bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and validation of SERPINE1 as a prognostic and immunological biomarker in pan-cancer and in ccRCC
Authors: Li Lingqin , Li Fan , Xu Zhehao , Li Liyang , Hu Haiyi , Li Yang , Yu Shicheng , Wang Mingchao , Gao Lei 
Published: August 2023

Background:SERPINE1, a serine protease inhibitor involved in the regulation of the plasminogen activation system, was recently identified as a cancer-related gene. However, its clinical significance and potential mechanisms in pan-cancer remain obscure.Methods: In pan-cancer multi-omics data from public datasets, including The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx), and online web tools were used to analyze the expression of SERPINE1 in different cancers and its correlation with prognosis, genetic alteration, DNA promoter methylation, biological processes, immunoregulator expression levels, immune cell infiltration into tumor, tumor mutation burden (TMB), microsatellite instability (MSI), immunotherapy response and drug sensitivity. Further, two single-cell databases, Tumor Immune Single-cell Hub 2 (TISCH2) and CancerSEA, were used to explore the expression and potential roles of SERPINE1 at a single-cell level. The aberrant expression of SERPINE1 was further verified in clear cell renal cell carcinoma (ccRCC) through qRT-PCR of clinical patient samples, validation in independent cohorts using The Gene Expression Omnibus (GEO) database, and proteomic validation using the Clinical Proteomic Tumor Analysis Consortium (CPTAC) database.Results: The expression of SERPINE1 was dysregulated in cancers and enriched in endothelial cells and fibroblasts. Copy number amplification and low DNA promoter methylation could be partly responsible for high SERPINE1 expression. High SERPINE1 expression was associated with poor prognosis in 21 cancers. The results of gene set enrichment analysis (GSEA) indicated SERPINE1 involvement in the immune response and tumor malignancy. SERPINE1 expression was also associated with the expression of several immunoregulators and immune cell infiltration and could play an immunosuppression role. Besides, SERPINE1 was found to be related with TMB, MSI, immunotherapy response and sensitivity to several drugs in cancers. Finally, the high expression of SERPINE1 in ccRCC was verified using qRT-PCR performed on patient samples, six independent GEO cohorts, and proteomic data from the CPTAC database.Conclusion: The findings of the present study revealed that SERPINE1 exhibits aberrant expression in various types of cancers and is associated with cancer immunity and tumor malignancy, providing novel insights for individualized cancer treatment.
Rapid test to detect insecticide resistance in field populations of Spodoptera frugiperda (Lepidoptera: Noctuidae)
Authors: Mao Kai-Kai , Li Hong-Ran , Zhu Jing-Yun , Jin Ming-Hui , Wang Peng , Peng Yan , Xiao Yu-Tao 
Published: August 2023

Introduction: The development of insecticide resistance in Spodoptera frugiperda populations is a serious threat to the crop industry. Given the spread of invasive resistant populations, prospective monitoring should be accelerated, and the development of diagnostic tools for rapid and accurate assessments of insecticide resistance is essential.Methods: First, the discriminating dose and diagnostic time of the kit were determined by the glass vial method based on a susceptible strain. Then, pests that were collected from field populations were used to determine their susceptibility to seven insecticides by using the diagnostic kit. Finally, the accuracy of the kit was verified based on correlation analyses and the likelihood of insecticide control failure was assessed.Results: Here, we describe a diagnostic kit that enables the rapid detection of resistance to chlorpyrifos, bifenthrin, deltamethrin, lambda-cyhalothrin, phoxim, chlorantraniliprole and chlorfenapyr within 1-2 h in S. frugiperda at diagnostic doses of 0.98, 0.84, 0.38, 1.64, 0.0082, 1.75 and 0.65 μg/cm2, respectively. The linear equation between mortalities under diagnostic doses and actual resistance ratios measured by the diet-overlay bioassay was determined. The high correlation indicates that the insecticide resistance levels diagnosed by the kit were consistent with the results of the diet-overlay bioassay. Moreover, we found a significant negative correlation between diagnostic mortality and the likelihood of control failure for bifenthrin (r = −0.899, p = 0.001), deltamethrin (r = −0.737, p = 0.024) and lambda-cyhalothrin (r = −0.871, p = 0.002).Discussion: The insecticide resistance diagnostic kit for S. frugiperda is a user-friendly tool (portable, short detection time). Its excellent performance qualifies the kit as a reliable screening tool for identifying effective insecticides in sustainable resistance management.
Comparative analysis of the medicinal plant Polygonatum kingianum (Asparagaceae) with related verticillate leaf types of the Polygonatum species based on chloroplast genomes
Authors: Shi Naixing , Yang Zefen , Miao Ke , Tang Lilei , Zhou Nian , Xie Pingxuan , Wen Guosong 
Published: August 2023

