bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treatment and survival analysis for 40-year SEER data on upper esophageal cancer
Authors: Wu Xi , Zhu Ming-Chuang , Li Guo-Liang , Xiong Peng , Sun Wei , Zhang Ni , Zhao Bo , Li Le-Qun , Fu Xiang-Ning , Zhu Min 
Published: July 2023

BackgroundUpper esophageal cancer (UEC) is rare in both Eastern and Western countries. The epidemiological characteristics and long-term survival of UEC patients are less known. In addition, the choice of optimal treatment for UEC has been controversial.MethodsCases of UEC (C15.3 and C15.0) arising during the period from 1973 to 2013 were identified and selected using the SEER database. Student's t-test and Pearson's chi-square test were used to compare the differences in parameters among different groups. Esophageal cancer-specific survival (ECSS) and overall survival (OS) rates were calculated by using the Kaplan–Meier method. Cox proportional hazard regression was used to analyze predictive factors.ResultsIn the past 40 years, the cases of UEC have gradually increased, and the proportion of adenocarcinoma (AD) has gradually increased (from 3.6% to 11.8%, p &lt; 0.001). There has been a significant increase (1973–1982 vs. 2004–2013) in median OS (7 months vs. 10 months, p &lt; 0.001) and median ECSS (7 months vs. 11 months, p &lt; 0.001) among UEC patients from 1973 to 2013. For the impact of different treatments, the results showed that the ECSS and OS of surgery without radiation (SWR) and radiation plus surgery (R+S) were superior to those of radiation without surgery (RWS). Subgroup analysis showed that ECSS and OS were highest among patients treated with SWR compared with R+S and RWS for patients with localized disease. For regional disease, ECSS and OS were highest among patients with R+S compared with SWR or RWS. Among patients with regional-stage squamous cell carcinoma (SCC), OS was higher with neoadjuvant radiotherapy or adjuvant radiotherapy compared with SWR. Multivariate analysis showed that radiotherapy sequence was dependently associated with OS among patients with regional-stage SCC.ConclusionAlthough the long-term survival of UEC remains poor, it has gradually increased since 1973. This should be closely related to the improvement of medical care over the past 40 years. Different treatment methods have a great influence on the long-term survival of UEC. For localized diseases, surgery may be a better choice. For regional disease, surgery plus adjuvant or neoadjuvant radiotherapy may be more beneficial to improve the long-term prognosis of UEC patients.
Short-term outcome of patients with adult IgA vasculitis: a single-center experience
Authors: Hočevar Alojzija , Ostrovršnik Jaka , Jurčić Vesna , Tomšič Matija , Rotar Žiga 
Published: July 2023

BackgroundFollow-up data on IgA vasculitis (IgAV) in adults are scarce. We aimed to investigate the outcome of adult IgAV in a well-defined cohort.MethodsData from histologically proven patients diagnosed between January 2010 and July 2022 with at least a 3-month follow-up were analyzed. The frequency and type of relapses and information on kidney function were extracted. Risk factors for IgAV relapse and decline in renal function were studied using the Cox hazards regression analysis. Mortality in IgAV was assessed using the Kaplan–Meier analysis and the standardized mortality ratio (SMR).ResultsIn total, 265 patients were followed for a median of 24 months. At baseline, 38.9, 29.8, and 44.5% had articular, gastrointestinal, and renal involvement, respectively. Initially, 189 (71.3%) patients received systemic glucocorticoids, and 32 (12.1%) patients received an additional immunomodulator. During follow-up, 42 (15.8%) patients relapsed. Relapses were more common in younger patients (HR 1.03 [95%CI 1.01–1.05]) and those without baseline glucocorticoid treatment (HR 3.70 [95%CI 2.0–6.67]). Furthermore, 74 (27.9%) patients had persistent abnormal urinalysis and a substantial (≥20%) decline in glomerular filtration rate (eGFR) was recorded in 41 (15.5%) patients. The factors associated with persistent abnormal urinalysis were an absence of IgAV joint involvement and baseline immunomodulatory treatment. Pre-existent chronic kidney disease and heart failure were associated with eGFR decline. The overall SMR was 1.4 (95%CI 1.14–1.71) compared to the Slovenian general population.ConclusionIgAV relapses occurred in 15% of patients, with younger patients with symptomatically managed IgAV experiencing it more frequently. Heart failure emerged as a predictor of persistent abnormal urinalysis and a decline in eGFR. Adults with IgAV had increased mortality compared to the general population.
Efficacy and safety of parecoxib and flurbiprofen axetil for perioperative analgesia in children: a network meta-analysis
Authors: Chen Xi , Chen Pan , Chen Xiao , Huang Min , Tang Kejing , He Qiuyi 
Published: July 2023

