bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants
Authors: Sang Shiye , Chen Wen , Zhang Di , Zhang Xuan , Yang Wenjing , Liu Changning 
Published: October 2021

Abstract
Background
Long non-coding RNAs (lncRNAs) play vital roles in many important biological processes in plants. Currently, a large fraction of plant lncRNA studies center at lncRNA identification and functional analysis. Only a few plant lncRNA studies focus on understanding their evolutionary history, which is crucial for an in-depth understanding of lncRNAs. Therefore, the integration of large volumes of plant lncRNA data is required to deeply investigate the evolution of lncRNAs.

Results
We present a large-scale evolutionary analysis of lncRNAs in 25 flowering plants. In total, we identified 199,796 high-confidence lncRNAs through data integration analysis, and grouped them into 5497 lncRNA orthologous families. Then, we divided the lncRNAs into groups based on the degree of sequence conservation, and quantified the various characteristics of 756 conserved Arabidopsis thaliana lncRNAs. We found that compared with non-conserved lncRNAs, conserved lncRNAs might have more exons, longer sequence length, higher expression levels, and lower tissue specificities. Functional annotation based on the A. thaliana coding-lncRNA gene co-expression network suggested potential functions of conserved lncRNAs including autophagy, locomotion, and cell cycle. Enrichment analysis revealed that the functions of conserved lncRNAs were closely related to the growth and development of the tissues in which they were specifically expressed.

Conclusions
Comprehensive integration of large-scale lncRNA data and construction of a phylogenetic tree with orthologous lncRNA families from 25 flowering plants was used to provide an oversight of the evolutionary history of plant lncRNAs including origin, conservation, and orthologous relationships. Further analysis revealed a differential characteristic profile for conserved lncRNAs in A. thaliana when compared with non-conserved lncRNAs. We also examined tissue specific expression and the potential functional roles of conserved lncRNAs. The results presented here will further our understanding of plant lncRNA evolution, and provide the basis for further in-depth studies of their functions.
Grapevine Rpv3-, Rpv10- and Rpv12-mediated defense responses against Plasmopara viticola and the impact of their deployment on fungicide use in viticulture
Authors: Wingerter Chantal , Eisenmann Birgit , Weber Patricia , Dry Ian , Bogs Jochen 
Published: October 2021

Abstract
Background
The high susceptibility of European grapevine cultivars (Vitis vinifera) to downy mildew (Plasmopara viticola) leads to the intensive use of fungicides in viticulture. To reduce this input, breeding programs have introgressed resistance loci from wild Vitis species into V. vinifera, resulting in new fungus-resistant grapevine cultivars (FRC). However, little is known about how these different resistance loci confer resistance and what the potential reduction in fungicide applications are likely to be if these FRCs are deployed. To ensure a durable and sustainable resistance management and breeding, detailed knowledge about the different defense mechanisms mediated by the respective Rpv (Resistance to P. viticola) resistance loci is essential.

Results
A comparison of the resistance mechanisms mediated by the Rpv3–1, Rpv10 and/or Rpv12-loci revealed an early onset of programmed cell death (PCD) at 8 hours post infection (hpi) in Rpv12-cultivars and 12 hpi in Rpv10-cultivars, whereas cell death was delayed in Rpv3-cultivars and was not observed until 28 hpi. These temporal differences correlated with an increase in the trans-resveratrol level and the formation of hydrogen peroxide shortly before onset of PCD. The differences in timing of onset of Rpv-loci specific defense reactions following downy mildew infection could be responsible for the observed differences in hyphal growth, sporulation and cultivar-specific susceptibility to this pathogen in the vineyard. Hereby, Rpv3- and Rpv12/Rpv3-cultivars showed a potential for a significant reduction of fungicide applications, depending on the annual P. viticola infection pressure and the Rpv-loci. Furthermore, we report on the discovery of a new P. viticola isolate that is able to overcome both Rpv3- and Rpv12-mediated resistance.

