bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-cell transcriptome sequencing reveals potential novel combination of biomarkers for antibody-based cancer therapeutics in hepatocellular carcinoma
Authors: Tang Hong , Yuan Jun , Gong Yuan-Feng , Zhang Cheng-Yang , Liu Ming , Luo Su-Xia
Published: September 2022

Background: Antibody-based cancer therapeutics is developing rapidly in recent years for its advantages in precisely targeting the tumor cells. However, tumor-specific cell surface antigens are still lacking, and the heterogeneity of tumor mass greatly impeded the development of effective drugs.

Methods: In the present study, single-cell RNA sequencing was used to dissect tumor heterogeneity in human hepatocellular carcinoma (HCC). Tissues from different spatial regions including the tumor, para-tumor, and distant normal liver tissues were dissociated into single cells, and the gene expressions were compared in a different subpopulation of cells from these regions and validated in independent cohorts.

Results: A total of 28 cell clusters with different distribution patterns and gene expression profiles were identified within a heterogenous tumor and its paired liver tissues. Differentially expressed genes encoding the plasma membrane in cells with hepatic lineage were further extracted from single-cell transcriptome sequencing and validated in TCGA database. A 3-gene signature was identified to be significantly upregulated in dominant HCC tumor cell subpopulations with prognostic significance and validated in multiple independent patient cohorts.

Conclusion: The composition of the three plasma membrane proteins on the surface of HCC tumor cells within a heterogenous tumor might indicate poor prognostic tumor subpopulations during cancer evolution and potential therapeutic targets.
Uniparental disomy screen of Irish rare disorder cohort unmasks homozygous variants of clinical significance in the TMCO1 and PRKRA genes
Authors: Molloy B. , Jones E. R. , Linhares N. D. , Buckley P. G. , Leahy T. R. , Lynch B. , Knerr I. , King M. D. , Gorman K. M.
Published: September 2022

A uniparental disomy (UPD) screen using whole genome sequencing (WGS) data from 164 trios with rare disorders in the Irish population was performed to identify large runs of homozygosity of uniparental origin that may harbour deleterious recessive variants. Three instances of whole chromosome uniparental isodisomy (UPiD) were identified: one case of maternal isodisomy of chromosome 1 and two cases of paternal isodisomy of chromosome 2. We identified deleterious homozygous variants on isodisomic chromosomes in two probands: a novel p (Glu59ValfsTer20) variant in TMCO1, and a p (Pro222Leu) variant in PRKRA, respectively. The overall prevalence of whole chromosome UPiD in our cohort was 1 in 55 births, compared to 1 in ∼7,500 births in the general population, suggesting a higher frequency of UPiD in rare disease cohorts. As a distinct mechanism underlying homozygosity compared to biallelic inheritance, the identification of UPiD has important implications for family planning and cascade testing. Our study demonstrates that UPD screening may improve diagnostic yields by prioritising UPiD chromosomes during WGS analysis.
Evaluation and characterization of expression quantitative trait analysis methods in the Hybrid Rat Diversity Panel
Authors: Pattee Jack , Vanderlinden Lauren A. , Mahaffey Spencer , Hoffman Paula , Tabakoff Boris , Saba Laura M.
Published: September 2022

The Hybrid Rat Diversity Panel (HRDP) is a stable and well-characterized set of more than 90 inbred rat strains that can be leveraged for systems genetics approaches to understanding the genetic and genomic variation associated with complex disease. The HRDP exhibits substantial between-strain diversity while retaining substantial within-strain isogenicity, allowing for the precise mapping of genetic variation associated with complex phenotypes and providing statistical power to identify associated variants. In order to robustly identify associated genetic variants, it is important to account for the population structure induced by inbreeding. To this end, we investigate the performance of four plausible approaches towards modeling quantitative traits in the HRDP and quantify their operating characteristics. In particular, we investigate three approaches based on genome-wide mixed model analysis, and one approach based on ordinary least squares linear regression. Towards facilitating study planning and design, we conduct extensive simulations to investigate the power of genetic association analyses in the HRDP, and characterize the impressive attained power. In simulation of eQTL data in the HRDP, we find that a mixed model approach that leverages leave-one-chromosome-out kinship estimation attains the highest power while controlling type I error.
Prenatal diagnosis of 21 fetuses with balanced chromosomal abnormalities (BCAs) using whole-genome sequencing
Authors: Fu Fang , Li Ru , Dang Xiao , Yu Qiuxia , Xu Ke , Gu Weiyue , Wang Dan , Yang Xin , Pan Min , Zhen Li , Zhang Yongling , Li Fatao , Jing Xiangyi , Li Fucheng , Li Dongzhi , Liao Can
Published: September 2022

