinical presentation has made it challenging to study or treat this syndrome. The (NZW×BXSB) F1 lupus-prone male mouse model of this disease is potentially useful to study mechanism and treatment modalities, but there is a lack of information about this model’s characterization and disease progression. Therefore, the aim was to examine this lupus model’s physical/clinical disease presentation and its immunological status.Materials and methodsClinical and physical status were observed in 8- and 16-week-old male and female (± 1 week) (NZW/LacJ x BXSB/MpJ) F1 mice (n = 8 per group). Young males (8 ± 1 week) without disease and female (16 ± 1 week) mice served as controls. Physical changes, quantitative values of autoantibodies, and blood cell parameters were determined. Necropsy and post-mortem histopathology were also performed.ResultsWith aging (≥ 12 weeks), significant increases in severe abdominal distension/swelling, inability to walk, paleness of paws and significant weight increase were observed compared to controls (p &lt; 0.05). The necropsy examination showed abdominal distension associated with serous effusion and histological examination identified severe edema and multi-organ abnormalities (spleen, lymph nodes, and kidney). Significant increases in anti-double-stranded DNA antibody (anti-dsDNA) was seen in old/sick compared to female (p = 0.0002) or young male (p = 0.0036) mice. Old mice developed immune thrombocytopenia compared to female (p = 0.0056) and young male (p = 0.0007) mice. Anti-platelet was detectable in old, sick mice. The mortality rate increased with aging; more than 35% of male mice died during this study between the ages of 13-18 weeks.ConclusionWe found that the (NZW/LacJ x BXSB/MpJ) F1 male mice spontaneously exhibit, over varying lengths of time, extremely severe and fatal clinical disease symptoms. This model may be too severe to be helpful in investigating SLE and testing potential treatment modalities.
Real-world effectiveness and protection of SARS-CoV-2 vaccine among patients hospitalized for COVID-19 in Xi’an, China, December 8, 2021, to January 20, 2022: A retrospective study
Authors: Li Xiaowei , Xu Yinjuan , Li Xiaomeng , Liu Wenbin , Yao Dan , Chen Weichao , Yu Hongchuan , He Langchong , Lu Shemin , Jiang Congshan , Zhu Wenhua , Meng Liesu 
Published: September 2022

IntroductionIn December 2021, a large-scale epidemic broke out in Xi’an, China, due to SARS-CoV-2 infection. This study reports the effect of vaccination on COVID-19 and evaluates the impact of different vaccine doses on routine laboratory markers.MethodsThe laboratory data upon admission, of 231 cases with COVID-19 hospitalized from December 8, 2021 to January 20, 2022 in Xi’an, including blood routine, lymphocyte subtypes, coagulative function tests, virus specific antibodies and blood biochemical tests were collected and analyzed.ResultsOf the 231 patients, 21 were not vaccinated, 158 were vaccinated with two doses and 52 with three doses. Unvaccinated patients had a higher proportion of moderate and severe symptoms than vaccinated patients, while two-dose vaccinated patients had a higher proportion than three-dose vaccinated patients. SARS-CoV-2 specific IgG levels were significantly elevated in vaccinated patients compared with unvaccinated patients. Particularly, unvaccinated patients had lower counts and percentages of lymphocytes, eosinophils and CD8+ T-lymphocytes, and elevated coagulation-related markers. In addition, vaccination had no effect on liver and kidney function.ConclusionsVaccination against SARS-CoV-2, inducing high IgG level and increased CD8+ T cells and eosinophils, and regulating coagulation function, can significantly attenuate symptoms of COVID-19, suggesting that the vaccine remains protective against SARS-CoV-2.
Eosinophilic gastrointestinal disorders in patients with inborn errors of immunity: Data from the USIDNET registry
Authors: Tran Paulina , Gober Laura , Garabedian Elizabeth K. , Fuleihan Ramsay L. , Puck Jennifer M. , Sullivan Kathleen E. , Spergel Jonathan M. , Ruffner Melanie A. 
Published: September 2022