Conclusion
This study reveals that differences in the timing of the defense reaction mediated by the Rpv3-, Rpv10- and Rpv12-loci, result in different degrees of natural resistance to downy mildew in field. Vineyard trials demonstrate that Rpv12/Rpv3- and Rpv3-cultivars are a powerful tool to reduce the dependence of grape production on fungicide applications. Furthermore, this study indicates the importance of sustainable breeding and plant protection strategies based on resistant grapevine cultivars to reduce the risk of new P. viticola isolates that are able to overcome the respective resistance mechanism.
Persistent eosinopenia is associated with in-hospital mortality among older patients: unexpected prognostic value of a revisited biomarker
Authors: Partouche Bethsabee , Pepin Marion , de Farcy Pauline Mary , Kahn Jean-Emmanuel , Sawczynski Bruno , Lechowski Laurent , Teillet Laurent , Barbot Frederic , Herr Marie , Davido Benjamin 
Published: October 2021

Abstract
Introduction
Infection is one of the major causes of mortality and morbidity in older adults. Available biomarkers are not associated with prognosis in older patients. This study aimed to analyze the value of eosinopenia (eosinophil count< 100/mm3) as a prognosis marker among older patients with suspected or confirmed bacterial infection.

Methods
A retrospective study was performed from 1 January to 31 December 2018 among patients in a geriatrics ward suffering from a bacterial infection treated with antibiotics. Biomarker data including the eosinophil count, neutrophil count and C-reactive protein (CRP) were collected within 4 days after patient diagnosis. Persistent eosinopenia was defined as a consistent eosinophil count< 100/mm3 between Day 2 and Day 4. The association of biomarkers with 30-day hospital mortality in a multivariate analysis was assessed and their predictive ability using the area under the ROC curve (AUC) was compared.

Results
Our study included 197 patients with a mean age of 90 ± 6 years. A total of 36 patients (18%) died during their stay in hospital. The patients who died were more likely to have persistent eosinopenia in comparison to survivors (78% versus 34%, p < 0.001). In the multivariate analysis, persistent eosinopenia was associated with in-hospital mortality with an adjusted HR of 8.90 (95%CI 3.46–22.9). The AUC for eosinophil count, CRP and neutrophil count between Day 2 and Day 4 were 0.7650, 0.7130, and 0.698, respectively.

Conclusion
Persistent eosinopenia within 4 days of diagnosis of bacterial infection appeared to be a predictor of in-hospital mortality in older patients.
The risk of preterm birth in combinations of socioeconomic position and mental health conditions in different age groups: a Danish nationwide register-based cohort study
Authors: Knudsen Camilla Klinge , Christesen Amanda Marie Somer , Heuckendorff Signe , Fonager Kirsten , Johansen Martin Nygård , Overgaard Charlotte 
Published: October 2021

Abstract
Background
Inequality in preterm birth is a world-wide challenge that has proved difficult for maternity care services to meet. Reducing the inequality requires identification of pregnant women at particularly high risk of preterm birth in order to target interventions. Therefore, the aim was to estimate the risk of preterm birth in women with different combinations of socioeconomic position, mental health conditions, and age.

Methods
In this nationwide register-based cohort study, we included all first-time mothers that gave birth to a singleton liveborn infant in Denmark between 2000 and 2016. The absolute and relative risk of preterm birth (< 37 weeks of gestation) was examined in different combinations of educational level (high, intermediate, and low) and mental health conditions (no, minor, and moderate/severe) in three age strata (≤23, 24–30, and ≥ 31 years). We estimated the relative risk using Poisson regression with a robust error variance. As additive interaction can help identify subgroups where limited resources can be of best use, we measured the attributable proportion to assess the risk that is due to interaction of the different exposures.

Results
Of the 415,523 included first-time mothers, 6.3% gave birth prematurely. The risk of preterm birth increased with decreasing educational level and increasing severity of mental health conditions in all age strata, but most in women aged ≥31 years. The highest absolute risk was 12.9% [95% CI: 11.2;14.8%] in women aged ≥31 years with low education and moderate/severe mental health conditions resulting in a relative risk of 2.23 [95% CI: 1.93–2.58] compared to the unexposed reference group in that age strata. We found positive additive interaction between low education and mental health conditions in women aged 24–30 and ≥ 31 years and between age ≥ 31 years and combinations of mental health conditions and educational levels.