Balanced chromosomal abnormalities (BCAs) are the most common chromosomal abnormalities and the frequency of congenital abnormalities is approximately twice as high in newborns with a de novo BCA, but a prenatal diagnosis based on BCAs is subject to evaluation. To detect translocation breakpoints and conduct a prenatal diagnosis, we performed whole-genome sequencing (WGS) in 21 subjects who were found BCAs, 19 balanced chromosome translocations and two inversions, in prenatal screening. In 16 BCAs on non-N-masked regions (non-NMRs), WGS detected 13 (81.2%, 13/16) BCAs, including all the inversions. All the breakpoints of 12 (12/14) cases of sufficient DNA were confirmed by Sanger sequencing. In 13 interrupted genes, CACNA1E (in case 12) and STARD7 (in case 17) are known causative and PDCL was found in subject (case 11) with situs inversus for the first time. Case 12 with abnormal ultrasound reached a definitive genetic diagnosis of CACNA1E-disease, while STARD7 exon deletion has never been found causative in patients. WGS provides the possibility of prenatal diagnosis in fetuses with BCAs, and its clinical significance also lies in providing data for postnatal diagnosis.
Screening and validation of platelet activation-related lncRNAs as potential biomarkers for prognosis and immunotherapy in gastric cancer patients
Authors: Yuan Mingjie , Jia Yanfei , Xing Yuanxin , Wang Yunshan , Liu Yunyun , Liu Xiangdong , Liu Duanrui
Published: September 2022

Background: Platelets (PLT) have a significant effect in promoting cancer progression and hematogenous metastasis. However, the effect of platelet activation-related lncRNAs (PLT-related lncRNAs) in gastric cancer (GC) is still poorly understood. In this study, we screened and validated PLT-related lncRNAs as potential biomarkers for prognosis and immunotherapy in GC patients.

Methods: We obtained relevant datasets from the Cancer Genome Atlas (TCGA) and Gene Ontology (GO) Resource Database. Pearson correlation analysis was used to identify PLT-related lncRNAs. By using the univariate, least absolute shrinkage and selection operator (LASSO) Cox regression analyses, we constructed the PLT-related lncRNAs model. Kaplan-Meier survival analysis, univariate, multivariate Cox regression analysis, and nomogram were used to verify the model. The Gene Set Enrichment Analysis (GSEA), drug screening, tumor immune microenvironment analysis, epithelial-mesenchymal transition (EMT), and DNA methylation regulators correlation analysis were performed in the high- and low-risk groups. Patients were regrouped based on the risk model, and candidate compounds and immunotherapeutic responses aimed at GC subgroups were also identified. The expression of seven PLT-related lncRNAs was validated in clinical medical samples using quantitative reverse transcription-polymerase chain reaction (qRT-PCR).

Results: In this study, a risk prediction model was established using seven PLT-related lncRNAs -(AL355574.1, LINC01697, AC002401.4, AC129507.1, AL513123.1, LINC01094, and AL356417.2), whose expression were validated in GC patients. Kaplan-Meier survival analysis, the receiver operating characteristic (ROC) curve analysis, univariate, multivariate Cox regression analysis verified the accuracy of the model. We screened multiple targeted drugs for the high-risk patients. Patients in the high-risk group had a poorer prognosis since low infiltration of immune killer cells, activation of immunosuppressive pathways, and poor response to immunotherapy. In addition, we revealed a close relationship between risk scores and EMT and DNA methylation regulators. The nomogram based on risk score suggested a good ability to predict prognosis and high clinical benefits.

Conclusion: Our findings provide new insights into how PLT-related lncRNAs biomarkers affect prognosis and immunotherapy. Also, these lncRNAs may become potential biomarkers and therapeutic targets for GC patients.
Genetic determinants of apixaban plasma levels and their relationship to bleeding and thromboembolic events
Authors: Attelind Sofia , Hallberg Pär , Wadelius Mia , Hamberg Anna-Karin , Siegbahn Agneta , Granger Christopher B. , Lopes Renato D. , Alexander John H. , Wallentin Lars , Eriksson Niclas
Published: September 2022

Apixaban is a direct oral anticoagulant, a factor Xa inhibitor, used for the prevention of ischemic stroke in patients with atrial fibrillation. Despite using recommended dosing a few patients might still experience bleeding or lack of efficacy that might be related to inappropriate drug exposure. We conducted a genome-wide association study using data from 1,325 participants in the pivotal phase three trial of apixaban with the aim to identify genetic factors affecting the pharmacokinetics of apixaban. A candidate gene analysis was also performed for pre-specified variants in ABCB1, ABCG2, CYP3A4, CYP3A5, and SULT1A1, with a subsequent analysis of all available polymorphisms within the candidate genes. Significant findings were further evaluated to assess a potential association with clinical outcome such as bleeding or thromboembolic events. No variant was consistently associated with an altered apixaban exposure on a genome-wide level. The candidate gene analyses showed a statistically significant association with a well-known variant in the drug transporter gene ABCG2 (c.421G > T, rs2231142). Patients carrying this variant had a higher exposure to apixaban [area under the curve (AUC), beta = 151 (95% CI 59–243), p = 0.001]. On average, heterozygotes displayed a 5% increase of AUC and homozygotes a 17% increase of AUC, compared with homozygotes for the wild-type allele. Bleeding or thromboembolic events were not significantly associated with ABCG2 rs2231142. This large genome-wide study demonstrates that genetic variation in the drug transporter gene ABCG2 is associated with the pharmacokinetics of apixaban. However, the influence of this finding on drug exposure was small, and further studies are needed to better understand whether it is of relevance for ischemic and bleeding events.
A novel immune cell signature for predicting osteosarcoma prognosis and guiding therapy
Authors: Pan Runsang , Pan Feng , Zeng Zhirui , Lei Shan , Yang Yan , Yang Yushi , Hu Chujiao , Chen Houping , Tian Xiaobin
Published: September 2022

