bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol.
Authors: LEAL Catarina , Fontaine Florence , Aziz Aziz , Egas Conceiçao , Clement Christophe , Trotel-Aziz Patricia 
Published: January 2021

Abstract
Background: Bacillus subtilis strains have been widely studied for their numerous benefits in agriculture, including viticulture. Providing several assets, B. subtilis spp. are described as promising plant-protectors against many pathogens and as influencers to adaptations in a changing environment. This study reports the draft genome sequence of the beneficial Bacillus subtilis PTA-271, isolated from the rhizospheric soil of healthy Vitis vinifera cv. Chardonnay at Champagne Region in France, attempting to draw outlines of its full biocontrol capacity.Results: The PTA-271 genome has a size of 4,001,755 bp, with 43.78% of G + C content and 3,945 protein coding genes. The draft genome of PTA-271 putatively highlights a functional swarming motility system hypothesizing a colonizing capacity and a strong interacting capacity, strong survival capacities and a set of genes encoding for bioactive substances. Predicted bioactive compounds are known to: stimulate plant growth or defenses such as hormones and elicitors, influence beneficial microbiota, and counteract pathogen aggressiveness such as effectors and many kinds of detoxifying enzymes.Conclusions: Plurality of the putatively encoded biomolecules by Bacillus subtilis PTA-271 genome suggests environmentally robust biocontrol potential of PTA-271, protecting plants against a broad spectrum of pathogens.
The seal louse (Echinophthirius horridus) in the Dutch Wadden Sea: investigation of vector-borne pathogens
Authors: Hirzmann Jörg , Ebmer David , Contreras Guillermo J. Sánchez , Rubio-García Ana , Magdowski Gerd , Gärtner Ulrich , Taubert Anja , Hermosilla Carlos 
Published: January 2021

Abstract
Background: Belonging to the anopluran family Echinophthiriidae, Echinophthirius horridus, the seal louse, has been reported to parasitize a broad range of representatives of phocid seals. So far, only few studies focused on vector function of echinophthiriid lice and knowledge on their role in pathogen transmission is still scarce. The current study aims to investigate the possible vector role of E. horridus parasitizing seals in the Dutch Wadden Sea.Methods: E. horridus seal lice were collected from 54 harbour seals (Phoca vitulina) and one grey seal (Halichoerus grypus) during their rehabilitation period at the Sealcentre Pieterburen, the Netherlands. DNA was extracted from pooled seal lice of individual seals for molecular detection of the seal heartworm Acanthocheilonema spirocauda, the rickettsial intracellular bacterium Anaplasma phagocytophilum, and the cell wall-less bacteria Mycoplasma spp. using PCR assays.Results: Seal lice from 35% of the harbour seals (19/54) and from the grey seal proved positive for A. spirocauda. The seal heartworm was molecularly characterised and phylogenetically analysed (rDNA, cox1). A nested PCR was developed for the cox1 gene to detect A. spirocauda stages in seal lice. A. phagocytophilum and a Mycoplasma species previously identified from a patient with disseminated ‘seal finger’ mycoplasmosis were detected the first time in seal lice. Conclusions: Our findings support the potential vector role of seal lice in transmission of A. spirocauda, and reveal new insights into the spectrum of pathogens occurring in seal lice. Studies on vector competence of E. horridus, especially for bacterial pathogens, are essentially needed in the future as these pathogens might have detrimental effects on the health of seal populations. Further, studies on the vector role of different echinophthiriid species infecting a wide range of pinniped hosts should be conducted to extend the knowledge of vector borne pathogens in seal lice.
SNX10 and PTGDS are Associated with the Progression and Prognosis of Cervical Squamous Cell Carcinoma
Authors: Jiang Pinping , Cao Ying , Gao Feng , Sun Wei , Liu Jinhui , Ma Ziyan , Xie Manxin , Fu Shilong 
Published: January 2021