Conclusion
The inequality in preterm birth increased with increasing age. To reduce inequality in preterm birth focused attention on women with higher age further combined with lower educational levels and mental health conditions is essential.
Correlation between low-level viremia and hepatitis B-related hepatocellular carcinoma and recurrence: a retrospective study
Authors: Sun Furong , Liu Zhifei , Wang Bingyuan 
Published: October 2021

Abstract
Background
Low-level viremia generally refers to detectable HBV DNA levels lower than 2000 IU/mL. Studies show that low-level viremia is a risk factor for hepatocellular carcinoma. The aim of this study was to explore the characteristics of low-level viremia patients with hepatitis B-related hepatocellular carcinoma and identify prognostic factors after curative hepatectomy.

Methods
Data from chronic hepatitis B patients with hepatocellular carcinoma receiving curative hepatectomy for the first time in the first hospital of China Medical University were studied. Patients were divided into two groups based on preoperative HBV DNA levels: group 1 (low-level viremia group, HBV DNA < 2000 IU/mL) and group 2 (HBV DNA ≥ 2000 IU/mL).

Results
Of the 212 patients, 104 patients were in group 1 and 108 patients were in group 2. There was a lower proportion of patients with HBsAg levels > 250 IU/mL (the upper limit of detection in our laboratory) in group 1 than in group 2 (71.2% vs. 86.1%, P < 0.01). The percentage of patients with a tumor diameter < 5 cm was 67.3% in group 1 and 37.0% in group 2 (P < 0.000). The percentage of tumor recurrence was 40.4% (42) in group 1 and 54.6% (59) in group 2 (P < 0.05). Median recurrence-free survival was 30.1 months in group 1 and 17.6 months in group 2 (P < 0.01). Multivariate analysis showed that a tumor diameter ≥ 5 cm (hazard ratio [HR] = 1.819, 95% confidence interval [CI] 1.193–2.775, P = 0.005), intrahepatic metastasis (HR = 1.916, 95% CI 1.077–3.407, P = 0.027), and an HBV DNA level ≥ 100 IU/mL (the lower limit of detection in our laboratory, HR = 2.943, 95% CI 1.916–4.520, P < 0.000) were independent prognostic factors associated with an increased risk of hepatocellular carcinoma recurrence.

Conclusion
Preoperative low-level viremia was related with a long tumor recurrence interval and complete virologic response after curative hepatectomy was associated with a lower risk of hepatocellular carcinoma recurrence.
Evidence on article 5.3 of FCTC (tobacco industry interference in tobacco control activities) in India- a qualitative scoping study
Authors: Goel Sonu , Kar Sitanshu Sekhar , Verma Madhur , Sivanantham Parthibane , Naik Bijay Nanda , Gupta Deepti 
Published: October 2021

AbstractBackgroundThe Tobacco Industry (henceforth TI) yearns to portray itself as being “socially responsible” and fights for the decision-making positions; that are it used to deter, delay or dilute tobacco control measures. There is little documented evidence of Tobacco Industry Interference (henceforth TII) from India, the scope of their interference and challenges faced by the experts for effective tobacco control. This research study seeks to cover this significant gap in the literature on the TI of India.MethodsA cross-sectional qualitative research design, based upon in-depth interviews (N = 26), was used to explore the key stakeholders’ opinions regarding TII in India. The interviews used a set of questions to collect information about the participant’s roles and responsibilities in tobacco control, the nature of TII faced by the participants, means of influence by TI, barriers and challenges to tobacco control efforts.ResultsMost of the respondents were engaged in tobacco control, training, advocacy and awareness generation activities for 5–10 years or more. The respondents defined the TI and its scope as per their experience with the help of the power ranking methodology. Most of them perceived TI as ‘manufacturers’ while others consider them as ‘advertisers’, ‘public relation companies’, ‘wholesalers’, ‘vendors’, and ‘Government firms with TI stocks. The research team identified six significant domains: influencing the policy and administrative decisions, Interference in the implementation of tobacco control laws and activities, false propaganda and hiding the truth, manipulating front action groups (FAG), rampant tobacco advertising and promotion activities and others under which TII activities were classified. Most respondents believed that TI players were interfering in the policy decisions, implementing the tobacco control laws and activities and manipulating the FAG. A detailed taxonomic classification of the TII strategies that emerged from our analysis was linked to article 5.3 of FCTC.ConclusionsThe study documented a significant level of TII in different domains, with stakeholders acting at various hierarchical levels. Thus providing insight into the tactics of the TI in order to enable stakeholders to anticipate and pre-empt the kinds of alliances the TI may attempt to build; stimulating academicians and researchers to undertake in-depth analysis into various strategies and therefore underscoring the need to ensuring transparency in official interaction with the TI and its representatives.
Does the rate of orthodontic tooth movement change during the estrus cycle? A systematic review based on animal studies
Authors: Almidfa Noura Saeed Sultan , Athanasiou Athanasios E. , Makrygiannakis Miltiadis A. , Kaklamanos Eleftherios G. 
Published: October 2021