BackgroundPolygonatum kingianum has been widely used as a traditional Chinese medicine as well as a healthy food. Because of its highly variable morphology, this medicinal plant is often difficult to distinguish from other related verticillate leaf types of the Polygonatum species. The contaminants in P. kingianum products not only decrease the products’ quality but also threaten consumer safety, seriously inhibiting the industrial application of P. kingianum.MethodsNine complete chloroplast (cp) genomes of six verticillate leaf types of the Polygonatum species were de novo assembled and systematically analyzed.ResultsThe total lengths of newly sequenced cp genomes ranged from 155,437 to 155,977 bp, including 86/87 protein-coding, 38 tRNA, and 8 rRNA genes, which all exhibited well-conserved genomic structures and gene orders. The differences in the IR/SC (inverted repeats/single-copy) boundary regions and simple sequence repeats were detected among the verticillate leaf types of the Polygonatum cp genomes. Comparative cp genomes analyses revealed that a higher similarity was conserved in the IR regions than in the SC regions. In addition, 11 divergent hotspot regions were selected, providing potential molecular markers for the identification of the Polygonatum species with verticillate leaf types. Phylogenetic analysis indicated that, as a super barcode, plastids realized a fast and efficient identification that clearly characterized the relationships within the verticillate leaf types of the Polygonatum species. In brief, our results not only enrich the data on the cp genomes of the genus Polygonatum but also provide references for the P. kingianum germplasm resource protection, herbal cultivation, and drug production.ConclusionThis study not only accurately identifies P. kingianum species, but also provides valuable information for the development of molecular markers and phylogenetic analyses of the Polygonatum species with verticillate leaf types.
Transcriptome and metabolome analysis reveals the effect of flavonoids on flower color variation in Dendrobium nobile Lindl.
Authors: Qiu Yujie , Cai Chengcheng , Mo Xu , Zhao Xinyi , Wu Lijuan , Liu Fan , Li Rui , Liu Chen , Chen Ji , Tian Mengliang 
Published: August 2023

IntroductionDendrobium nobile L. is a rare orchid plant with high medicinal and ornamentalvalue, and extremely few genetic species resources are remaining in nature. In the normal purple flower population, a type of population material with a white flower variation phenotype has been discovered, and through pigment component determination, flavonoids were preliminarily found to be the main reason for the variation.MethodsThis study mainly explored the different genes and metabolites at different flowering stages and analysed the flower color variation mechanism through transcriptome- and flavonoid-targeted metabolomics. The experimental materials consisted of two different flower color phenotypes, purple flower (PF) and white flower (WF), observed during three different periods.Results and discussionThe results identified 1382, 2421 and 989 differentially expressed genes (DEGs) in the white flower variety compared with the purple flower variety at S1 (bud stage), S2 (chromogenic stage) and S3 (flowering stage), respectively. Among these, 27 genes enriched in the ko00941, ko00942, ko00943 and ko00944 pathways were screened as potential functional genes affecting flavonoid synthesis and flower color. Further analysis revealed that 15 genes are potential functional genes that lead to flavonoid changes and flower color variations. The metabolomics results at S3 found 129 differentially accumulated metabolites (DAMs), which included 8 anthocyanin metabolites, all of which (with the exception of delphinidin-3-o-(2’’’-o-malonyl) sophoroside-5-o-glucoside) were found at lower amounts in the WF variety compared with the PF variety, indicating that a decrease in the anthocyanin content was the main reason for the inability to form purple flowers. Therefore, the changes in 19 flavone and 62 flavonol metabolites were considered the main reasons for the formation of white flowers. In this study, valuable materials responsible for flower color variation in D. nobile were identified and further analyzed the main pathways and potential genes affecting changes in flavonoids and the flower color. This study provides a material basis and theoretical support for the hybridization and molecular-assisted breeding of D. nobile.
The association of alcohol use and positive and negative urgency to same day objective binge eating in emerging adults
Authors: Fischer Sarah , Wonderlich Joseph , Miller Leo A. , Breithaupt Lauren , Frietchen Rachel , Cao Li , Nelson Jillian D. , Izquierdo Alyssa 
Published: August 2023