Dysregulation of immune cell infiltration in the tumor microenvironment contributes to the progression of osteosarcoma (OS). In the present study, we explored genes related to immune cell infiltration and constructed a risk model to predict the prognosis of and guide therapeutic strategies for OS. The gene expression profile of OS was obtained from TARGET and Gene Expression Omnibus, which were set as the discovery and verification cohorts. CIBERSORT and Kaplan survival analyses were used to analyze the effects of immune cells on the overall survival rates of OS in the discovery cohort. Differentially expressed gene (DEG) analysis and protein–protein interaction (PPI) networks were used to analyze genes associated with immune cell infiltration. Cox regression analysis was used to select key genes to construct a risk model that classified OS tissues into high- and low-risk groups. The prognostic value of the risk model for survival and metastasis was analyzed by Kaplan–Meier survival analyses, receiver operating characteristic curves, and immunohistochemical experiments. Immunological characteristics and response effects of immune checkpoint blockade (ICB) therapy in OS tissues were analyzed using the ESTIMATE and Tumor Immune Dysfunction and Exclusion algorithms, while sensitivity for both targeted and chemotherapy drugs was analyzed using the OncoPredict algorithm. It was demonstrated that the high infiltration of resting dendritic cells in OS tissues was associated with poor prognosis. A total of 225 DEGs were found between the high- and low-infiltration groups of OS tissues, while 94 genes interacted with others. Through COX analyses, among these 94 genes, four genes (including AOC3, CDK6, COL22A1, and RNASE6) were used to construct a risk model. This risk model showed a remarkable prognostic value for survival rates and metastasis in both the discovery and verification cohorts. Even though a high microsatellite instability score was observed in the high-risk group, the ICB response in the high-risk group was poor. Furthermore, using OncoPredict, we found that the high-risk group OS tissues were resistant to seven drugs and sensitive to 25 drugs. Therefore, our study indicates that the resting dendritic cell signature constructed by AOC3, CDK6, COL22A1, and RNASE6 may contribute to predicting osteosarcoma prognosis and thus therapy guidance.
Loss of early B cell protein λ5 decreases bone mass and accelerates skeletal aging
Authors: Khass Mohamed , Rashid Harunur , Burrows Peter D. , Javed Amjad , Schroeder Harry W.
Published: September 2022

The early B cell protein λ5 is an essential component of the surrogate light chain and the preB cell receptor (preBCR), which is critical for optimal B cell development. To investigate the effect of λ5 and/or B cells on bone acquisition over time, we developed a panel of JH-/-, λ5-/-, JH-/- λ5-/-, and wild-type (WT) BALB/c mice and then studied postnatal bone development and aging in these mice at one, six, twelve, and twenty-two months of age. The trabecular bone volume over total volume (BV/TV) in JH-/- mice was similar to WT mice at all ages. In contrast, at six months of age and thereafter, λ5-/- and JH-/-λ5-/- mice demonstrated a severe decrease in trabecular bone mass. Surprisingly, bone mass in six-month-old λ5-/- and JH-/-λ5-/- mice was similar to or even lower than in aged (twenty-two-months) WT mice, suggesting accelerated skeletal aging. The postnatal development and the acquisition of cortical bone mass in JH-/-λ5-/- mice were generally comparable to WT. However, JH-/-λ5-/- mice showed a significant decrease in cortical BV/TV at six- and twelve months of age. To examine the contribution of λ5 and B cells to postnatal bone synthesis, we separately transplanted whole bone marrow cells from JH-/-λ5-/- and WT mice into irradiated JH-/-λ5-/- and WT recipients. WT recipients of JH-/-λ5-/- marrow cells failed to show acquisition of trabecular bone mass, whereas transplanting WT marrow cells into JH-/-λ5-/- recipients led to the recovery of trabecular bone mass. Transfer of WT marrow cells into JH-/-λ5-/- mice promoted synthesis of new cortical and trabecular bone. Our findings indicate that λ5 plays a major role in preserving bone mass during postnatal development and skeletal aging which is distinct from its role in B cell development. The absence of both λ5 and B cells in JH-/-λ5-/- mice leads to delayed acquisition of cortical bone during postnatal development. Dissecting the mechanism(s) by which λ5 regulates bone homeostasis may provide new avenues for the treatment of age-related loss of bone mass and osteoporosis.
Circulating pyruvate is a potent prognostic marker for critical COVID-19 outcomes
Authors: Ceperuelo-Mallafré Victòria , Reverté Laia , Peraire Joaquim , Madeira Ana , Maymó-Masip Elsa , López-Dupla Miguel , Gutierrez-Valencia Alicia , Ruiz-Mateos Ezequiel , Buzón Maria José , Jorba Rosa , Vendrell Joan , Auguet Teresa , Olona Montserrat , Vidal Francesc , Rull Anna , Fernández-Veledo Sonia
Published: September 2022

Background

Coronavirus-19 (COVID-19) disease is driven by an unchecked immune response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus which alters host mitochondrial-associated mechanisms. Compromised mitochondrial health results in abnormal reprogramming of glucose metabolism, which can disrupt extracellular signalling. We hypothesized that examining mitochondrial energy-related signalling metabolites implicated in host immune response to SARS-CoV-2 infection would provide potential biomarkers for predicting the risk of severe COVID-19 illness.