Abstract
Background: Cervical cancer (CC) is the primary cause of death in women. This study sought to investigate the potential mechanism and prognostic genes of CC. Methods: We downloaded four gene expression profiles from GEO. The RRA method was used to integrate and screen differentially expressed genes (DEGs) between CC and normal samples. Functional analysis was performed by clusterprofiler. We built PPI network by Search Tool for the Retrieval of Interacting Genes Database (STRING) and selected hub modules via Molecular COmplex Detection (MCODE). CMap database was used to find molecules with therapeutic potential for CC. The hub genes were validated in GEO datasets, Gene Expession Profiling Interactive Analysis (GEPIA), immunohistochemistry, Cox regression analysis, TCGA methylation analysis and ONCOMINE were carried out. ROC curve analysis and GSEA were also performed to describe the prognostic significance of hub genes. Results: Functional analysis revealed that 147 DEGs were significantly enriched in binding, cell proliferation, transcriptional activity and cell cycle regulation. PPI network screened 30 hub genes, with CDK1 having the strongest connectivity with CC. Cmap showed that apigenin, thioguanine and trichostatin A might be used to treat CC(P<0.05). Eight genes (APOD, CXCL8, MMP1, MMP3, PLOD2, PTGDS, SNX10 and SPP1) were screened out through GEPIA. Of them, only PTGDS and SNX10 had not appeared in previous studies about CC. The validation in GEO showed that PTGDS showed low expression in tumor tissues while SNX10 showed high expression in tumor tissues. Their expression profiles were consistent with the results in immunohistochemistry. ROC curve analysis indicated that the model had a good diagnostic efficiency(AUC=0.738). GSEA showed that the two genes were associated with the chemokine signaling pathway(P<0.05). TCGA methylation analysis showed that patients with lowly-expressed and highly-methylated PTGDS had a worse prognosis than those with highly-expressed and lowly-methylated PTGDS (p=0.037). Cox regression analysis showed that SNX10 and PTGDS were independent prognostic indicators for OS among CC patients(P=0.007 and 0.003). Conclusions: PTGDS and SNX10 showed abnormal expression and methylation in CC. Both genes might have high prognostic value of CC patients.
Morphological study of the vastus medialis oblique in recurrent patellar dislocation based on magnetic resonance images
Authors: Shu Lei , Yang Xu , He Hangyuan , Chen Biao , Chen Liaobin , Ni Qubo 
Published: January 2021

Abstract
Background: To investigate the morphological parameters of the vastus medialis obliquus (VMO) muscle and delineate its importance in the maintenance of patellofemoral joint stability.Methods: The magnetic resonance imaging (MRI) data of seventy-five knees (fifty-four patients) with recurrent lateral patella dislocation (LPD) and seventy-five knees (seventy patients) without recurrent LPD were retrospectively analysed. Five morphological parameters related to the VMO (elevation in the sagittal plane and coronal plane, craniocaudal extent, muscle-fibre angulation, cross-sectional area ratio) and two patella tilt parameters (patella tilt angle, bisect offset ratio) were measured in MR images. The independent-samples t test or chi-square test was used for statistical comparisons.Results: The mean ages of the patients in the recurrent LPD group and control group were 22.1 ± 9.9 years and 24.0 ± 6.5 years, respectively. Eighteen out of seventy-five (24%) patients MRI showed VMO injuries. Compared with the control group, the patients with recurrent LPD showed significantly higher sagittal VMO elevation (10.4 ± 2.3 mm vs 4.1 ± 1.9 mm), coronal VMO elevation (15.9 ± 5.7 mm vs 3.9 ± 3.7 mm), muscle-fibre angulation (35.4 ± 8.0° vs 27.9 ± 6.3°), patella tilt angle (25.9 ± 10.7° vs 9.1 ± 5.2°), and bisect offset ratio values (0.9 ± 0.3 vs 0.5 ± 0.1) and significantly lower craniocaudal extent (13.7 ± 5.3 mm vs 16.7 ± 5.1 mm) and cross-sectional area ratio values (0.05 ± 0.02 vs 0.07 ± 0.02).Conclusions: The results showed that abnormalities in the VMO and patella tilt were clearly present in recurrent LPD patients compared with normal people.
Differences on Pyrexia Related Immune Responses between SARS-CoV-2 and Influenza-A-infected Children: A Retrospective Study
Authors: Kou Shanglong , Zhan Senlin , Li Xiaohe , Zhang Mingxia , Deng Guofang , Pan Yanchao , Yuan Jing 
Published: January 2021