AbstractBackgroundAs the fluctuation of sex hormone levels in menstruating women results in periodical effects in bone metabolism, understanding the implications for tooth movement could be of benefit to the orthodontist. This type of research presents practical and ethical problems in humans, but animal models could provide useful information. Our objective was to systematically investigate the available evidence on the question whether the rate of orthodontic tooth movement varies between the different stages of the estrus cycle in animals.MethodsUnrestricted searches in 7 databases and manual searching of the reference lists in relevant studies were performed up to February 2021 (Medline [PubMed], CENTRAL [Cochrane Library; includes records from Embase, CINAHL, ClinicalTrials.gov, WHO's ICTRP, KoreaMed, Cochrane Review Groups’ Specialized Registers, and records identified by handsearching], Cochrane Database of Systematic Reviews [Cochrane Library], Scopus, Web of Knowledge [including Web of Science Core Collection, KCI Korean Journal Database, Russian Science Citation Index, SciELO Citation Index and Zoological Record], Arab World Research Source [EBSCO] and ProQuest Dissertation and Theses [ProQuest]). Our search focused on prospective controlled animal studies, whose samples included female subjects of any species that were quantitatively comparing the amount of tooth movement in the different stages of the estrus cycle. Following study retrieval and selection, relevant data was extracted, and the risk of bias was assessed using the SYRCLE’s Risk of Bias Tool.ResultsFrom the finally assessed records, 3 studies met the inclusion criteria. Two of the studies experimented on Wistar rats, whereas the other on cats. Tooth movement was induced by expansion or coil springs. The rate of orthodontic tooth movement was increased during the stages of the estrus cycle when oestrogen and/or progesterone levels were lower. The risk of bias in the retrieved studies was assessed to be unclear.ConclusionHormonal changes during the estrus cycle may affect the rate of orthodontic tooth movement. Although these animal experiment results should be approached cautiously regarding their translational potential, it could be useful to consider the possible impact of these physiological changes in the clinical setting until more information becomes available.Registration: PROSPERO (CRD42021158069).
Effectiveness of oral health education intervention among 12–15-year-old school children in Dharan, Nepal: a randomized controlled trial
Authors: Subedi Krishna , Shrestha Ashish , Bhagat Tarakant , Baral Dharanidhar 
Published: October 2021