IntroductionObjective binge eating and problematic alcohol use often co-occur and are common behaviors in emerging adults. Both behaviors are thought to be driven by affect regulation processes. Objective binge eating often occurs in the context of increasing or acute negative affect, and often occurs in solitude. Alcohol use in emerging adults can also be associated with negative affect regulation. However, in contrast to objective binge eating, a large body of research indicates that there are positively valenced pathways to alcohol use in this age group. Emerging adults often drink socially, to enhance enjoyment, and in the context of positive mood. We propose that one pathway to objective binge eating in this developmental period is through alcohol use itself, such that emerging adults who consume alcohol and who are more likely to act impulsively in the context of positive emotion (i.e., have high levels of positive urgency) may be more likely to binge eat following drinking.MethodsWe collected data using ecological momentary assessment in 106 undergraduates on positive and negative affect, motives for drinking and eating, and alcohol use and objective binge eating, in addition to baseline questionnaires of impulsivity.ResultsThere were no significant changes in affect prior to drinking in this sample. Alcohol use at one time point significantly increased odds of objective binge eating at a later time point in the same day. Individual differences in positive urgency, the tendency to act rashly while experiencing positive affect, were also associated with increased odds of objective binge eating that occurred after alcohol use. Individual differences in negative urgency, the tendency to act rashly after experiencing negative affect, did not have a main effect on objective binge episodes, but did interact with alcohol use to increase the odds of objective binge eating following drinking. The vast majority of drinking episodes prior to objective binge eating were social drinking episodes, and participants most commonly endorsed "to have fun" as a reason for drinking.DiscussionResults suggest that alcohol consumption may increase risk for objective binge eating in emerging adults.
Stability and genetic insights of the co-existence of blaCTX-M-65, blaOXA-1, and mcr-1.1 harboring conjugative IncI2 plasmid isolated from a clinical extensively-drug resistant Escherichia coli ST744 in Shanghai
Authors: Feng Jun , Wu Huanyu , Zhuang Yuan , Luo Jiayuan , Chen Yong , Wu Yitong , Fei Jiayi , Shen Qi , Yuan Zhengan , Chen Min 
Published: August 2023

BackgroundCo-existence of colistin, β-lactam and carbapenem in multidrug-resistant Enterobacteriaceae isolates poses a serious threat to public health. In this study, we investigated and characterized the co-occurrence of blaCTX-M-65, blaOXA-1, and mcr-1.1 strain isolated from a clinical extensively-drug-resistant Escherichia coli ST744 in Shanghai.MethodsAntimicrobial susceptibility test was carried out by agar dilution methods. Whole genome sequencing was conducted, and resistance genes, and sequence types of colistin in E. coli isolates were analyzed. Plasmid stability and amino acid mutations were assessed in E. coli isolates.ResultsA colistin resistant E. coli ST744, named ECPX221, was identified out of 145 fecal samples collected. The strain carries a 60,168 IncI2 plasmid with the mcr-1.1 gene. The strain also has blaCTX-M-65, blaOXA-1, dfrA14, qnrS1, cmlA5, arr2, ampC, aph(4)-Ia, sul1, and aadA5 resistance genes. The plasmid pECPX221 was capable of conjugation with an efficiency of 2.6 × 10−2. Notably, 45% of the transconjugants were determined as mcr-1.1-harboring in the colistin-free environment after 60 generation of passage. No mutations occurred in pmrB, mgrB, and phoPQ gene in the mcr-1.1-harboring transconjugants. Bioinformatic analysis indicated pECPX221 shared highly similar backbone with the previously reported mcr-1.1-harboring pAH62-1, pMFDS1339.1, pSCZE4, and p2018-10-2CC. Furthermore, sequencing and phylogenetic analyses revealed a similarity between other MCR-1-homolog proteins, indicating that ECPX221 was colistin resistant.ConclusionThe stable transferable mcr-1.1-harboring plasmid found in the E. coli ST744 strain indicated the high risk to disseminate the extensively-drug-resistance phenotype among Enterobacteriaceae.
Willingness of people living with HIV to receive a second COVID-19 booster dose: a multicenter cross-sectional study in China
Authors: Lan Xinquan , Su Bin , Liang Shijie , Yu Maohe , Qiao Ying , Wang Li , Song Moxin , Wang Yuxiao , Xu Junjie 
Published: August 2023

