bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening, cloning and expression patterns of phosphorus-related genes of Burkholderia multivorans WS-FJ9 at different phosphorus levels
Authors: Liu Yuqing , Wang Yahui , Kong Weiliang , Liu Wanhui , Xie Xingli , Wu Xiaoqin 
Published: January 2020

Abstract
As important plant growth promoting rhizobacteria, phosphate-solubilizing bacteria (PSB) fix nitrogen, dissolve potassium, promote growth, improve the soil micro-environment, and enhance soil fertility. A high-efficiency PSB strain from the pine tree rhizosphere, Burkholderia multivorans WS-FJ9, was screened in our laboratory. In this study, using a Bio Screener fully automatic microbial growth curve meter to determine the growth of the WS-FJ9 strain in phosphate-removing medium, the growth and mineral phosphate solubilization of WS-FJ9 were obtained by Mo-Sb colorimetry and organophosphate-degradation plate assays. Second-generation sequencing technology was used to obtain genomic information and analyze possible phosphorus decomposition genes. The related expression of these genes under different phosphorus levels was determined by quantitative real-time PCR. The results showed that WS-FJ9 had strong adaptability and capacity for mineral phosphate solubilization at low phosphorus levels, which is characterized by its low phosphorus induction and high phosphorus inhibition. And the amount of solubilized mineral phosphate could exceed 140 mg/L. The total length of the genome of WS-FJ9 was 7,497,552 bp after splicing, and the GC content was 67.37%. Eight phosphate-related genes were selected to determine their expression patterns at different phosphorus levels. Among them, AP-2, GspE and GspF were only related to organic phosphorus, HlyB was only related to inorganic phosphorus, and PhoR, PhoA, AP-1 and AP-3 were related to both. The WS-FJ9 strain utilizes multiple pathways for mineral phosphate solubilization, and the degradation processes of different phosphorus sources are interrelated and independent, indicating that WS-FJ9 strain can adapt to different phosphorus source environments and has good potential for future applications.
National mapping of soil-transmitted helminth and schistosome infections in Ethiopia
Authors: Leta Gemechu Tadesse , Mekete Kalkidan , Wuletaw Yonas , Gebretsadik Abeba , Sime Heven , Mekasha Sindew , Woyessa Adugna , Shafi Oumer , Vercruysse Jozef , Grimes Jack ET , Gardiner Iain , French Michael , Levecke Bruno , Drake Lesley , Harrison Wendy , Fenwick Alan 
Published: January 2020

Abstract
Background: The geographical distributions of both soil-transmitted helminths (STHs; Ascarislumbricoides, Trichuristrichiura, and the hookworms (Necatoramericanus and Ancylostomaduodenale) and schistosomes (SCH; Schistosomamansoni and S. haematobium) are pivotal to be able to effectively design and implement mass drug administration (MDA) programs. The objective of this mapping was to provide up-to-date data on the distribution of both STH and SCH for Ethiopia to inform the national control program.Methodology: Between 2013 and 2015, we assessed the distributions of STHs and SCH in a nationwide survey covering 153,238 school-aged children (aged five to 15 years), from 786woredas (districts), representing all nine Regional States and two City Administrations of Ethiopia. From these surveys, nationwide disease maps were developed which allow recommendations to be made on the implementation of MDA programs.Principal findings: The prevalence of any STH infection across the study population was 21.7%, with A. lumbricoides (12.8%) the most prevalent, followed by hookworms (7.5%) and T. trichiura (5.9%). The prevalence for any SCH was 3.8%, with S. mansoni (3.5%) the dominant and S. haematobium was less prevalent (0.3%).STHs were more prevalent in southwest Ethiopia, whereas SCH found mostly in the west and northeast of the country. The prevalence of moderate-to-heavy intensity infections was 2% for STHs and 1.6% for SCH. Based on the disease maps and on WHO guidance for STH, 279 woredas were classified as highly endemic and therefore qualify for treatment twice per year and 215 woredas were moderate endemic and qualify for treatment once per year. For SCH, 69 woredas were classified as highly endemic and qualify for treatment once per year and 153 woredas were moderate endemic and qualify for treatment every two years. Conclusions/Significance: the results confirm that Ethiopia is endemic for both STHs and SCH, posing a significant public health problem. Following the WHO recommendations on mass drug administration, 18 and 14 million school-aged children are in need of MDA for STHs and SCH respectively.
Refining sleep measurement using the Motionwatch8©: How many days of monitoring do we need to get reliable estimates of sleep quality for older adults with Mild Cognitive Impairment?
Authors: Falck Ryan S. , Barha Cindy K. , Chan Patrick C.Y. , Liu-Ambrose Teresa 
Published: January 2020