Methods

We used a semi-targeted serum metabolomics approach in 273 patients with different severity grades of COVID-19 recruited at the acute phase of the infection to determine the relative abundance of tricarboxylic acid (Krebs) cycle-related metabolites with known extracellular signaling properties (pyruvate, lactate, succinate and α-ketoglutarate). Abundance levels of energy-related metabolites were evaluated in a validation cohort (n=398) using quantitative fluorimetric assays.

Results

Increased levels of four energy-related metabolites (pyruvate, lactate, a-ketoglutarate and succinate) were found in critically ill COVID-19 patients using semi-targeted and targeted approaches (p<0.05). The combined strategy proposed herein enabled us to establish that circulating pyruvate levels (p<0.001) together with body mass index (p=0.025), C-reactive protein (p=0.039), D-Dimer (p<0.001) and creatinine (p=0.043) levels, are independent predictors of critical COVID-19. Furthermore, classification and regression tree (CART) analysis provided a cut-off value of pyruvate in serum (24.54 µM; p<0.001) as an early criterion to accurately classify patients with critical outcomes.

Conclusion

Our findings support the link between COVID-19 pathogenesis and immunometabolic dysregulation, and show that fluorometric quantification of circulating pyruvate is a cost-effective clinical decision support tool to improve patient stratification and prognosis prediction.
SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK
Authors: Aramyan Sona , McGregor Kirk , Sandeep Samarth , Haczku Angela
Published: September 2022

The pulmonary surfactant protein A (SP-A) is a constitutively expressed immune-protective collagenous lectin (collectin) in the lung. It binds to the cell membrane of immune cells and opsonizes infectious agents such as bacteria, fungi, and viruses through glycoprotein binding. SARS-CoV-2 enters airway epithelial cells by ligating the Angiotensin Converting Enzyme 2 (ACE2) receptor on the cell surface using its Spike glycoprotein (S protein). We hypothesized that SP-A binds to the SARS-CoV-2 S protein and this binding interferes with ACE2 ligation. To study this hypothesis, we used a hybrid quantum and classical in silico modeling technique that utilized protein graph pruning. This graph pruning technique determines the best binding sites between amino acid chains by utilizing the Quantum Approximate Optimization Algorithm (QAOA)-based MaxCut (QAOA-MaxCut) program on a Near Intermediate Scale Quantum (NISQ) device. In this, the angles between every neighboring three atoms were Fourier-transformed into microwave frequencies and sent to a quantum chip that identified the chemically irrelevant atoms to eliminate based on their chemical topology. We confirmed that the remaining residues contained all the potential binding sites in the molecules by the Universal Protein Resource (UniProt) database. QAOA-MaxCut was compared with GROMACS with T-REMD using AMBER, OPLS, and CHARMM force fields to determine the differences in preparing a protein structure docking, as well as with Goemans-Williamson, the best classical algorithm for MaxCut. The relative binding affinity of potential interactions between the pruned protein chain residues of SP-A and SARS-CoV-2 S proteins was assessed by the ZDOCK program. Our data indicate that SP-A could ligate the S protein with a similar affinity to the ACE2-Spike binding. Interestingly, however, the results suggest that the most tightly-bound SP-A binding site is localized to the S2 chain, in the fusion region of the SARS-CoV-2 S protein, that is responsible for cell entry Based on these findings we speculate that SP-A may not directly compete with ACE2 for the binding site on the S protein, but interferes with viral entry to the cell by hindering necessary conformational changes or the fusion process.
Development of a novel hypoxia-immune–related LncRNA risk signature for predicting the prognosis and immunotherapy response of colorectal cancer
Authors: Luan Likun , Dai Youguo , Shen Tao , Yang Changlong , Chen Zhenpu , Liu Shan , Jia Junyi , Li Zhenhui , Fang Shaojun , Qiu Hengqiong , Cheng Xianshuo , Yang Zhibin
Published: September 2022

Background

Colorectal cancer (CRC) is one of the most common digestive system tumors worldwide. Hypoxia and immunity are closely related in CRC; however, the role of hypoxia-immune–related lncRNAs in CRC prognosis is unknown.

Methods

Data used in the current study were sourced from the Gene Expression Omnibus and The Cancer Genome Atlas (TCGA) databases. CRC patients were divided into low- and high-hypoxia groups using the single-sample gene set enrichment analysis (ssGSEA) algorithm and into low- and high-immune groups using the Estimation of STromal and Immune cells in MAlignant Tumours using Expression data (ESTIMATE) algorithm. Differentially expressed lncRNAs (DElncRNAs) between low- and high-hypoxia groups, low- and high-immune groups, and tumor and control samples were identified using the limma package. Hypoxia-immune–related lncRNAs were obtained by intersecting these DElncRNAs. A hypoxia-immune–related lncRNA risk signature was developed using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analyses. The tumor microenvironments in the low- and high-risk groups were evaluated using ssGSEA, ESTIMATE, and the expression of immune checkpoints. The therapeutic response in the two groups was assessed using TIDE, IPS, and IC50. A ceRNA network based on signature lncRNAs was constructed. Finally, we used RT-qPCR to verify the expression of hypoxia-immune–related lncRNA signatures in normal and cancer tissues.