ObjectiveThe aim of this study was to systematically review the efficacy and safety of parecoxib and flurbiprofen axetil for perioperative analgesia in children through Bayesian network meta-analysis.MethodsWe systematically searched PubMed, Embase, Cochrane Library, Web of Science, Sinomed, CNKI, VIP, and Wanfang Data databases on 18 July 2022 to obtain randomized controlled trials comparing perioperative parecoxib or flurbiprofen with placebo or standard treatment for pediatric analgesia. The outcomes were the postoperative pain score and the incidence of adverse events. The Gemtc package of R-4.0.3 and Stata 17.0 were used for Bayesian network meta-analysis.ResultsWe retrieved 942 articles and 49 randomized controlled trials involving 3,657 patients who met the inclusion criteria. Compared with children who received placebo treatment, those who received flurbiprofen axetil had lower pain sores at each time point within 24 h postoperatively, and those who received parecoxib had lower pain sores at each time point within 12 h postoperatively. Compared with children who received tramadol treatment, both the children who received flurbiprofen axetil or parecoxib had lower pain scores at 8 h postoperatively. The ranking results demonstrated that flurbiprofen axetil had significant superiority in reducing pain scores at 2, 4, and 12 h postoperatively, and parecoxib had significant superiority in reducing pain scores at 0, 0.5, 1, 6, 8, and 24 h postoperatively. In terms of safety, compared with children who received placebo, those who received flurbiprofen axetil or parecoxib had a lower incidence of total adverse events and postoperative agitation. Compared with tramadol, flurbiprofen axetil and parecoxib both significantly reduced the incidence of total adverse events and postoperative nausea and vomiting. Compared with flurbiprofen axetil or fentanyl, parecoxib significantly reduced the incidence of postoperative nausea and vomiting. The ranking results showed that parecoxib was advantageous in decreasing the incidence of total adverse events and postoperative nausea and vomiting.ConclusionFlurbiprofen axetil was most effective at reducing pain scores at 2, 4, and 12 h postoperatively. Parecoxib had an advantage in terms of reducing pain scores at 0, 0.5, 1, 6, 8, and 24 h postoperatively, as well as the incidence of total adverse events and postoperative nausea and vomiting.Systematic trial registrationhttps://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=348886, PROSPERO (CRD42022348886).
Identification of a miRNA–mRNA regulatory network for post-stroke depression: a machine-learning approach
Authors: Qiu Huaide , Shen Likui , Shen Ying , Mao Yiming 
Published: July 2023

