bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decision-making fusion of InSAR technology and offset tracking to study the deformation of large gradients in mining areas-Xuemiaotan mine as an example
Authors: Ma Jianquan , Yang Juncheng , Zhu Zhanrong , Cao Husheng , Li Shibo , Du Xiaolan 
Published: August 2022

The multi-level disturbance of underground and surface caused by coal mining activities intensifies the deterioration of the ecological environment in the mining area. Among them, the uneven settlement caused by coal mining is the most intuitive manifestation of surface environmental damage. The uneven settlement in the mining area has the characteristics of large settlement magnitude and severe deformation. Therefore, based on 15 Sentinel-1A image data, this paper uses three methods: SBAS InSAR, continuous D-InSAR and offset tracking technology to monitor the surface deformation of the mining area. The results show that the continuous D-InSAR technology SBAS-InSAR technology is applied to the small deformation in the edge area of the subsidence basin. The mining area with low gradient subsidence of SBAS-InSAR can obtain better performance than continuous D-InSAR technology. The offset tracking technique is used to monitor the large gradient deformation in the center of the subsidence basin. Therefore, this paper proposes to expand the quantitative analysis through the spatial coherence threshold and the accuracy and successful image elements of the interference fringe displacement. Combine the advantages of the three methods and overcome the shortcomings of each method, fuse the deformation information of the three methods, and obtain the deformation law of the whole surface subsidence. The results show that the mean absolute error (MAE1-1) of continuity D-InSAR is 0.92 m, the mean absolute error (MAE2-1) of SBAS-InSAR is 0.94 m, and the mean absolute error (MAE3-1) of Offset-tracking is 0.25 m. The results of this fusion method are in good agreement with the measured data, and the mean absolute error (MAE4-1) of vertical displacement is 7 cm. Therefore, the fusion method has advantages over individual methods and provides a new idea in monitoring the large gradient deformation of coal mining subsidence in mining areas.
Comparison of empagliflozin and vildagliptin for efficacy and safety in type 2 diabetes mellitus in the Pakistani population
Authors: Khan Asima , Khan Izhan A. , Abidi Hussain , Ahmed Mansoor 
Published: August 2022

BackgroundDiabetes mellitus (DM) is a chronic disease that needs early management to prevent complications and premature mortality. Therefore, it is essential to select evidence-based drugs available to control diabetes and limit the progression to related complications. This study aimed to compare the efficacy and safety of empagliflozin and vildagliptin in people with type 2 DM.MethodsThis was an open-label, parallel randomized controlled trial (NCT 05359432) conducted at two tertiary care hospitals in Karachi, Pakistan. After obtaining consent, participants were randomized into two groups. The first group was given empagliflozin (10 mg once or two times daily) with metformin, and the second group got vildagliptin (50 mg once or two times daily) with metformin. HbA1c, high-density lipoprotein (HDL) levels, systolic blood pressure, fasting blood glucose, and body weight were measured at the baseline and 24-week visits.ResultsA total of 120 patients fulfilled the selection criteria and then underwent randomization to be placed into empagliflozin and vildagliptin groups. The mean change in HbA1c (-0.97% ± 0.68 for empagliflozin and -0.82% ± 1.57 for vildagliptin) was statistically similar in both groups (p-value = 0.980). No statistically significant difference was observed between the two groups for safety parameters such as eGFR (p = 0.46), serum ALT (p = 0.13), LDL (p = 0.23), total cholesterol (p = 0.49), and triglycerides (p = 0.49).ConclusionResults of the study highlight that vildagliptin and empagliflozin have a significant beneficial effect in reducing HbA1c, fasting blood glucose, systolic blood pressure, and weight of participants. Both drugs had no differences when compared on safety parameters.
The prevalence of thyroid nodules and its factors among Chinese adult women: A cross-sectional study
Authors: Dong Xiaoqian , Li Ying , Xie Jianfei , Li Lijun , Wan Ziyu , Kang Yue , Luo Yating , Wang Jiangang , Duan Yinglong , Ding Siqing , Cheng Andy SK 
Published: August 2022