Results

Using differential expression analysis, and univariate Cox and LASSO regression analyses, ZNF667-AS1, LINC01354, LINC00996, DANCR, CECR7, and LINC01116 were selected to construct a hypoxia-immune–related lncRNA signature. The performance of the risk signature in predicting CRC prognosis was validated in internal and external datasets, as evidenced by receiver operating characteristic curves. In addition, we observed significant differences in the tumor microenvironment and immunotherapy response between low- and high-risk groups and constructed a CECR7–miRNA–mRNA regulatory network in CRC. Furthermore, RT-qPCR results confirmed that the expression patterns of the six lncRNA signatures were consistent with those in TCGA-CRC cohort.

Conclusion

Our study identified six hypoxia-immune–related lncRNAs for predicting CRC survival and sensitivity to immunotherapy. These findings may enrich our understanding of CRC and help improve CRC treatment. However, large-scale long-term follow-up studies are required for verification.
Immunogenicity profiling and distinct immune response in liver transplant recipients vaccinated with SARS-CoV-2 inactivated vaccines
Authors: Duan Binwei , Zhang Gongming , Wang Wenjing , Yin Jiming , Liu Mengcheng , Zhang Jing , Chen Dexi , Ouyang Yabo , Li Guangming
Published: September 2022

SARS-CoV-2 vaccination has been recommended for liver transplant (LT) recipients. However, our understanding of inactivated vaccine stimulation of the immune system in regulating humoral and cellular immunity among LT recipients is inadequate. Forty-six LT recipients who received two-dose inactivated vaccines according to the national vaccination schedule were enrolled. The clinical characteristics, antibody responses, single-cell peripheral immune profiling, and plasma cytokine/chemokine/growth factor levels were recorded. Sixteen (34.78%) LT recipients with positive neutralizing antibody (nAb) were present in the Type 1 group. Fourteen and 16 LT recipients with undetected nAb were present in the Type 2 and Type 3 groups, respectively. Time from transplant and lymphocyte count were different among the three groups. The levels of anti-RBD and anti-S1S2 decreased with decreasing neutralizing inhibition rates. Compared to the Type 2 and Type 3 groups, the Type 1 group had an enhanced innate immune response. The proportions of B, DNT, and CD3+CD19+ cells were increased in the Type 1 group, whereas monocytes and CD4+ T cells were decreased. High CD19, high CD8+CD45RA+ cells, and low effector memory CD4+/naïve CD4+ cells of the T-cell populations were present in the Type 1 group. The Type 1 group had higher concentrations of plasma CXCL10, MIP-1 beta, and TNF-alpha. No severe adverse events were reported in all LT recipients. We identified the immune responses induced by inactivated vaccines among LT recipients and provided insights into the identification of immunotypes associated with the responders.
Research hotspot and trend analysis in the diagnosis of inflammatory bowel disease: A machine learning bibliometric analysis from 2012 to 2021
Authors: Liu Chuan , Yu Rong , Zhang Jixiang , Wei Shuchun , Xue Fumin , Guo Yingyun , He Pengzhan , Shang Lining , Dong Weiguo
Published: September 2022

Aims

This study aimed to conduct a bibliometric analysis of the relevant literature on the diagnosis of inflammatory bowel disease (IBD), and show its current status, hot spots, and development trends.

Methods

The literature on IBD diagnosis was acquired from the Science Citation Index Expanded of the Web of Science Core Collection. Co-occurrence and cooperation relationship analysis of authors, institutions, countries, journals, references, and keywords in the literature were carried out through CiteSpace software and the Online Analysis platform of Literature Metrology. At the same time, the relevant knowledge maps were drawn, and the keywords cluster analysis and emergence analysis were performed.

Results

14,742 related articles were included, showing that the number of articles in this field has increased in recent years. The results showed that PEYRIN-BIROULET L from the University Hospital of Nancy-Brabois was the author with the most cumulative number of articles. The institution with the most articles was Mayo Clin, and the United States was far ahead in the article output and had a dominant role. Keywords analysis showed that there was a total of 818 keywords, which were mainly focused on the research of related diseases caused or coexisted by IBD, such as colorectal cancer and autoimmune diseases, and the diagnosis and treatment methods of IBD. Emerging analysis showed that future research hotspots and trends might be the treatment of IBD and precision medicine.

Conclusion

This research was the first bibliometric analysis of publications in the field of IBD diagnosis using visualization software and data information mining, and obtained the current status, hotspots, and development of this field. The future research hotspot might be the precision medicine of IBD, and the mechanism needed to be explored in depth to provide a theoretical basis for its clinical application.
The role of the complement system in kidney glomerular capillary thrombosis
Authors: Yoshida Yoko , Nishi Hiroshi
Published: September 2022

The complement system is part of the innate immune system. The crucial step in activating the complement system is the generation and regulation of C3 convertase complexes, which are needed to generate opsonins that promote phagocytosis, to generate C3a that regulates inflammation, and to initiate the lytic terminal pathway through the generation and activity of C5 convertases. A growing body of evidence has highlighted the interplay between the complement system, coagulation system, platelets, neutrophils, and endothelial cells. The kidneys are highly susceptible to complement-mediated injury in several genetic, infectious, and autoimmune diseases. Atypical hemolytic uremic syndrome (aHUS) and lupus nephritis (LN) are both characterized by thrombosis in the glomerular capillaries of the kidneys. In aHUS, congenital or acquired defects in complement regulators may trigger platelet aggregation and activation, resulting in the formation of platelet-rich thrombi in the kidneys. Because glomerular vasculopathy is usually noted with immunoglobulin and complement accumulation in LN, complement-mediated activation of tissue factors could partly explain the autoimmune mechanism of thrombosis. Thus, kidney glomerular capillary thrombosis is mediated by complement dysregulation and may also be associated with complement overactivation. Further investigation is required to clarify the interaction between these vascular components and develop specific therapeutic approaches.
At what size do anti-injury shelters start to play a positive role in the culture of Portunus trituberculatus?
Authors: He Jie , Yu Huaihua , Wan Litao , Zhang Dongxu , Xu Wenjun
Published: September 2022