Abstract
Background: The ongoing pandemic of COVID‐19 has led to an unprecedented global crisis with problems of fragmentation in healthcare services in many severely affected countries. A key issue is distinguishing the clinical manifestations of COVID-19 from other respiratory infectious disease, especially in children and teens.Methods: To provide precise and comprehensive information on SARS-CoV-2 infected children, a total 62 hospitalized patients, aged from 1 to 14 years old and confirmed with the infection of either SARS-CoV-2 or influenza A virus, were enrolled from September 2019 to February 2020. The epidemiological, clinical and laboratory characteristics, as well as the outcomes of these pediatric patients were collected, followed by comparisons and regression analysis on clinical features and hematological parameters among the COVID-19 patients and the flu patients.Results: We reported that SARS-CoV-2 infected children showed less fever (43.33% vs 100%, p<0.001) with mild elevation of the body temperature (p<0.001), as well as attenuated inflammatory responses in comparison with patients with influenza A infection. We further showed the significant correlations between initial body temperature and multiple immune parameters (white blood cell counts and inflammatory markers) among SARS-CoV-2 infected children. Conclusions: Children with SARS-CoV-2 infection were more likely to have mild symptoms and relatively slow progression with a hypo-inflammatory response. Furthermore, the correlation results suggested that distinct immune responses were involved during SARS-CoV-2 infection.
Dietary Intakes of Total Polyphenol and Its Subclasses in Association with the Incidence of Chronic Kidney Diseases: A Prospective Population-based Cohort Study
Authors: Mirmiran Parvin , Yuzbashian Emad , Rahbarinejad Pegah , Asghari Golaleh , Azizi Fereidoun 
Published: January 2021

Abstract
Background: As chronic kidney disease (CKD) is amongst the current global health challenges, this study is aiming to evaluate the long-term intake of total polyphenol and its subclasses in association with CKD incidence. Methods: For the purpose of this study, a sample of 3021 Iranian adults (47% men, aged 20-79 years) with no CKD diagnosis at baseline, were selected from the Tehran Lipid and Glucose Study population. The total intake of polyphenol and its major subclasses were assessed by a validated food frequency questionnaire and categorized as flavonoids, phenolic acids, stilbenes, and lignans. Although the morphological abnormalities of the kidneys or 3-month persistent urinalysis can distinctively define CKD, the glomerular filtration rate (eGFR) reduction is accepted as a more precise index of renal function. Therefore, eGFR <60 mL/min/1.73m2 was the exclusive index of CKD diagnosis in the current study. The eGFR was calculated by the Modification of Diet in Renal Disease Study equation. Cox-regression analysis was used to assess the hazard ratio and 95% confidence intervals of CKD in quartiles of the total polyphenols.Results: In this study, 355 CKD cases over 11,058.464 person-years was reported. The median (IQR) age of participants was 36 years (27-46) at baseline. Moderate intake of lignans (≤6.8 mg) was negatively associated with the incidence of CKD in the adjusted model. No significant associations were detected between higher amounts of lignin and total polyphenols (HR: 0.97, 95% CI 0.67-1.40) and CKD incidence. Conclusions: Based on the current findings, moderate intake of lignin possess CKD-protective properties by approximately 32%. No independent associations were observed between higher amounts of lignins and CKD incidence.
An exploratory study to estimate cost-effectiveness threshold value for life saving treatments in western Iran
Authors: Moradi Najmeh , Woldemichael Abraha , Malekian Parisa , Rotavandi Delnia Moradi , Rezaei Satar 
Published: January 2021