ObjectiveTo determine the prevalence of thyroid nodules in Chinese adult women. To analyze the relationships between lifestyle, metabolic syndrome and thyroid nodules.MethodsWe conducted a retrospective cross-sectional study in the tertiary hospital from 2017 to 2019. Included participants underwent thyroid color Doppler ultrasonography, lipids examination, and dietary evaluation.ResultsTotally 2,784 participants were included, and 933 participants were found to have thyroid nodule(s) by B-ultrasound. The prevalence of thyroid nodules was 33.3%. Women in 50-59 years (OR: 1.746, 95% CI [1.356-2.249]), older than 60 (2.147 [1.540-2.993]) and occupations with mainly manual work (1.780 [1.367-2.317]) were risk factors for thyroid nodules, while moderate dietary diversity (0.624 [0.476-0.817]) and normal triglycerides level (0.739 [0.604-0.905]) were protective factors.ConclusionWomen over 50 and those whose jobs are mainly manual should enhance screening, follow-up and health management of thyroid nodules. Higher dietary diversity is protective measures against thyroid nodules for adult women and should consider dietary balance and the food varieties, not just increased quantities.
Integrated risk scores from N6-methyladenosine-related lncRNAs are potential biomarkers for predicting the overall survival of bladder cancer patients
Authors: Huang Xin , Wang Hao-Fei , Huang Shuang 
Published: August 2022

Background: N6-methyladenosine (m6A) is the most common form of mRNA- and long noncoding RNA (lncRNA)-specific internal modification encountered in eukaryotes, with important effects on mRNA stability, translation, and splicing. The role of m6A-modified lncRNAs (m6A-lncRNAs) in bladder cancer (BLCA) is rarely reported. This study aimed to evaluate an efficient prognostic model of BLCA in patients, based on m6A-lncRNAs, and to discover potential biological targets.Methods: Differentially expressed lncRNAs were investigated in 433 BLCA samples derived from The Cancer Genome Atlas (TCGA) database. Kaplan–Meier and univariate Cox regression analyses were performed to screen for m6A-lncRNAs with prognostic roles in BLCA. We implemented Pearson correlation analysis to analyze 18 potentially prognostic lncRNAs and 20 known m6A-associated genes. Next, the data were imputed using least absolute shrinkage and selection operator (LASSO) Cox regression to establish an m6A-lncRNA prognostic signature.Results: We established an integrated risk score (RS) containing five m6A-lncRNAs and constructed a nomogram that had the ability to forecast the overall survival (OS) of patients with BLCA. We showed that the predictive accuracy of the RS for BLCA prognosis was high, which was confirmed by the area under the receiver operating characteristic (ROC) curve. We analyzed the correlation between tumor immune infiltrating cells and RS in high- and low-risk patients with BLCA and used tumor immune dysfunction and exclusion to predict the effect of immunotherapy. We screened out the most relevant modules of RS through the weighted gene co-expression network analysis network and explored their potential biological functions using GO and KEGG analyses.Conclusion: Our findings demonstrate that, compared with nomograms constructed using a single prognostic factor, the integrated RS represents a superior model for predicting survival in patients with BLCA, which may improve the clinical management of BLCA.
Identification of Nitrogen Starvation-Responsive miRNAs to Reveal the miRNA-Mediated Regulatory Network in Betula luminifera
Authors: Lin Yan , Chu Sasa , Xu Xiaoshan , Han Xiao , Huang Huahong , Tong Zaikang , Zhang Junhong 
Published: August 2022