Based on the existing research, special plastic baskets were used as anti-injury shelters to explore the hidden behavior and molting growth of Portunus trituberculatus (Swimming crab) different initial body weights (Group A: 5.74 ± 0.11 g, Group B: 12.06 ± 0.15 g, Group C: 24.82 ± 0.41 g, Group D: 49.55 ± 1.12 g and Group E: 94.32 ± 1.19 g). The results showed that the shelter occupancy rate (SOR) during the daytime with all different body weights were significantly higher than that at night (P < 0.05), and the SOR was proportional to the crab’s body weight, among them, SOR in group E was as high as 71.52%. Meanwhile, the territorial consciousness of smaller body weight crabs (Groups A, B and C) was poor, and there was a phenomenon in which multiple individuals occupied the same shelter at the same time, while the individuals with the body weight of approximately 50 g and above (Groups D and E) had strong territorial consciousness, and most of them occupied one shelter alone. In all groups, more individuals chose to molt in the shelter on condition that there existed shelter, and the rate of molting in group B was high up to 81.15% and that in other groups was about 60%. Although the existence of shelter had no significant influence on the molting interphase (MI) of swimming crab in each group, the body weight growth rate (WGR) and carapace width growth rate (WGRC) after molting were increased by shelter compared with those without shelter. In addition, shelter could improve the survival rate (SR) in each group, and the effect of shelter on individuals with large body weight was relatively more obvious, in which the SR in Group D was significantly improved (P < 0.05). In general, the shelter can play a positive role in the whole growth of swimming crab. Therefore, it is necessary to set up the shelter in advance before the seedlings are put into production, which is helpful to increase the yield of swimming crab.
Variability of Near-Surface Salinity in the Nordic Seas Over the Past Three Decades (1991-2019)
Authors: Park Ji-Eun , Kim Hyun-Cheol , Cho Kyoung-Ho
Published: September 2022

The Nordic Seas have been widely implicated by deep water formation as a part of Atlantic Meridional Overturning Circulation. This study explores the spatiotemporal variations in the near-surface salinity over the Nordic Seas associated with surface freshening factors by using monthly TOPAZ4 reanalysis data from 1991 to 2019. We first show that reliability of TOPAZ4 data compared to the salinity products of other reanalysis data, satellite data, and in-situ measurements in the Nordic Seas. The salinity variability was larger in the Greenland Sea (GS) than in the Norwegian Sea (NS) on both time scales of seasonal and interannual. The seasonal change of GS salinity was coincident with the seasonality of sea ice extent. The longer-time variations are decomposed by empirical orthogonal function (EOF) analysis. The GS salinity is mainly affected by current advection (29%) and sea ice extent (11%). The interannual response of salinity to the sea ice extent over the GS differs by season. NS salinity variability responds to the strength of the Subpolar Gyre associated with a large-scale atmospheric system that caused the freshening event in the mid-1990s. The propagation of the northward Atlantic Water core is observed over the period of about 3 years from the Faroe Shetland Channel to the Fram Strait at a speed of 2.6-6.5° year-1. Other freshening factors such as sea ice export from the Arctic, freshwater flux at the Fram Strait, and net precipitation are also discussed. For the past three decades, the continuous trend appeared only in the sea ice extent, which might be a signal of climate changes over high latitude. However, there was no significant trend other than the periodic change in a few years to the decadal time scale in the salinity of GS and NS. As preconditioning for deep convection, near-surface salinity within Greenland Sea Gyre was influenced by salinity fluctuation in both GS and NS.
Effect of micro-magnesium oxide admixture on rheological and compressive strength properties of class G well cement
Authors: Chen Weiqing , Mahmoud Ahmed Abdulhamid , Elkatatny Salaheldin
Published: September 2022