ObjectiveThe study aimed to explore the miRNA and mRNA biomarkers in post-stroke depression (PSD) and to develop a miRNA–mRNA regulatory network to reveal its potential pathogenesis.MethodsThe transcriptomic expression profile was obtained from the GEO database using the accession numbers GSE117064 (miRNAs, stroke vs. control) and GSE76826 [mRNAs, late-onset major depressive disorder (MDD) vs. control]. Differentially expressed miRNAs (DE-miRNAs) were identified in blood samples collected from stroke patients vs. control using the Linear Models for Microarray Data (LIMMA) package, while the weighted correlation network analysis (WGCNA) revealed co-expressed gene modules correlated with the subject group. The intersection between DE-miRNAs and miRNAs identified by WGCNA was defined as stroke-related miRNAs, whose target mRNAs were stroke-related genes with the prediction based on three databases (miRDB, miRTarBase, and TargetScan). Using the GSE76826 dataset, the differentially expressed genes (DEGs) were identified. Overlapped DEGs between stroke-related genes and DEGs in late-onset MDD were retrieved, and these were potential mRNA biomarkers in PSD. With the overlapped DEGs, three machine-learning methods were employed to identify gene signatures for PSD, which were established with the intersection of gene sets identified by each algorithm. Based on the gene signatures, the upstream miRNAs were predicted, and a miRNA–mRNA network was constructed.ResultsUsing the GSE117064 dataset, we retrieved a total of 667 DE-miRNAs, which included 420 upregulated and 247 downregulated ones. Meanwhile, WGCNA identified two modules (blue and brown) that were significantly correlated with the subject group. A total of 117 stroke-related miRNAs were identified with the intersection of DE-miRNAs and WGCNA-related ones. Based on the miRNA-mRNA databases, we identified a list of 2,387 stroke-related genes, among which 99 DEGs in MDD were also embedded. Based on the 99 overlapped DEGs, we identified three gene signatures (SPATA2, ZNF208, and YTHDC1) using three machine-learning classifiers. Predictions of the three mRNAs highlight four miRNAs as follows: miR-6883-5p, miR-6873-3p, miR-4776-3p, and miR-6738-3p. Subsequently, a miRNA–mRNA network was developed.ConclusionThe study highlighted gene signatures for PSD with three genes (SPATA2, ZNF208, and YTHDC1) and four upstream miRNAs (miR-6883-5p, miR-6873-3p, miR-4776-3p, and miR-6738-3p). These biomarkers could further our understanding of the pathogenesis of PSD.
Quality appraisal of clinical practice guidelines for motor neuron diseases or related disorders using the AGREE II instrument
Authors: Ou Jia-Yin , Liu Jun-Jun , Xu Jing , Li Jia-Yu , Liu Yang , Liu You-Zhang , Lu Li-Ming , Pan Hua-Feng , Wang Lin 
Published: July 2023

ObjectivesThis study aimed to systematically assess the quality of CPGs for motor neuron diseases (MNDs) or related disorders and identify the gaps that limit evidence-based practice.MethodsFour scientific databases and six guideline repositories were searched for eligible CPGs. Three researchers assessed the eligible CPGs using the Appraisal of Guidelines Research and Evaluation II instrument. The distribution of the level of evidence and strength of recommendation of these CPGs were determined. The univariate regression analysis was used to explore the characteristic factors affecting the quality of CPGs.ResultsFifteen CPGs met the eligibility criteria: 10 were for MND and 5 were for spinal muscular atrophy. The mean overall rating score was 44.5%, and only 3 of 15 CPGs were of high quality. The domains that achieved low mean scores were applicability (24.4%), rigor of development (39.9%), and stakeholder involvement (40.3%). Most recommendations were based on low-quality evidence and had a weak strength. The CPGs that were updated, meant for adults, and evidence based, and used a CPG quality tool and a grading system were associated with higher scores in certain specific domains and overall rating.ConclusionThe overall quality of CPGs for MNDs or related disorders was poor and recommendations were largely based on low-quality evidence. Many areas still need improvement to develop high-quality CPGs, and the use of CPG quality tools should be emphasized. A great deal of research on MNDs or related disorders is still needed to fill the large evidence gap.
Effects of exercise based on ACSM recommendations on bone mineral density in individuals with osteoporosis: a systematic review and meta-analyses of randomized controlled trials
Authors: Cui Wenlai , Li Dong , Jiang Yueshuai , Gao Yang 
Published: July 2023