RationaleEosinophilic gastrointestinal disorders (EGID), including eosinophilic esophagitis (EoE), are inflammatory disorders of the gastrointestinal mucosa mediated by complex immune mechanisms. Although there have been initial reports of EGID in patients with inborn errors of immunity (IEI), little is known about the presentation of EGID in immunodeficient individuals.MethodsWe queried the U.S. Immunodeficiency Network (USIDNET) for patient records including the terms eosinophilic esophagitis, gastritis, enteritis, or colitis. We analyzed 74 patient records from the database, including diagnoses, demographics, infectious history, laboratory findings, genetic studies, therapeutic interventions, and clinical outcomes.ResultsWe examined 74 patient records. A total of 61 patients had isolated EoE, and 13 had distal gastrointestinal involvement consistent with EGID. The most common IEI were common variable immunodeficiency (43.2%), some form of combined immunodeficiency (21.6%), chronic granulomatous disease (8.1%), hyper-IgE syndrome (6.8%), and autoimmune lymphoproliferative syndrome (6.8%). The median age at presentation with IEI was 0.5 years (IQR 1.725, max 39 years) and 56.76% were male. Approximately 20% of the patients in the cohort received a hematopoietic stem cell transplantation for treatment of IEI, but the timing of the HSCT in relationship to the EGID diagnosis was unknown.ConclusionsHere, we report EGID in a diverse cohort of IEI patients, suggesting that both non-EoE EGID and EoE can be seen as comorbid conditions with a variety of IEI. Our data suggests that EGID may be more common in patients with IEI than would be expected based on estimates of EGID in the general population.
Bioinformatics and systems-biology analysis to determine the effects of Coronavirus disease 2019 on patients with allergic asthma
Authors: Fang Hongwei , Sun Zhun , Chen Zhouyi , Chen Anning , Sun Donglin , Kong Yan , Fang Hao , Qian Guojun 
Published: September 2022

BackgroundThe coronavirus disease (COVID-19) pandemic has posed a significant challenge for global health systems. Increasing evidence shows that asthma phenotypes and comorbidities are major risk factors for COVID-19 symptom severity. However, the molecular mechanisms underlying the association between COVID-19 and asthma are poorly understood. Therefore, we conducted bioinformatics and systems biology analysis to identify common pathways and molecular biomarkers in patients with COVID-19 and asthma, as well as potential molecular mechanisms and candidate drugs for treating patients with both COVID-19 and asthma.MethodsTwo sets of differentially expressed genes (DEGs) from the GSE171110 and GSE143192 datasets were intersected to identify common hub genes, shared pathways, and candidate drugs. In addition, murine models were utilized to explore the expression levels and associations of the hub genes in asthma and lung inflammation/injury.ResultsWe discovered 157 common DEGs between the asthma and COVID-19 datasets. A protein–protein-interaction network was built using various combinatorial statistical approaches and bioinformatics tools, which revealed several hub genes and critical modules. Six of the hub genes were markedly elevated in murine asthmatic lungs and were positively associated with IL-5, IL-13 and MUC5AC, which are the key mediators of allergic asthma. Gene Ontology and pathway analysis revealed common associations between asthma and COVID-19 progression. Finally, we identified transcription factor–gene interactions, DEG–microRNA coregulatory networks, and potential drug and chemical-compound interactions using the hub genes.ConclusionWe identified the top 15 hub genes that can be used as novel biomarkers of COVID-19 and asthma and discovered several promising candidate drugs that might be helpful for treating patients with COVID-19 and asthma.
IgE receptor responsiveness of basophils in chronic inducible urticaria
Authors: Mizuno Mayuko , Oda Yoshiko , Imamura Shinya , Washio Ken , Fukumoto Takeshi , Fukunaga Atsushi 
Published: September 2022

IntroductionChronic inducible urticaria (CIndU) is a subgroup of chronic urticaria induced by a specific stimulus. We evaluated basophil characteristics in patients with CIndU and compared with those in patients with chronic spontaneous urticaria (CSU) and healthy controls (HCs).MethodsBlood was collected from patients, and a basophil activation test (BAT) was performed. Basophil responsiveness and surface marker expression in patients with CIndU were compared with those in patients with CSU and HCs. For some patients with CIndU, blood was collected before and after wheals were induced. In these cases, we compared the responsiveness of basophils before and after the appearance of wheals.ResultHCs (n=23) and patients with CIndU (n=24) or CSU (n=38) were enrolled in the study. The degree of basophil activation at steady state in patients with CIndU was higher than in HCs. Basophil responsiveness via high-affinity IgE receptor (FcϵRI) stimulation with anti-IgE or anti-FcϵRI antibody in patients with CIndU was equivalent to that in HCs, and higher than that in patients with CSU. No abnormalities in IgE and FcϵRI expressions on the surface of basophils in patients with CIndU were observed. When we induced wheals in some patients with CIndU and performed a BAT before and after the appearance of wheals, no significant changes were found.ConclusionPeripheral blood basophils in CIndU were slightly activated at steady state, but no abnormalities in basophil responsiveness. In future, a higher number of cases should be enrolled to confirm the role of basophils and refine therapeutic targets for CIndU.