BackgroundThe coronavirus disease 2019 (COVID-19) pandemic has significantly affected the global population, with People Living with HIV (PLWH) being particularly vulnerable due to their compromised immune systems. Although vaccination is a crucial preventative measure against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, little is understood about the willingness of PLWH to receive a second COVID-19 booster dose and the factors that may influence this decision. This study investigates the willingness of PLWH in China to receive a second COVID-19 booster dose and its influencing factors, comparing these with a group of healthy individuals.MethodsA multicenter cross-sectional study was conducted across five Chinese cities, namely, Beijing, Tianjin, Zhengzhou, Hohhot, and Harbin. Participants were recruited through five community-based organizations. Data were collected via participant self-administered questionnaires included demographic information, willingness to receive a second COVID-19 booster dose, and knowledge about HIV and COVID-19 vaccination. Factors influencing vaccination willingness were identified using multivariable logistic regression analyzes.ResultsA total of 156 PLWH and 151 healthy individuals were included in the study. After adjusting for potential confounders, it was found that PLWH demonstrated a lower willingness to receive a second COVID-19 booster dose compared to healthy individuals (77.6% vs. 88.7%, p = 0.009). Lower willingness was associated with HIV positive status (Adjusted Odds Ratio [AOR]: 0.39, 95%CI: 0.20, 0.75), perceived barriers (AOR: 0.05, 95%CI: 0.01, 0.26), and perceived severity (AOR: 0.32, 95%CI: 0.12, 0.90).ConclusionPLWH in China demonstrated a lower willingness to receive a second COVID-19 booster dose compared to healthy individuals. The findings suggest that perceptions and understanding of the COVID-19 vaccination and its necessity for protection against SARS-CoV-2 could influence this willingness. Efforts should be made to strengthen and disseminate knowledge about HIV and COVID-19 vaccinations among this population. In addition, developing interventions and policies that target specific subgroups and address misconceptions about vaccination could be instrumental in improving vaccination rates among PLWH.
Determinants of post-stroke cognitive impairment and dementia: association with objective measures and patient-reported outcomes
Authors: Oliveira Lara C. , Bonkhoff Anna K. , Ponciano Ana , Tuozzo Carissa , Viswanathan Anand , Rost Natalia S. , Etherton Mark R. 
Published: August 2023

BackgroundPost-stroke cognitive impairment and dementia (PSCID) is a sequel of ischemic stroke (IS), highly prevalent and linked to poor long-term outcomes. Thus, early recognition of the clinical determinants of PSCID is urgent for identifying high-risk individuals who are susceptible to PSCID. And investigating objective measures of PSCID in relation to patient-reported outcome measures (PROMs) is essential for understanding the impact of IS. Here we identify the clinical determinants associated with PSCID and the relationship of PSCID to patient-reported outcomes in a population with IS.MethodsThis was a cohort study. We enrolled 138 patients who were admitted to our hospital between February 2017 and February 2020, with IS and no pre-stroke diagnosis of dementia. Clinical variables were acquired on admission. At 3 months, patients underwent a follow-up evaluation including the Telephone Interview for Cognitive Status (TICS), modified Rankin scale (mRS), Barthel Index (BI), and PROMs, using the Patient-Reported Outcomes Measurement information System Global Health (PROMIS GH). MCI/Dementia was defined as a TICS score of &lt;36. Regression analyses were used to identify clinical, functional, and patient-reported outcome determinants of the 3-month TICS score. Analyses were adjusted for age, stroke severity, and prior IS.ResultsAt follow-up, 113 participants (82%) were found to have MCI/Dementia. Patients with PSCID were more likely to be older, and at 3-months post-stroke they had lower rates of PROMIS GH T Mental (mean 47.69 vs. 52.13) and T Physical (mean 46.75 vs. 50.64). In multivariable linear regression analyses, increasing age (β = −0.07, p = 0.03) and Peripheral Artery Disease (PAD; β = −3.60, p = 0.03) were independently associated with a lower TICS score. Functional and patient-reported outcomes were also associated with worse TICS, including mRS ≥ 2, BI, T Mental, Global Mental, T Physical, and Global Physical in adjusted analyses. Individual components of PROMs were also associated with TICS, including quality of life, mental health, social satisfaction, and physical activities.ConclusionsIn patients with IS, increased age and a pre-admission diagnosis of PAD are independently associated with worse objective measures of PSCID. Worse functional and patient-reported outcomes are also strongly linked to PSCID.
Evaluation of the mechanical properties and clinical application of nickel–titanium shape memory alloy anal fistula clip
Authors: Deng Heng , Li Ming , Fang Xiaoli , Zhang Jun , Wang Jianmin , Tang Kun , Tang Ran , Jia Ru , Han Ying , Shi Yang , Dong Yu'ang 
Published: August 2023

