bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phaseolus vulgaris alphaendornavirus-1 is frequent in bean germplasm in Slovakia and shows low molecular variability
Authors: Mrkvová Michaela , Achs Adam , Alaxin Peter , Šubr Zdeno , Predajňa Lukáš , Zetochová Erika , Hauptvogel Pavol , Šoltys Katarína , Candresse Thierry , Glasa Miroslav 
Published: June 2023

Phaseolus vulgaris alphaendornavirus-1 (PvEV-1, family Endornaviridae) was identified by ribodepleted total RNA high-throughput sequencing in the virome of two bean plants (Phaseouls vulgaris L.) grown in a garden in western Slovakia. Two nearly complete PvEV-1 genomes (ca. 14.06 kb, named PV1 and PV2) were assembled, showing 99.9% nucleotide identity, while their nucleotide identity with the reference PvEV-1 genome (NC_039217) reached 98.4%. Two primer pairs spanning the viral helicase encoding region and sequence upstream of the RNA-dependent RNA polymerase were designed and used to confirm the presence of the virus in the original bean samples by RT-PCR. A subsequent search for PvEV-1 presence in Slovakia was focused on two groups of samples: 1) bean plants grown under open field conditions and sampled during the vegetation period and 2) bean accessions grown from seeds obtained from a Slovak and French bean germplasm collection. Based on RT-PCR results, 4 out of 15 bean samples from open fields and 12 out of 21 bean accessions from the curated germplasm collection tested PvEV-1-positive. Interestingly, sequencing of RT-PCR products revealed that all amplified isolates are identical in the two amplified genomic portion which is also identical to those of the PV1 and PV2 isolates. These results suggest a relatively high incidence of PvEV-1 in bean in Slovakia. This is the first evidence and characterization of PvEV-1 from bean plants in Europe.
Application of multi-criteria decision analysis techniques and decision support framework for informing select agent designation for agricultural animal pathogens
Authors: Pillai Segaran P. , West Todd , Anderson Kevin , Fruetel Julia A. , McNeil Carrie , Hernandez Patricia , Ball Cameron , Beck Nataly , Morse Stephen A. 
Published: June 2023

The United States Department of Agriculture (USDA), Division of Agricultural Select Agents and Toxins (DASAT) established a list of biological agents and toxins (Select Agent List) that potentially threaten agricultural health and safety, the procedures governing the transfer of those agents, and training requirements for entities working with them. Every 2 years the USDA DASAT reviews the Select Agent List, using subject matter experts (SMEs) to perform an assessment and rank the agents. To assist the USDA DASAT biennial review process, we explored the applicability of multi-criteria decision analysis (MCDA) techniques and a Decision Support Framework (DSF) in a logic tree format to identify pathogens for consideration as select agents, applying the approach broadly to include non-select agents to evaluate its robustness and generality. We conducted a literature review of 41 pathogens against 21 criteria for assessing agricultural threat, economic impact, and bioterrorism risk and documented the findings to support this assessment. The most prominent data gaps were those for aerosol stability and animal infectious dose by inhalation and ingestion routes. Technical review of published data and associated scoring recommendations by pathogen-specific SMEs was found to be critical for accuracy, particularly for pathogens with very few known cases, or where proxy data (e.g., from animal models or similar organisms) were used to address data gaps. The MCDA analysis supported the intuitive sense that select agents should rank high on the relative risk scale when considering agricultural health consequences of a bioterrorism attack. However, comparing select agents with non-select agents indicated that there was not a clean break in scores to suggest thresholds for designating select agents, requiring subject matter expertise collectively to establish which analytical results were in good agreement to support the intended purpose in designating select agents. The DSF utilized a logic tree approach to identify pathogens that are of sufficiently low concern that they can be ruled out from consideration as a select agent. In contrast to the MCDA approach, the DSF rules out a pathogen if it fails to meet even one criteria threshold. Both the MCDA and DSF approaches arrived at similar conclusions, suggesting the value of employing the two analytical approaches to add robustness for decision making.
Breast Tumor-Derived Exosomal MicroRNA-200b-3p Promotes Specific Organ Metastasis Through Regulating CCL2 Expression in Lung Epithelial Cells
Authors: Gu Pengfei , Sun Mayu , Li Lei , Yang Yang , Jiang Zheshun , Ge Yang , Wang Wenbo , Mu Wei , Wang Hui 
Published: June 2023