Purpose: To analyze the effects of different exercise dose on lumbar spine and femoral neck bone mineral density (BMD) in individuals with osteoporosis (OP).Design: A systematic search was conducted in four electronic databases, namely, PubMed, Embase, Web of Science, and Cochrane, with the topic of the impact of exercise on BMD in individuals with OP. Randomized controlled trials comparing exercise intervention with no intervention were identified, and changes in lumbar spine and femoral neck BMD were reported and evaluated using standardized mean difference (SMD) and 95% confidence interval (95% CI). The intervention measures in the studies were evaluated and categorized as high adherence with the exercise testing and prescription recommendations for individuals with OP developed by the American College of Sports Medicine (ACSM) or low/uncertainty adherence with ACSM recommendations. A random effects model was used to conduct meta-analyses and compare the results between subgroups.Results: A total of 32 studies involving 2005 participants were included in the analyses, with 14 studies categorized as high adherence with ACSM recommendations and 18 studies categorized as low or uncertain adherence. In the analyses of lumbar spine BMD, 27 studies with 1,539 participants were included. The combined SMD for the high adherence group was 0.31, while the combined SMD for the low or uncertain adherence group was 0.04. In the analyses of femoral neck BMD, 23 studies with 1,606 participants were included. The combined SMD for the high adherence group was 0.45, while the combined SMD for the low or uncertain adherence group was 0.28. Within resistance exercise, the subgroup with high ACSM adherence had a greater impact on lumbar spine BMD compared to the subgroup with low or uncertain ACSM adherence (SMD: 0.08 &gt; −0.04). Similarly, for femoral neck BMD, resistance exercise with high ACSM adherence had a higher SMD compared to exercise with low or uncertain ACSM adherence (SMD: 0.49 &gt; 0.13).Conclusion: The results suggest that exercise interventions with high adherence to ACSM recommendations are more effective in improving lumbar spine and femoral neck BMD in individuals with OP compared to interventions with low or uncertain adherence to ACSM recommendations.Systematic Review Registration: PROSPERO, identifier CRD42023427009
Brassinosteroids affect wood development and properties of Fraxinus mandshurica
Authors: Lu Han , Chen Mingjun , Fu Meng , Yan Jialin , Su Wenlong , Zhan Yaguang , Zeng Fansuo 
Published: July 2023

IntroductionXylem development plays a crucial role in wood formation in woody plants. In recent years, there has been growing attention towards the impact of brassinosteroids (BRs) on this xylem development. In the present study, we evaluated the dynamic variation of xylem development in Fraxinus mandshurica (female parent, M8) and a novel interspecific hybrid F. mandshurica × Fraxinus sogdiana (1601) from May to August 2020.MethodsWe obtained RNA-Seq transcriptomes of three tissue types (xylem, phloem, and leaf) to identify the differences in xylem-differentially expressed genes (X-DEGs) and xylem-specifically expressed genes (X-SEGs) in M8 and 1601 variants. We then further evaluated these genes via weighted gene co-expression network analysis (WGCNA) alongside overexpressing FmCPD, a BR biosynthesis enzyme gene, in transient transgenic F. mandshurica.ResultsOur results indicated that the xylem development cycle of 1601 was extended by 2 weeks compared to that of M8. In addition, during the later wood development stages (secondary wall thickening) of 1601, an increased cellulose content (14%) and a reduced lignin content (11%) was observed. Furthermore, vessel length and width increased by 67% and 37%, respectively, in 1601 compared with those of M8. A total of 4589 X-DEGs were identified, including enzymes related to phenylpropane metabolism, galactose metabolism, BR synthesis, and signal transduction pathways. WGCNA identified hub X-SEGs involved in cellulose synthesis and BR signaling in the 1601 wood formation–related module (CESA8, COR1, C3H14, and C3H15); in contrast, genes involved in phenylpropane metabolism were significantly enriched in the M8 wood formation–related module (CCoAOMT and CCR). Moreover, overexpression of FmCPD in transient transgenic F. mandshurica affected the expression of genes associated with lignin and cellulose biosynthesis signal transduction. Finally, BR content was determined to be approximately 20% lower in the M8 xylem than in the 1601 xylem, and the exogenous application of BRs (24-epi brassinolide) significantly increased the number of xylem cell layers and altered the composition of the secondary cell walls in F. mandshurica.DiscussionOur findings suggest that BR biosynthesis and signaling play a critical role in the differing wood development and properties observed between M8 and 1601 F. mandshurica.
Identification of new potential molecular actors related to fiber quality in flax through Omics
Authors: Chabi Malika , Goulas Estelle , Galinousky Dmitry , Blervacq Anne-Sophie , Lucau-Danila Anca , Neutelings Godfrey , Grec Sébastien , Day Arnaud , Chabbert Brigitte , Haag Katharina , Müssig Jörg , Arribat Sandrine , Planchon Sébastien , Renaut Jenny , Hawkins Simon 
Published: July 2023