Because of the immobility, plants encounter a series of stresses, such as varied nutrient concentrations in soil, which regulate plant growth, development, and phase transitions. Nitrogen (N) is one of the most limiting factors for plants, which was exemplified by the fact that low nitrogen (LN) has a great adverse effect on plant growth and development. In the present study, we explored the potential role of microRNAs (miRNAs) in response to LN stress in Betula luminifera. We identified 198 miRNAs using sRNA sequencing, including 155 known and 43 novel miRNAs. Among them, 98 known miRNAs and 31 novel miRNAs were differentially expressed after 0.5 h or 24 h of LN stress. Based on degradome data, 122 differential expressed miRNAs (DEmiRNAs) including 102 known miRNAs and 20 novel miRNAs targeted 203 genes, comprising 321 miRNA–target pairs. A big proportion of target genes were transcription factors and functional proteins, and most of the Gene Ontology terms were enriched in biological processes; moreover, one Kyoto Encyclopedia of Genes and Genomes term “ascorbate and aldarate metabolism” was significantly enriched. The expression patterns of six miRNAs and their corresponding target genes under LN stress were monitored. According to the potential function for targets of DEmiRNAs, a proposed regulatory network mediated by miRNA–target pairs under LN stress in B. luminifera was constructed. Taken together, these findings provide useful information to elucidate miRNA functions and establish a framework for exploring N signaling networks mediated by miRNAs in B. luminifera. It may provide new insights into the genetic engineering of the high use efficiency of N in forestry trees.
Differential gene expression profiling reveals potential biomarkers and pharmacological compounds against SARS-CoV-2: Insights from machine learning and bioinformatics approaches
Authors: Hoque M. Nazmul , Sarkar Md. Murshed Hasan , Khan Md. Arif , Hossain Md. Arju , Hasan Md. Imran , Rahman Md. Habibur , Habib Md. Ahashan , Akter Shahina , Banu Tanjina Akhtar , Goswami Barna , Jahan Iffat , Nafisa Tasnim , Molla Md. Maruf Ahmed , Soliman Mahmoud E. , Araf Yusha , Khan M. Salim , Zheng Chunfu , Islam Tofazzal 
Published: August 2022

The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has created an urgent global situation. Therefore, it is necessary to identify the differentially expressed genes (DEGs) in COVID-19 patients to understand disease pathogenesis and the genetic factor(s) responsible for inter-individual variability and disease comorbidities. The pandemic continues to spread worldwide, despite intense efforts to develop multiple vaccines and therapeutic options against COVID-19. However, the precise role of SARS-CoV-2 in the pathophysiology of the nasopharyngeal tract (NT) is still unfathomable. This study utilized machine learning approaches to analyze 22 RNA-seq data from COVID-19 patients (n = 8), recovered individuals (n = 7), and healthy individuals (n = 7) to find disease-related differentially expressed genes (DEGs). We compared dysregulated DEGs to detect critical pathways and gene ontology (GO) connected to COVID-19 comorbidities. We found 1960 and 153 DEG signatures in COVID-19 patients and recovered individuals compared to healthy controls. In COVID-19 patients, the DEG–miRNA, and DEG–transcription factors (TFs) interactions network analysis revealed that E2F1, MAX, EGR1, YY1, and SRF were the highly expressed TFs, whereas hsa-miR-19b, hsa-miR-495, hsa-miR-340, hsa-miR-101, and hsa-miR-19a were the overexpressed miRNAs. Three chemical agents (Valproic Acid, Alfatoxin B1, and Cyclosporine) were abundant in COVID-19 patients and recovered individuals. Mental retardation, mental deficit, intellectual disability, muscle hypotonia, micrognathism, and cleft palate were the significant diseases associated with COVID-19 by sharing DEGs. Finally, the detected DEGs mediated by TFs and miRNA expression indicated that SARS-CoV-2 infection might contribute to various comorbidities. Our results provide the common DEGs between COVID-19 patients and recovered humans, which suggests some crucial insights into the complex interplay between COVID-19 progression and the recovery stage, and offer some suggestions on therapeutic target identification in COVID-19 caused by the SARS-CoV-2.
Metagenomic shotgun sequencing and metabolomic profiling identify specific human gut microbiota associated with diabetic retinopathy in patients with type 2 diabetes
Authors: Li Lihua , Yang Kaibo , Li Cong , Zhang Han , Yu Honghua , Chen Kang , Yang Xiaohong , Liu Lei 
Published: August 2022

BackgroundDiabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM) and is one of the leading causes of blindness among DM patients. However, the molecular mechanism involving DR remains unclear.MethodsA case–control study with age-, sex-, and duration-matched diabetic patients and controls was conducted, which included 15 type 2 DM (T2DM) patients with DR and 15 T2DM patients without DR. Shotgun sequencing and non-targeted metabolomic profiling analyses of fecal samples were performed, and comprehensive bioinformatics analyses were conducted.ResultsUsing metagenomic analyses, we identified 293,460 unique genes in the non-DR group, while that in the DR group was 283,235, and the number of overlapping genes was 1,237,914. Regarding phylum levels, Actinobacteria decreased but Bacteroidetes increased in the DR group when compared with those in the control group. Regarding genus levels, Bifidobacterium and Lactobacillus decreased. Cellular processes, environmental information processes, and metabolism-related pathways were found at higher levels in the gut microbiome of DR patients. Using metabolomic analyses, we found 116 differentially expressed metabolites with a positive ion model and 168 differentially expressed metabolites with a negative ion model between the two groups. Kyoto Encyclopedia of Genes and Genomes annotation revealed six pathways with different levels between DR and diabetic controls, namely, cellular processes, environmental information processing, genetic information processing, human diseases, organismal systems and metabolism. Moreover, lysine biosynthesis and lysine degradation were enriched using a positive model, but histidine metabolism and β-alanine metabolism were enriched using a negative model.ConclusionsTogether, the metagenomic profiles of DR patients indicated different gut microbiota compositions and characteristic fecal metabolic phenotypes in DR patients. Our findings of microbial pathways therefore provided potential etiological and therapeutic targets for DR patients.
Antioxidant effect of grape seed extract corrects experimental autoimmune encephalomyelitis behavioral dysfunctions, demyelination, and glial activation
Authors: Mabrouk Maha , El Ayed Mohamed , Démosthènes Amélie , Aissouni Youssef , Aouani Ezzedine , Daulhac-Terrail Laurence , Mokni Meherzia , Bégou Mélina 
Published: August 2022

Background and purposeMultiple sclerosis (MS), a multifactorial autoimmune disease of the central nervous system (CNS), is characterized by demyelination and chronic inflammation, as well as axonal and neuronal loss. There is no cure for MS, and despite a significant improvement in the therapeutic management of patients during the last 20 years, some symptoms are still resistant to treatment, and the evolution of the disease to progressive form seems still ineluctable. The etiology of MS is complex and still not fully understood. However, inflammation is a major driver of physiopathology and oxidative stress contributes to CNS lesions and promotes existing inflammatory response. Plant polyphenols are endowed with many therapeutic benefits through alleviating oxidative stress and inflammation, thus providing neuroprotection in MS. We presently evaluated the curative effect of grape seed extract (GSE) in an experimental autoimmune encephalomyelitis (EAE) mouse model of MS.Experimental approachSix-week-old C57Bl/6J females were subjected to the EAE paradigm (using myelin oligodendrocyte glycoprotein peptide fragment (35-55), complete Freund’s adjuvant, and pertussis toxin) and then chronically treated with GSE from day 10 to day 30 post-induction. Clinical score and body weight were monitored daily, while evaluation of sensitive, motor, cognitive, and anxiety-related behaviors was performed weekly. Then, the GSE effect was evaluated on whole brain and spinal cord samples through the evaluation of oxidative stress damage, antioxidant capacities, myelin alteration, astroglial and microglial proliferation, and sirtuin expression.Key resultsGrape seed extract curative chronic treatment corrected the clinical course of EAE, as well as the mechanical hypersensitivity, and avoided the development of EAE mouse thermal cold allodynia. The neuropathological evaluation showed that GSE reduced oxidative stress in the brain and spinal cord by decreasing the lipid and protein oxidation through correction of the three main antioxidant enzyme activities, namely, superoxide dismutase, catalase, and glutathione peroxidase, as well as restoring normal myelin protein expression and correcting microglial and astroglial protein overexpression and sirtuin downregulation.Conclusion and implicationsThese data strongly support GSE as an effective therapeutic approach in MS treatment.
Long term complete response of advanced hepatocellular carcinoma to glypican-3 specific chimeric antigen receptor T-Cells plus sorafenib, a case report
Authors: Sun Hongwei , Xing Chongyun , Jiang Songfu , Yu Kang , Dai Shengjie , Kong Hongru , Jin Yuepeng , Shan Yunfeng , Yang Wenjun , Wang Zhen , Xiao Jun , Wang Huamao , Wang Wei , Li Zonghai , Shi Keqing 
Published: August 2022