Graphical AbstractSchematic diagram of tumor-derived exosomes induced organotropism and immunosuppression.
Current understanding of disease control and its application in patients with chronic rhinosinusitis
Authors: Zhou Jiahui , Yuan Fan , Huang Tianhao , Zhu Li , Wu Dawei 
Published: June 2023

BackgroundDisease control is a primary treatment goal for patients with chronic rhinosinusitis (CRS). This study aims to summarize the evaluation parameters of disease control and then identify predictors of poorly controlled CRS.MethodsA systematic review of the literature was performed on PubMed, Google Scholar, Scopus, and Cochrane databases to identify studies relating to disease control in CRS.ResultsThe concept of disease control in patients with CRS involved the longitudinal assessment of the disease state and was also an important goal of treatment. As a metric of the disease state, the disease control reflected the ability to keep disease manifestations within certain limits, the efficacy after treatment, and the impact on quality of life. Validated measurements, such as EPOS2012 criteria, EPOS2020 criteria, Sinus Control Test, and patient/physician-reported global level of CRS control, have been utilized in clinical practice. These existing disease control instruments incorporated various disease manifestations and categorized patients into two (well-controlled and poor-controlled), three (uncontrolled, partly controlled, and controlled), or five (not at all, a little, somewhat, very, and completely) control categories. Eosinophilia, high computerized tomography score, bilateral sinonasal disease, asthma, allergic rhinitis, female gender, aspirin intolerance, revision surgery, low serum amyloid A, and specific T cell subtype would predict poorly controlled CRS.ConclusionThe concept of disease control and its application were gradually developed in patients with CRS. The existing disease control instruments demonstrated a lack of uniformity regarding the controlled criteria and included parameters.
Alterations of the gut microbiota associated with the occurrence and progression of viral hepatitis
Authors: Yang Xing , Mai Huanzhuo , Zhou Jie , Li Zhuoxin , Wang Qing , Lan Liuyan , Lu Fang , Yang Xiping , Guo Baodong , Ye Li , Cui Ping , Liang Hao , Huang Jiegang 
Published: June 2023

BackgroundGut microbiota is the largest population of microorganisms and is closely related to health. Many studies have explored changes in gut microbiota in viral hepatitis. However, the correlation between gut microbiota and the occurrence and progression of viral hepatitis has not been fully clarified.MethodsPubMed and BioProject databases were searched for studies about viral hepatitis disease and 16S rRNA gene sequencing of gut microbiota up to January 2023. With bioinformatics analyses, we explored changes in microbial diversity of viral hepatitis, screened out crucial bacteria and microbial functions related to viral hepatitis, and identified the potential microbial markers for predicting risks for the occurrence and progression of viral hepatitis based on ROC analysis.ResultsOf the 1389 records identified, 13 studies met the inclusion criteria, with 950 individuals including 656 patient samples (HBV, n = 546; HCV, n = 86; HEV, n = 24) and 294 healthy controls. Gut microbial diversity is significantly decreased as the infection and progression of viral hepatitis. Alpha diversity and microbiota including Butyricimonas, Escherichia-Shigella, Lactobacillus, and Veillonella were identified as the potential microbial markers for predicting the risk of development of viral hepatitis (AUC&gt;0.7). Microbial functions including tryptophan metabolism, fatty acid biosynthesis, lipopolysaccharide biosynthesis, and lipid metabolism related to the microbial community increased significantly as the development of viral hepatitis.ConclusionsThis study demonstrated comprehensively the gut microbiota characteristics in viral hepatitis, screened out crucial microbial functions related to viral hepatitis, and identified the potential microbial markers for predicting the risk of viral hepatitis.
Drug-coated balloon therapy is more effective in treating late drug-eluting stent in-stent restenosis than the early occurring one—a systematic review and meta-analysis
Authors: Kulyassa Péter , Engh Marie Anne , Vámosi Péter , Fehérvári Péter , Hegyi Péter , Merkely Béla , Édes István Ferenc 
Published: June 2023