Rheological property tuning is one key aspect of oil-well cement, not only affecting the cement slurry placement but also indirectly impacting other cementing properties such as the bonding strength and compressive strength. However, the research is scant on the rheological properties of blending magnesium oxide with class G oil-well cement, despite some studies having been conducted on its impacts on shrinkage compensation, compressive strength, bonding strength, and permeability properties of oil-well cement. This work studies the effects of micro-sized magnesium oxide on the rheological properties and compressive strength of the formulated API Class G oil-well cement slurries. Two types of micro-sized magnesium oxide (50 μm and 100 μm) were used as the mineral admixture at different dosages (3%, 9%). The base formulated slurry sample was incorporated with the silica flour and several commercialized additives such as retarder, fluid loss control agent, and defoamer. A batch of flow tests have been conducted by the use of a digital viscometer at two different temperatures, 25 and 88°C. The compressive strength has also been measured after curing the samples with the same formulation and conditions for 7 days. The variations of the rheological properties (plastic viscosity, yield stress, and gel strength), shear stress–shear rate correlations, and shear-thinning/thickening behavior are impacted by the temperature, the type, and dosage of magnesium oxide. The plastic viscosity of the tested slurries decreased by 27.0% (type II, 9%, 25°C) and 15.1% (type II, 3%, 88°C), respectively, and the yield stress increased by 258.5% (type II, 3%, 88°C) and 53.9% (type II, 9%, 25°C). The gel strength generally increases as the magnesium oxide dosage increases. However, all tested slurry samples show shear-thinning behavior and non-Newtonian characteristics. Among the tested slurry samples, it is found that better rheological performance is achieved when incorporating magnesium oxide with a smaller particle size. On the other side, the specimens of mixed magnesium oxide with a bigger particle size and medium dosage outperform their rival with a smaller particle size in compressive strength.
Worsening of asthma control after COVID-19
Authors: Agondi Rosana Câmara , Menechino Natália , Marinho Ana Karolina Barreto Berselli , Kalil Jorge , Giavina-Bianchi Pedro
Published: September 2022

Background

SARS-CoV-2 enters lung cells via angiotensin-converting enzyme 2 (ACE2) receptor. Several studies suggest that interleukin-13, an important cytokine involved in T2 inflammation, reduces ACE2 expression, and therefore, asthma would not be a significant risk factor for the development of severe COVID-19. However, several asthma-related risk factors should be valued during the concurrent occurrence of asthma and COVID-19. The purpose of this study was to compare the evolution of asthma in patients who had COVID-19 with those who did not have the disease.

Methods

This was an observational and retrospective study involving asthmatic patients followed up at a tertiary center. Patients were assessed for severity of asthma, atopy, comorbidities, and COVID-19. Worsening of asthma was considered when, during the period of Sept 2020 to Oct 2021, patients referred an increasing of asthma symptoms and a need to increment their maintenance therapy.

Results

This study included 208 asthmatic patients, the mean age was 52.75 years, 79.81% were atopic asthmatics, and 59 (28.37%) had laboratory-confirmed coronavirus disease. Of all patients infected with the SARS-CoV-2, eleven (18.64%) needed hospitalization and required oxygen supply with an O2 mask. Comparing the worsening of asthma between patients who had COVID-19 and those who had not the disease, there was a statistically significant difference, 33.90 vs. 11.41%, respectively (p < 0.001). There was no statistical significance regarding asthma comorbidities.

Conclusion

This study assessed a group of asthmatic patients that had COVID-19, and that although the respiratory symptoms related to COVID-19 were mild to moderate, a subgroup of these asthmatic patients evolved with a chronic worsening of their asthma requiring an increment in asthma medication to control the disease.
The association between Herpes simplex virus type 2 and asthma: A cross-sectional study from National Health and Nutrition Examination Survey 1999–2016
Authors: Zhang Xiaofei , Jiang Yalin , Qian Hui , Qu Xiangkun , Han Kexing
Published: September 2022

Background

The association between Herpes simplex virus type 2 (HSV-2) infection, a common infectious disease that increases the incidence of multisystem diseases, and asthma was less well studied. The aim of this study was to investigate the association between HSV-2 infection and the prevalence of asthma.

Materials and methods

We used data from National Health and Nutrition Examination Survey (NHANES) 1999–2016 for analysis. The study population included was limited to those aged 20–45 years and contained complete information on HSV-2 infection and asthma. We calculated the prevalence of HSV-2, asthma, and HSV-2 combined with asthma separately. The association between HSV-2 infection and asthma was analyzed using multiple logistic regression. We also performed stratified analyses to reduce bias and to find sensitive cohorts.

Results

The prevalence of HSV-2 infection was decreasing with change in time period (P for trend < 0.01), but the prevalence of asthma was increasing (P for trend < 0.01). The prevalence of HSV-2 infection was higher in those with asthma than in non-asthma participants. A positive association was found between HSV-2 infection and asthma [odds ratio (OR) = 1.15, 95% CI: 1.04–1.27]. Subgroup analysis showed that this positive association was more pronounced in participants who were male, White, 30 years ≤ age ≤ 40 years, body mass index (BMI) ≤ 28 kg/m2, 1.39 ≤ ratio of family income to poverty (PIR) < 3.49 and smokers.

Conclusion

There was a positive association between HSV-2 infection and asthma, and participants who were male, White race, 30 years ≤ age < 40 years, BMI ≥ 28 kg/m2, 1.39 ≤ PIR < 3.49, and smokers should receive more attention.
Predicting the sentiment of South Korean Twitter users toward vaccination after the emergence of COVID-19 Omicron variant using deep learning-based natural language processing
Authors: Eom Gayeong , Yun Sanghyun , Byeon Haewon
Published: September 2022