Abstract
Background: Cost-effectiveness analysis provides a crucial means for evidence-informed decision-making on resource allocation. This study aims to elicit individuals' willingness to pay (WTP) for one additional quality-adjusted life-year (QALY) gained from life-saving treatment and associated factors in Kermanshah city, western Iran.Methods: We conducted a cross-sectional study on a total of 847 adults aged 18 years and above to elicit their WTP for one additional QALY gained by oneself and a family member using a hypothetical life-saving treatment. We used a multistage sampling technique to select the samples, and the Iranian version of EQ-5D-3L, and visual analogue scale (VAS) measures to obtain the participants’ health utility value. The Tobit regression model was used to identify the factors affecting WTP per QALY values.Results: The mean WTP value and standard deviation (SD) was US$ 862 (3,224) for the respondents. The mean utility values using EQ-5D-3L and VAS methods for respondents were 0.779 and 0.800, respectively. Besides, the WTP for the additional QALY gained by the individual participants using the EQ-5D-3L and VAS methods were respectively US$ 1,202 and US$ 1,101, while the estimated value of the family members was US$ 1,355 (SD= 3,993). The Tobit regression models indicated that monthly income, education level, sex, and birthplace were statistically significantly associated (p < 0.05) with both the WTP for the extra QALY values using the EQ-5D-3L and the VAS methods. Educational level and monthly income also showed statistically significant relationships with the WTP for the additional QALY gained by the family members (p < 0.05). Conclusion: Our findings indicated that the participants' WTP value of the additional QALY gained from the hypothetical life-saving treatment was in the range of 0.20 to 0.24 of the gross domestic product (GDP) per capita of Iran. This value is far lower than the World Health Organization (WHO) recommended CE threshold value of one. This wide gap reflects the challenges the health system is facing and requires further research for defining the most appropriate CE threshold at the local level.
Nanomaterials induce different levels of oxidative stress, depending on the used model system: Comparison of in vitro and in vivo effects
Authors: Karkossa Isabel , Bannuscher Anne , Hellack Bryan , Wohlleben Wendel , Laloy Julie , Stan Miruna S. , Dinischiotu Anca , Wiemann Martin , Luch Andreas , Haase Andrea , von Bergen Martin , Schubert Kristin 
Published: January 2021

Abstract
Background: The immense variety and constant development of nanomaterials (NMs) raise the demand for a facilitated risk assessment, for which knowledge on NMs mode of actions (MoAs) is required. For this purpose, a comprehensive data basis is of paramountcy that can be obtained using omics. Furthermore, the establishment of suitable in vitro test systems is indispensable to follow the 3R concept and to master the high number of NMs. In the present study, we aimed at comparing NM effects in vitro and in vivo using a multi-omics approach. We applied an integrated data evaluation strategy based on proteomics and metabolomics to four silica NMs and one titanium dioxide-based NM. For in vitro investigations, rat alveolar epithelial cells (RLE-6TN) and rat alveolar macrophages (NR8383) were treated with different doses of NMs, and the results were compared to effects on rat lungs after short-term inhalations and instillations at varying doses with and without a recovery period.Results: Since the production of reactive oxygen species (ROS) is described to be a critical biological effect of NMs, and enrichment analyses confirmed oxidative stress as a significant effect upon NM treatment in vitro in the present study, we focused on different levels of oxidative stress. Thus, we found opposite changes for proteins and metabolites that are related to the production of reduced glutathione in alveolar epithelial cells and alveolar macrophages, illustrating that NMs MoAs depend on the used model system. Interestingly, in vivo, pathways related to inflammation were affected to a greater extent than oxidative stress responses. Hence, the assignment of the observed effects to the levels of oxidative stress was different in vitro and in vivo as well. However, the overall classification of “active” and “passive” NMs was consistent in vitro and in vivo.Conclusions: The consistent classification indicates both tested cell lines to be suitable for NM toxicity assessment even though the induced levels of oxidative stress strongly depend on the used model systems. Thus, the here presented results highlight that model systems need to be carefully revised to decipher the extent to which they can replace in vivo testing.
What is the impact of the Rashomon Approach in primary care education? : An educational case report of Implementing Dialogue and Improvisation into Medical Education
Authors: Takamura Akiteru , Imafuku Rintaro 
Published: January 2021