Drug-eluting stent in-stent restenosis (DES-ISR) remains one of the important assignments to be resolved in interventional cardiology, as it is present in 5%–10% of total percutaneous coronary intervention cases. Drug-coated balloon (DCB) utilization is promising, as it comes with long-term protection from recurrent restenosis in optimal conditions without the hazard of higher risk for stent thrombosis and in-stent restenosis. We aim to reduce the need for recurrent revascularization in DES-ISR, specifying the population in which the DCB therapy should be used. In this meta-analysis, the results of studies containing data on the time frame between drug-eluting stent implantation and the clinical presentation of in-stent restenosis and concomitant drug-coated balloon treatment were summarized. A systematic search was performed in Medline, Central, Web of Science, Scopus and Embase databases on November 11th, 2021. The QUIPS tool was used to assess the risk of bias in the included studies. The occurrence of a major cardiac adverse events (MACE) composite endpoint, containing target lesion revascularization (TLR), myocardial infarction, and cardiac death, and each of these separately, was assessed at 12 months after the balloon treatment. Random effects meta-analysis models were used for statistical analysis. Data of 882 patients from four studies were analyzed. Across the included studies, a 1.68 OR (CI 1.57–1.80, p &lt; 0.01) for MACE and a 1.69 OR (CI 1.18–2.42 p &lt; 0.01) for TLR were observed, both in favor of late DES-ISR. The main limitation of the study is the relatively low patient number. Nevertheless, this analysis shows the first statistically significant results for the effect of DCB treatment in the early or late presentation of DES-ISR. As to date, intravascular imaging (IVI) remains limitedly accessible, other landmarks as the time frame of in-stent restenosis development are to be pursued to advance therapeutic outcomes. In consideration of other biological, technical and mechanical factors, time frame of occurrence as a prognostic factor could reduce the burden of recurrent revascularization in patients at an already high risk.Systematic Review Registration: identifier [CRD42021286262].
Growth response of syndromic versus non-syndromic children born small for gestational age (SGA) to growth hormone therapy: a Belgian study
Authors: Becker Marianne , Thomas Muriel , Brachet Cécile , Heinrichs Claudine , Dotremont Hilde , De Schepper Jean , Lysy Philippe , Beckers Dominique ,   the BESPEED group
Published: June 2023

IntroductionA substantial proportion of SGA patients present with a syndrome underlying their growth restriction. Most SGA cohorts comprise both syndromic and non-syndromic patients impeding delineation of the recombinant human growth hormone (rhGH) response. We present a detailed characterization of a SGA cohort and analyze rhGH response based on adult height (AH).MethodsClinical and auxological data of SGA patients treated with rhGH, who had reached AH, were retrieved from BELGROW, a national database of all rhGH treated patients held by BESPEED (BElgian Society for PEdiatric Endocrinology and Diabetology). SGA patients were categorized in syndromic or non-syndromic patients.Results272 patients were included, 42 classified as syndromic (most frequent diagnosis (n=6): fetal alcohol syndrome and Silver-Russell syndrome). Compared with non-syndromic patients, syndromic were younger [years (median (P10/P90)] 7.43 (4.3/12.37) vs 10.21 (5.43/14.03), p=0.0005), shorter (height SDS -3.39 (-5.6/-2.62) vs -3.07 (-3.74/-2.62), p=0.0253) and thinner (BMI -1.70 (-3.67/0.04) vs -1.14 (-2.47/0.27) SDS, p=0.0054) at start of rhGH treatment. First year rhGH response was comparable (delta height SDS +0.54 (0.24/0.94) vs +0.56 (0.26/0.92), p=0.94). Growth pattern differed with syndromic patients having a higher prepubertal (SDS +1.26 vs +0.83, p=0.0048), but a lower pubertal height gain compared to the non-syndromic group (SDS -0.28 vs 0.44, p=0.0001). Mean rhGH dose was higher in syndromic SGA patients (mg/kg body weight/day 0.047 (0.039/0.064) vs 0.043 (0.035/0.056), p=0.0042). AH SDS was lower in syndromic SGA patients (-2.59 (-4.99/-1.57) vs -2.32 (-3.3/-1.2), p=0.0107). The majority in both groups remained short (&lt;-2 SDS: syndromic 71%, non-syndromic 63%). Total height gain was comparable in both groups (delta height SDS +0.76 (-0.70/1.48) vs +0.86 (-0.12/1.86), p=0.41).ConclusionsCompared to non-syndromic SGA patients, syndromic SGA patients were shorter when starting rhGH therapy, started rhGH therapy earlier, and received a higher dose of rhGH. At AH, syndromic SGA patients were shorter than non-syndromic ones, but their height gain under rhGH therapy was comparable.
Assessing of programmed cell death gene signature for predicting ovarian cancer prognosis and treatment response
Authors: Lian Xin , Liu Bing , Wang Caixia , Wang Shuang , Zhuang Yuan , Li Xiao 
Published: June 2023