Although the full vaccination rate of South Korea compared to other countries, concerns about the effectiveness of the vaccine are growing as new COVID variants such as Alpha, Beta, Gamma, Delta, and Omicron appear over time. In this study, we collected Twitter data in South Korea that contained keywords like vaccines after the outbreak of the Omicron variant from 27 November 2021 to 14 February 2022. First, we analyzed the relationship between potential keywords associated with vaccination after the appearance of the Omicron variant in Twitter using network analysis. Second, we developed an efficient model for predicting the emotion of speech regarding vaccination after the COVID-19 Omicron variant pandemic by using deep learning algorithms. We constructed sentiment analysis models regarding vaccination after the COVID-19 Omicron pandemic by using five algorithms [i.e., support vector machine (SVM), recurrent neural networks (RNNs), long short-term memory models (LSTMs), bidirectional encoder representations from transformers (BERT), and Korean BERT (KoBERT)]. The results confirmed that KoBERT showed the best performance (71%) in all predictive performance indicators (accuracy, precision, and F1 score). It is necessary to prepare measures to alleviate the negative factorss of the public about vaccination in the long-term pandemic situation and help the public recognize the efficacy and safety of vaccination by using big data based on the results of this study.
A multidisciplinary approach to the diagnosis of antisynthetase syndrome
Authors: Wells Matthew , Alawi Sughra , Thin Kyaing Yi Mon , Gunawardena Harsha , Brown Adrian R. , Edey Anthony , Pauling John D. , Barratt Shaney L. , Adamali Huzaifa I.
Published: September 2022

Antisynthetase syndrome is a subtype of idiopathic inflammatory myopathy, strongly associated with the presence of interstitial lung disease. Diagnosis is made by identifying myositis-specific antibodies directed against aminoacyl tRNA synthetase, and relevant clinical and radiologic features. Given the multisystem nature of the disease, diagnosis requires the careful synthesis of subtle clinical and radiological features with the interpretation of specialized autoimmune serological testing. This is provided in a multidisciplinary environment with input from rheumatologists, respiratory physicians, and radiologists. Differentiation from other idiopathic interstitial lung diseases is key; treatment and prognosis differ between patients with antisynthetase syndrome and idiopathic interstitial lung disease. In this review article, we look at the role of the multidisciplinary team and its individual members in the initial diagnosis of the antisynthetase syndrome, including the role of physicians, radiologists, and the wider team.
Long-term renal and cardiovascular outcome of living kidney donors: A single-center retrospective observation study
Authors: Colucci Vincenza , Gallo Pasquale , Simone Simona , Morrone Luigi , Alfieri Carlo Maria , Gesualdo Loreto , Castellano Giuseppe
Published: September 2022

Background

The nephrectomy for donation reduces the renal parenchyma and glomerular filtration rate (GFR). It is important to understand the clinical consequences of kidney donation by a living donor.

Methods

In this single-center, observational, retrospective study, we defined the renal and cardiovascular outcomes of living kidney donors. We analyzed data of 124 donors who donated at the Kidney Transplant Center (TC) of Bari between February 2002 and December 2018. Biometric data collected at visit 0, that is, at the time of the study of the donor candidate, and at visit 1, or rather at the last nephrological checkup (October-2018/August-2019) were compared.

Results

An overall drop in GFR of 29 mL/min was observed over the analyzed period of 81+/-59 months. At visit 1, two donors developed chronic renal failure, including one in ESKD who underwent a kidney transplant. No relationship between age at donation and GFR drop was found. A trend toward an increase in obese people was reported; 28% of patients had compensated dyslipidemia and 35% were treated for hypertension. During the follow-up time, 3% had major cardiovascular events and 24% were lost to follow-up. One patient died.

Conclusion

The age of the donor does not represent a basic element for reducing GFR or for the occurrence of major cardiovascular events. Furthermore, older donor candidates, in optimal health, should not be excluded from the donation. It is important to promote careful and timely follow-up of the donor, preventing the most common clinical consequences of nephrectomy, in consideration of the poor compliance of a large part of donors over the long-term post-donation period.
Epidemiological analysis of septic shock in the plateau region of China
Authors: Li Qianwei , Chai Wenzhao , Wang Xiaoting , Cheng Li , Cai Xin , Fu Jianlei , Pan Wenjun , Lin Guoying
Published: September 2022

Purpose

Little epidemiological data exist on patients with severe infection in the plateau region of China, and the data that do exist are lacking in quality. Using the medical records of patients with severe infection in the Department of Intensive Medicine (intensive care unit; ICU) of the People's Hospital of Tibet Autonomous Region, this study analyzed the epidemiological and clinical characteristics of patients with septic shock in plateau area (Tibet), with the ultimate aim of reducing the incidence and mortality from this condition.

Methods

Clinical data on 137 patients with septic shock in the studied ICU from November 2017 to October 2019 were retrospectively analyzed using SPSS, Version 21.0.

Results

Among the 137 patients with septic shock, there were 47 survivors and 90 in-hospital or post-discharge deaths. There were 91 male patients and 46 female patients. The incidence of septic shock was 11.3%, and mortality rate was 65.7%. Median age was 55 years old, median APACHE-II score on the day of admission was 17, median SOFA score was 11, and median number of organ injuries was one. APACHE-II score (P = 0.02), SOFA score (P < 0.001), and the number of organ injuries (P < 0.001) were higher among patients who died than among survivors. The infections were mainly pulmonary and abdominal, and the main pathogen was gram-negative bacteria.

Conclusion

The incidence and mortality of septic shock in ICU wards in Tibet are very high. The APACHE-II score, SOFA score, and the number of organ damage on the first day after diagnosis are independent risk factors for septic shock. To some extent, this study reflects the epidemiological characteristics of septic shock in the plateau region of China (≥ 3,650 m above sea level) and provides data that can support the prevention and treatment of sepsis in the future. More and deeper epidemiological studies of septic shock are necessary.