AbstractBackgroundSchool-aged adolescents are in particular need of preventive program to ensure positive long-term oral health and hygiene. The objective of this study was to assess the effectiveness of an oral health education (OHE) intervention on oral hygiene knowledge, attitude and practices (KAP), plaque control and gingival health among 12–15 years old school children in Dharan sub-metropolitan city, Nepal.MethodsA randomized controlled trial was conducted with parallel study groups, comprising 12–15-year-old school children, 120 in each group. OHE was given to the experimental group at baseline, third and sixth months and to the control group after completion of the study. Interview of the participants were done using a 23-item questionnaire for assessment of oral hygiene KAP. For each question, correct answer was scored as 1 and wrong answer was scored zero. An overall composite score was then created, by adding the individual scores. Oral examination was done using mouth mirror and WHO probe to record Turesky–Gilmore–Glickman modification of the Quigley-Hein plaque index, Gingival index and Dentition status and treatment needs. Analysis was done using chi-square test for categorical data and independent t test, Mann–Whitney U test, repeated measures ANOVA and post hoc Tukey’s test for quantitative data. The level of significance was set atP < 0.05.ResultsThere was 54.58% improvement in overall oral hygiene KAP in experimental group (P = 0.001) whereas no improvement was seen in control group at the end of the study. The mean plaque score was improved by 57.67% (P = 0.001) in experimental group in comparison to 4.56% in control group. Gingival index was improved by 49.90% (P = 0.001) in experimental group in comparison to 0.7% in control group. Caries experience was increased in both groups but no significant difference was seen.ConclusionsThe study concluded that oral health education was effective in improving oral hygiene KAP, plaque control and gingival health.Trial registrationThe trial was retrospectively registered with Clinical Trial Registry India (CTRI) with identifier no. CTRI/2018/05/013985, registered on 05/21/2018. (http://www.ctri.nic.in/Clinicaltrials/pdf_generate.php?trialid=23651&EncHid=&modid=&compid=%27,%2723651det%27). Institutional Review Committee, B. P. Koirala Institute of Health Sciences (BPKIHS), Dharan, Nepal provided the ethical approval (Ref. No.: 292/074/075-IRC).
The benefit of combining curcumin, bromelain and harpagophytum to reduce inflammation in osteoarthritic synovial cells
Authors: Brochard Sybille , Pontin Julien , Bernay Benoit , Boumediene Karim , Conrozier Thierry , Baugé Catherine 
Published: October 2021

Abstract
Background
Osteoarthritis (OA) is the most common form of arthritis, affecting millions of people worldwide and characterised by joint pain and inflammation. It is a complex disease involving inflammatory factors and affecting the whole joint, including the synovial membrane. Since drug combination is widely used to treat chronic inflammatory diseases, a similar strategy of designing plant-derived natural products to reduce inflammation in OA joints may be of interest. In this study, we characterised the response of OA synovial cells to lipopolysaccharide (LPS) and investigated the biological action of the combination of curcumin, bromelain and harpagophytum in this original in vitro model of osteoarthritis.

Methods
Firstly, human synovial cells from OA patients were stimulated with LPS and proteomic analysis was performed. Bioinformatics analyses were performed using Cytoscape App and SkeletalVis databases. Additionally, cells were treated with curcumin, bromelain and harpagophytum alone or with the three vegetal compounds together. The gene expression involved in inflammation, pain or catabolism was determined by RT-PCR. The release of the encoded proteins by these genes and of prostaglandin E2 (PGE2) were also assayed by ELISA.

Results
Proteomic analysis demonstrated that LPS induces the expression of numerous proteins involved in the OA process in human OA synovial cells. In particular, it stimulates inflammation through the production of pro-inflammatory cytokines (Interleukin-6, IL-6), catabolism through an increase of metalloproteases (MMP-1, MMP-3, MMP-13), and the production of pain-mediating neurotrophins (Nerve Growth Factor, NGF). These increases were observed in terms of mRNA levels and protein release. LPS also increases the amount of PGE2, another inflammation and pain mediator. At the doses tested, vegetal extracts had little effect: only curcumin slightly counteracted the effects of LPS on NGF and MMP-13 mRNA, and PGE2, IL-6 and MMP-13 release. In contrast, the combination of curcumin with bromelain and harpagophytum reversed lots of effects of LPS in human OA synovial cells. It significantly reduced the gene expression and/or the release of proteins involved in catabolism (MMP-3 and -13), inflammation (IL-6) and pain (PGE2 and NGF).

Conclusion
We have shown that the stimulation of human OA synovial cells with LPS can induce protein changes similar to inflamed OA synovial tissues. In addition, using this model, we demonstrated that the combination of three vegetal compounds, namely curcumin, bromelain and harpagophytum, have anti-inflammatory and anti-catabolic effects in synovial cells and may thus reduce OA progression and related pain.