BackgroundProgrammed cell death (PCD) is an overwhelming factor affecting tumor cell metastasis, but the mechanism of PCD in ovarian cancer (OV) is still uncertain.MethodsTo define the molecular subtypes of OV, we performed unsupervised clustering based on the expression level of prognosis related PCD genes in the Cancer Genome Atlas (TCGA)-OV. COX and least absolute shrinkage and selection operator (LASSO) COX analysis were used to identify the OV prognostic related PCD genes, and the genes identified according to the minimum Akaike information criterion (AIC) were the OV prognostic characteristic genes. According to the regression coefficient in the multivariate COX analysis and gene expression data, the Risk Score of OV prognosis was constructed. Kaplan-Meier analysis was conducted to assess the prognostic status of OV patients, and receiver operating characteristic (ROC) curves were conducted to assess the clinical value of Risk Score. Moreover, RNA-Seq date of OV patient derived from Gene Expression Omnibus (GEO, GSE32062) and the International Cancer Genome Consortium (ICGC) database (ICGC-AU), verifying the robustness of the Risk Score via Kaplan-Meier and ROC analysis.Pathway features were performed by gene set enrichment analysis and single sample gene set enrichment analysis. Finally, Risk Score in terms of chemotherapy drug sensitivity and immunotherapy suitability was also evaluated in different groups.Results9-gene composition Risk Score system was finally determined by COX and LASSO COX analysis. Patients in the low Risk Score group possessed improved prognostic status, immune activity. PI3K pathway activity was increased in the high Risk Score group. In the chemotherapy drug sensitivity analysis, we found that the high Risk Score group might be more suitable for treatment with PI3K inhibitors Taselisib and Pictilisib. In addition, we found that patients in the low-risk group responded better to immunotherapy.ConclusionRisk Score of 9-gene composition of PCD signature possesses promising clinical potential in OV prognosis, immunotherapy, immune microenvironment activity, and chemotherapeutic drug selection, and our study provides the basis for an in-depth investigation of the PCD mechanism in OV.
Community structure and plant diversity under different degrees of restored grassland in mining areas of the Qilian Mountains, Northwestern China
Authors: Yang Xiaomei , Feng Qi , Liu Wei , Xia Honghua , Zhang Jutao , Yang Linshan , Zhang Chengqi , Wang Zhiyang , Feng Yonglin 
Published: June 2023

Background: Mining activities are known to exert significant effects on the structure and function of grassland ecosystems. However, the role of mining grasslands restoration in altering the plant community and soil quality remains poorly understood, especially in alpine regions. Here, we investigated species diversity in grasslands with dynamic changes and different restoration levels in the Tianzhu alpine mining area locating in the Qilian Mountains.Methods: The plant community structure and species composition of the grasslands with different restoration levels were analyzed by the sample method. We used five different restoration levels: very low recovered degree (VLRD), low recovered degree (LRD), medium recovered degree (MRD), and high recovered degree (HRD), and selected natural grassland (NGL, CK) as the control.Results: Plant community structure and species composition were significantly higher than those under the VLRD in the Tianzhu alpine mining area (p &lt; 0.05), with HRD &gt; MRD &gt; LRD &gt; VLRD. There were 11 families, 18 genera, and 17 species of plants, mainly in the families of Leguminosae, Asteraceae, Gramineae, Rosaceae, and Salicaceae; among them, Salicaceae and Gramineae played a decisive role in the stability of the community. The ecotype community showed that perennial herbaceous plants were the most dominant, with annual herbaceous plants being the least dominant, and no tree and shrub layers were observed; the dominance index was the highest in VLRD at 0.32, the richness index was the highest in HRD at 2.73, the diversity of HRD was higher at 1.93, soil pH and EC showed a decreasing trend, and SMC, SOC, TN, NO3-N, NH4-N, AN, TP, and AP content showed an increasing trend with the increase of grassland restoration.Conclusion: In summary, with the increase of restored grassland in the Tianzhu alpine mining area, plant diversity gradually increased and plant community structure gradually diversified, which was close to the plant diversity of NGL. The protection of partially VLRD and LRD grasslands in the mining area should be emphasized, and the mine grassland should be used rationally and scientifically restored.
Thriving in uncertainty: examining the relationship between perceived environmental uncertainty and corporate eco-innovation through the lens of dynamic capabilities
Authors: Han Xiang , Yue Beibei , He Zhiwei 
Published: June 2023