ObjectiveThe study investigates the mechanical properties of a nickel–titanium shape memory alloy anal fistula clip (NiTi-AFC), studies the surgical method of treating anal fistula, and evaluates its clinical efficacy.MethodsThe anal fistula clip was formed in nickel–titanium alloy with a titanium content of 50.0%–51.8%. The mechanical properties and chemical properties were tested. A total of 31 patients with anal fistula were enrolled between 1 January 2020 and 1 January 2023. All patients underwent internal orifice closure surgery using NiTi-AFC, and anorectal magnetic resonance or ultrasound was performed before surgery and 6 months after surgery for diagnosis and evaluation. Fistula cure rates, length of stay, perianal pain, and Wexner incontinence scores were retrospectively compared between patients treated with NiTi-AFC and patients treated with other surgical methods.ResultNiTi-AFC has a density of 6.44–6.50 g·cm−3, with a shape-restoring force of 63.8 N. The corrosion rate of NiTi-AFC in 0.05% hydrochloric acid solution at atmospheric pressure and 20°C is approximately 6.8 × 10−5 g·(m·h)−1. A total of 31 patients (male/female: 19/12, age: 43.7 ± 17.8 years) were included. Among them, 22.6% (7) had multiple anal fistula, 16.1% (5) had high anal fistula, and 48.3% (15) had perianal fistula Crohn's disease. In total, 12.9% (4/31) did not achieve primary healing, underwent fistula resection, and eventually recovered. A retrospective analysis showed that the fistula healing rate, length of stay, and anal pain of NiTi-AFC treatment were similar to those of other traditional surgeries, but the Wexner incontinence score was significantly lower.ConclusionNiTi-AFC has shape memory properties, corrosion resistance, superelastic effect, and surface cell adhesion. It is applied to internal orifice closure surgery of anal fistula, with good therapeutic effect, and can protect the anal function.
Sociodemographic variations in the uptake of faecal immunochemical tests in primary care: a retrospective study
Authors: Bailey James A , Morton Alastair J , Jones James , Chapman Caroline J , Oliver Simon , Morling Joanne R , Patel Heetan , Banerjea Ayan , Humes David J 
Published: August 2023

BackgroundFaecal immunochemical test (FIT) usage for symptomatic patients is increasing, but variations in use caused by sociodemographic factors are unknown. A clinical pathway for colorectal cancer (CRC) was introduced in primary care for symptomatic patients in November 2017. The pathway was commissioned to provide GPs with direct access to FITs.AimTo identify whether sociodemographic factors affect FIT return in symptomatic patients.Design and settingA retrospective study was undertaken in Nottingham, UK, following the introduction of FIT as triage tool in primary care. It was mandated for all colorectal referrals (except rectal bleeding or mass) to secondary care. FIT was used, alongside full blood count and ferritin, to stratify CRC risk.MethodAll referrals from November 2017 to December 2021 were retrospectively reviewed. Sociodemographic factors affecting FIT return were analysed by multivariate logistic regression.ResultsA total of 35 289 (90.7%) patients returned their index FIT, while 3631 (9.3%) did not. On multivariate analysis, males were less likely to return an FIT (odds ratio [OR] 1.11, 95% confidence interval [CI] = 1.03 to 1.19). Patients aged ≥65 years were more likely to return an FIT (OR 0.78 for non-return, 95% CI = 0.72 to 0.83). Unreturned FIT more than doubled in the most compared with the least deprived quintile (OR 2.20, 95% CI = 1.99 to 2.43). Patients from Asian (OR 1.82, 95% CI = 1.58 to 2.10), Black (OR 1.21, 95% CI = 0.98 to 1.49), and mixed or other ethnic groups (OR 1.29, 95% CI = 1.05 to 1.59) were more likely to not return an FIT compared with patients from a White ethnic group. A total of 599 (1.5%) CRCs were detected; 561 in those who returned a first FIT request.ConclusionFIT return in those suspected of having CRC varied by sex, age, ethnic group, and socioeconomic deprivation. Strategies to mitigate effects on FIT return and CRC detection should be considered as FIT usage expands.