The clinical efficacy of current therapies for Hepatocellular carcinoma (HCC) are unsatisfactory. In recent years, chimeric antigen receptor (CAR) T-cell therapies have been developed for solid tumors including advanced HCC (aHCC), but limited progress has been made. Glypican-3 is a promising immunotherapeutic target for HCC since it is specifically highly expressed in HCC. A previous study indicated that GPC3-targeted CAR T-(CAR-GPC3) cells were well-tolerated and had prolonged survival for HCC patients and that Sorafenib could increase the antitumor activities of CAR-GPC3 T-cells against HCC in mouse models. Here, we report a patient with aHCC who achieved a complete response (CR) and a long survival period after the combination therapy of CAR-GPC3 T-cell plus sorafenib.A 60-year-old Asian male diagnosed with hepatitis B virus (HBV) related HCC developed liver recurrence and lung metastasis after liver tumor resection and trans-arterial chemoembolization therapy. The patient also previously received microwave ablation therapy for lung metastasis. After the enrollment, the patient underwent leukapheresis for CAR-GPC3 T-cells manufacturing. Seven days after leukapheresis, the patient started to receive 400 mg of Sorafenib twice daily. The patient received 4 cycles of CAR-GPC3 T cells (CT011) treatment and each cycle was divided into two infusions. Prior to each cycle of CT011 treatment, lymphodepletion was performed. The lymphodepletion regimen was cyclophosphamide 500 mg/m2/day for 2 to 3 days, and fludarabine 20-25 mg/m2/day for 3 to 4 days. A total of 4×109 CAR-GPC3 T cells were infused. The CT011 plus Sorafenib combination therapy was well tolerated. All the ≥ grade 3 AEs were hematological toxicities which were deemed an expected event caused by the preconditioning regimen. This patient obtained partial responses from the 3rd month and achieved CR in the 12th month after the first cycle of CT011 infusion according to the RECIST1.1 assessment. The tumor had no progression for more than 36 months and maintained the CR status for more than 24 months after the first infusion.
Improved induced innate immune response after cART initiation in people with HIV
Authors: Hove-Skovsgaard Malene , Møller Dina Leth , Hald Annemette , Gerstoft Jan , Lundgren Jens , Ostrowski Sisse Rye , Nielsen Susanne Dam 
Published: August 2022

IntroductionImpairment of the innate immune function may contribute to the increased risk of bacterial and viral infections in people with HIV (PWH). In this study we aimed to investigate the induced innate immune responses in PWH prior to and after initiation of combinational antiretroviral therapy (cART). Furthermore, we aimed to investigate if the induced innate immune responses before initiation of cART were associated with CD4+ T-cell recovery one year after initiating cART.Material and methodThe induced innate immune response was assessed by the TruCulture®whole blood technique in 32 PWH before cART initiation and after 1, 6 and 12 months. To mimic bacterial and viral infections we used a panel of three stimuli (lipopolysaccharide (LPS), resiquimod (R848), and polyinosinic:polycytidylic acid (Poly I:C)) to stimulate the extracellular Toll-like receptor (TLR) 4 and the intracellular TLR7/8 and TLR3, respectively. The following cytokine responses were analyzed by Luminex 200: Tumor Necrosis Factor (TNF)-α, Interleukin (IL)-1b, IL-6, IL-8, IL-10, IL-12p40, IL17A, Interferon (IFN)-α, and IFN-γ.ResultsAt baseline PWH with nadir CD4+ T-cell count &lt;350 cell/µL had lower levels of LPS-, R848-, and Poly I:C-induced IL-6 and IFN-γ, LPS- and R848-induced TNF-α and IL-12, LPS induced IL-1b, and R848-induced IL-10 than PWH with nadir CD4+ T-cell count &gt;350 cells/µL. The majority (&gt;50%) had induced cytokine concentrations below the reference intervals at baseline which was most pronounced for the LPS- and Poly I:C-induced responses. The induced responses in the whole population improved after 12 months of cART, and more PWH had induced cytokine concentrations within the reference intervals after 12 months. However, the majority of PWH still had LPS-induced INF-α, INF-γ and Poly I:C-induced TNF-α and IL-6 below the reference interval. The induced innate immune responses before cART initiation were not associated with the CD4+ T-cell recovery after 12 months of cART.ConclusionThe innate immune response was impaired in PWH, with a more pronounced impairment in PWH with low nadir CD4+ T-cell count. Initiation of cART improved the innate immune response, but compared to the reference intervals, some impairment remained in PWH without viral replication.