Abstract
Background:The excessive sub-divided or concrete pre-determined objectives found in the technological approach in contemporary medical education curricula may hinder the students’ spontaneous learning about diverse needs and values in care. However, medical professionals must learn the diversity for care or a variety of social factors of the patients influencing decision making in daily practice.Methods:We introduced a new method of curriculum development called the Rashomon approach. For testing the Rashomon approach, educational activities to teach the diversity in primary care were developed in four modules: 1) explication of the competency without specifying sub-objectives; 2) dialogue among multiple professional students; 3) visits and interviews of the patients; 4) dialogue with teachers' improvisation. The students’ outcomes and responses were quantitatively and qualitatively analyzed.Results:A total of 135 medical students joined this study in 2017. The descriptive data suggested that the key concepts of diversity in primary care were fully recognized and that the pre-determined general goals were achieved. Scores on the understanding of social factors in medicine, respect for other professionals, professional identity, and satisfaction with the course were very high.Conclusion:Instead of the technological approach, the Rashomon approach, in which only a general goal guides educational activities was used in this research. Improvisation and dialogue fit the approach and were potentially effective activities to learn the multifaceted practice of medicine. In an era of competency-based education, the Rashomon approach could be a very useful framework in primary care education.
The assessment of general movements in term and late-preterm infants diagnosed with neonatal encephalopathy, as a predictive tool of cerebral palsy by two years of age - A scoping review.
Authors: Seesahai Judy , Rotter Thomas , Luther Maureen , Maddalena Patricia , Church Paige Terrien , Asztalos Elizabeth , Banihani Rudaina 
Published: January 2021

Abstract
BACKGROUND The General Movements Assessment is a non-invasive and cost-effective tool with demonstrated reliability for identifying infants at risk for cerebral palsy. Early detection of cerebral palsy allows for implementation of early intervention, and is associated with better functional outcomes. No review to date has summarized the utility of the General Movements Assessment to predict cerebral palsy in term and late-preterm infants diagnosed with neonatal encephalopathy.METHODS We conducted a scoping review involving infants born greater than or equal to 34 weeks gestational age to identify all available evidence and delineate research gaps. We extracted data on sensitivity, specificity, positive and negative predictive value and described the strengths and limitations of the results. We searched five databases (MEDLINE, Embase, PsychINFO, Scopus and CINAHL). Two reviewers conducted all screening and data extraction independently. The articles were categorized according to key findings and a critical appraisal performed.RESULTS From the electronic database search, only two studies, case series, met all of the inclusion criteria. The total number of participants were 60. Neither of the final eligible studies included late-preterm neonates. Both studies reported on sensitivity, specificity, positive predictive and negative predictive value. The newer study reported that in the time period between term and 4-5 months post-term, that any cramped synchronized movements in this time period had results of 100% sensitivity and variable results for specificity, positive predictive value and negative predictive value. Neither of the studies had infants that received therapeutic hypothermia for Neonatal Encephalopathy.CONCLUSIONS The finding of cramped synchronized General Movements is a strong predictor for the diagnosis of cerebral palsy by two years of age in the term population with neonatal encephalopathy. The deficit of high quality research limits the applicability and so the general movements assessment should not be used in isolation when assessing this population.Systematic review registrationTitle registration with Joanna Briggs Institute. URL: http://joannabriggswebdev.org/research/registered_titles.aspx
The semi-dwarfing gene Rht-dp from dwarf Polish wheat (Triticum polonicum L.) is the “Green Revolution” gene Rht-B1b
Authors: Chai Songyue , Yao Qin , Zhang Xu , Xiao Xue , Fan Xing , Zeng Jian , Sha Lina , Kang Houyang , Zhang Haiqin , Li Jun , Zhou Yonghong , Wang Yi 
Published: January 2021

Abstract
Background: The wheat dwarfing gene increases lodging resistance, the grain number per spike and harvest index. Dwarf Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, DPW), initially collected from Tulufan, Xinjiang, China, carries a semi-dwarfing gene Rht-dp on chromosome 4BS. However, Rht-dp and its dwarfing mechanism are unknown.Results: Homologous cloning and mapping revealed that Rht-dp is the ‘Green Revolution’ gene Rht-B1b. A haplotype analysis in 59 tetraploid wheat accessions showed that Rht-B1b was only present in T. polonicum. Transcriptomic analysis of two pairs of near-isogenic lines (NILs) of DPW×Tall Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, TPW) revealed 41 differentially expressed genes (DEGs) as potential dwarfism-related genes. Among them, 28 functionally annotated DEGs were classed into five sub-groups: hormone-related signalling transduction genes, transcription factor genes, cell wall structure-related genes, reactive oxygen-related genes, and nitrogen regulation-related genes. Conclusions: These results indicated that Rht-dp is Rht-B1b, which regulates pathways related to hormones, reactive oxygen species, and nitrogen assimilation to modify the cell wall structure, and then limits cell wall loosening and inhibits cell elongation, thereby causing dwarfism in DPW.