Introduction: Objective environmental uncertainty has important impacts on entrepreneurial decision-making, but entrepreneurs’ perception of uncertainty may be a more crucial factor. This is because objective environmental uncertainty may need to be filtered through entrepreneurs’ perceptions to influence their decision-making. Therefore, exploring how entrepreneurs’ perceived environmental uncertainty (PEU) affects their corporate eco-innovation behavior has significant theoretical and practical implications.Methods: Drawing on the dynamic capability view, we utilize data from the 2016 China Private Enterprise Survey (CPES) on 2,733 small and medium-sized enterprises (SEMs) to highlight the impact of entrepreneurs’ PEU on corporate eco-innovation. We also examine the moderating effect of government intervention (government subsidies and government official visiting) on this relationship.Results: Our study reveals a positive impact of entrepreneurs’ PEU on corporate eco-innovation, confirming the critical role of dynamic capability in corporate strategic adjustment under uncertain conditions. Additionally, we find that government intervention (government subsidies and official visits) has a positive moderating effect on this relationship, with entrepreneurs’ PEU and eco-innovation being mediated by corporate dynamic capability.Discussion: The study contributes to the literature on environmental uncertainty, dynamic capabilities, and eco-innovation, and provides practical implications for SMEs in developing countries. The findings highlight the importance of subjective perceptions of environmental uncertainty over objective uncertainty. The study also demonstrates that environmental uncertainty is not inherently negative, but can be managed strategically with dynamic adjustment and government support.
Downregulation of interleukin 6 signaling might reduce the risk of periodontitis: a drug target Mendelian randomization study
Authors: Nolde Michael , Alayash Zoheir , Reckelkamm Stefan Lars , Kocher Thomas , Ehmke Benjamin , Holtfreter Birte , Baurecht Hansjörg , Georgakis Marios K. , Baumeister Sebastian-Edgar 
Published: June 2023

AimInterleukin 6 (IL-6) is considered to play a role in the dysbiotic host response in the development of periodontitis. While the inhibition of the IL-6 receptor using monoclonal antibodies is a well-established therapy for some diseases, so far, its potential benefit in patients with periodontitis has not been examined. We tested the association of genetically proxied downregulation of IL-6 signaling with periodontitis to explore whether downregulation of IL-6 signaling could represent a viable treatment target for periodontitis,Materials and methodsAs proxies for IL-6 signaling downregulation, we selected 52 genetic variants in close vicinity of the gene encoding IL-6 receptor that were associated with lower circulating C-reactive protein (CRP) levels in a genome-wide association study (GWAS) of 575 531 participants of European ancestry from the UK Biobank and the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. Associations with periodontitis were tested with inverse-variance weighted Mendelian randomization in a study of 17 353 cases and 28 210 controls of European descent in the Gene-Lifestyle Interactions in Dental Endpoints (GLIDE) consortium. In addition, the effect of CRP reduction independent of the IL-6 pathway was assessed.ResultsGenetically proxied downregulation of IL-6 signaling was associated with lower odds of periodontitis (odds ratio (OR) = 0.81 per 1-unit decrement in log-CRP levels; 95% confidence interval (CI): [0.66;0.99]; P = 0.0497). Genetically proxied reduction of CRP independent of the IL-6 pathway had a similar effect (OR = 0.81; 95% CI: [0.68; 0.98]; P = 0.0296).ConclusionIn conclusion, genetically proxied downregulation of IL-6 signaling was associated with lower odds of periodontitis and CRP might be a causal target for the effect of IL-6 on the risk of periodontitis.