One of the biggest challenges for a more widespread utilization of plant fibers is to better understand the different molecular factors underlying the variability in fineness and mechanical properties of both elementary and scutched fibers. Accordingly, we analyzed genome-wide transcription profiling from bast fiber bearing tissues of seven different flax varieties (4 spring, 2 winter fiber varieties and 1 winter linseed) and identified 1041 differentially expressed genes between varieties, of which 97 were related to cell wall metabolism. KEGG analysis highlighted a number of different enriched pathways. Subsequent statistical analysis using Partial Least-Squares Discriminant Analysis showed that 73% of the total variance was explained by the first 3 X-variates corresponding to 56 differentially expressed genes. Calculation of Pearson correlations identified 5 genes showing a strong correlation between expression and morphometric data. Two-dimensional gel proteomic analysis on the two varieties showing the most discriminant and significant differences in morphometrics revealed 1490 protein spots of which 108 showed significant differential abundance. Mass spectrometry analysis successfully identified 46 proteins representing 32 non-redundant proteins. Statistical clusterization based on the expression level of genes corresponding to the 32 proteins showed clear discrimination into three separate clusters, reflecting the variety type (spring-/winter-fiber/oil). Four of the 32 proteins were also highly correlated with morphometric features. Examination of predicted functions for the 9 (5 + 4) identified genes highlighted lipid metabolism and senescence process. Calculation of Pearson correlation coefficients between expression data and retted fiber mechanical measurements (strength and maximum force) identified 3 significantly correlated genes. The genes were predicted to be connected to cell wall dynamics, either directly (Expansin-like protein), or indirectly (NAD(P)-binding Rossmann-fold superfamily protein). Taken together, our results have allowed the identification of molecular actors potentially associated with the determination of both in-planta fiber morphometrics, as well as ex-planta fiber mechanical properties, both of which are key parameters for elementary fiber and scutched fiber quality in flax.
A biomarker discovery framework for childhood anxiety
Authors: Bosl William J. , Bosquet Enlow Michelle , Lock Eric F. , Nelson Charles A. 
Published: July 2023

IntroductionAnxiety is the most common manifestation of psychopathology in youth, negatively affecting academic, social, and adaptive functioning and increasing risk for mental health problems into adulthood. Anxiety disorders are diagnosed only after clinical symptoms emerge, potentially missing opportunities to intervene during critical early prodromal periods. In this study, we used a new empirical approach to extracting nonlinear features of the electroencephalogram (EEG), with the goal of discovering differences in brain electrodynamics that distinguish children with anxiety disorders from healthy children. Additionally, we examined whether this approach could distinguish children with externalizing disorders from healthy children and children with anxiety.MethodsWe used a novel supervised tensor factorization method to extract latent factors from repeated multifrequency nonlinear EEG measures in a longitudinal sample of children assessed in infancy and at ages 3, 5, and 7 years of age. We first examined the validity of this method by showing that calendar age is highly correlated with latent EEG complexity factors (r = 0.77). We then computed latent factors separately for distinguishing children with anxiety disorders from healthy controls using a 5-fold cross validation scheme and similarly for distinguishing children with externalizing disorders from healthy controls.ResultsWe found that latent factors derived from EEG recordings at age 7 years were required to distinguish children with an anxiety disorder from healthy controls; recordings from infancy, 3 years, or 5 years alone were insufficient. However, recordings from two (5, 7 years) or three (3, 5, 7 years) recordings gave much better results than 7 year recordings alone. Externalizing disorders could be detected using 3- and 5 years EEG data, also giving better results with two or three recordings than any single snapshot. Further, sex assigned at birth was an important covariate that improved accuracy for both disorder groups, and birthweight as a covariate modestly improved accuracy for externalizing disorders. Recordings from infant EEG did not contribute to the classification accuracy for either anxiety or externalizing disorders.ConclusionThis study suggests that latent factors extracted from EEG recordings in childhood are promising candidate biomarkers for anxiety and for externalizing disorders if chosen at appropriate ages.