Abstract
BackgroundMild cognitive impairment (MCI) is a transition stage between healthy cognition and dementia, and is linked to poorer sleep. Objective, reliable, and low-burden field methods to measure older adult sleep are also currently needed. The MotionWatch8© (MW8) wrist-worn actigraph provides estimates of sleep with 14 days of observation; however, there may be underlying differences in the reliability of sleep estimates based on MCI status. We therefore investigated the number of MW8 monitoring days required to estimate sleep in older adults with MCI and without. MethodsOlder adults (55+ years; N=151) wore the MW8 for ≥14 days. The Montreal Cognitive Assessment was used to categorize participants with probable MCI (scores of <26/30) and participants without MCI (≥26/30). We calculated intra-class reliability coefficients for 1-, 7-, and 14-days of wear-time, and performed Spearman-Brown predictions to determine the number of monitoring days needed for an ICC=0.80.ResultsOlder adults with MCI were older (p<0.01), more likely to be male (p=0.03), and had shorter sleep duration (p<0.01). Spearman-Brown analyses indicated that the number of monitoring days needed for an ICC=0.80 in older adults with probable MCI was 7 days for sleep duration, 4 days for fragmentation, and 4 days for efficiency; adults without MCI required 4 days for duration, 6 days for fragmentation, and 3 days for efficiency. ConclusionsOur results indicate that while the reliability of MW8 estimates of sleep differs based on cognitive status, 7 days of MW8 monitoring provides reliable estimates of sleep for adults with MCI and those without.
Evaluation of Oxidant and Anti-Oxidant Activity in Rheumatoid Arthritis Patients and Their Effects on Rheumatoid Arthritis Disease Activity
Authors: Toosi Taraneh Dormohammadi , Dehghani Abbas , Rezaei Ramin , Asgardoon Mohammad Hossein , Mirmiranpour Hossein , Rostamian Abdolrahman , Movasseghi Safieh , Pezeshki Shaghayegh , Hashemi Payam , Esteghamati Alireza 
Published: January 2020

Abstract
BackgroundRheumatoid arthritis (RA) is the most common cause of systemic inflammatory arthritis which causes joint destruction. The pathogenesis of RA is not fully understood, but it seems imbalance between oxidant and antioxidant process, plays a significant role on it. As a result, suppression of these mechanisms would be helpful to subside inflammation and eventually control of the disease activity. The aim of this study was to evaluate the level of oxidant and antioxidant and their effects on disease activity in RA patients.MethodsIn the following case-control study, we evaluated the levels of Malondialdehyde (MDA) and oxidized Low-Density Lipoproteins (ox.LDL) as oxidative factors and Catalase (CAT), Glutathione Peroxide (GSH-Px) and Superoxide Dismutase (SOD) as antioxidants. Also tumor Necrosis Factor (TNF)-α, Interleukin (IL) 1β and IL6 were measured as inflammatory factors.Results43 RA patients and 43 healthy people were enrolled. Significant differences were found in the average levels of MDA, ox.LDL, CAT, GPX, SOD, TNFα, IL1beta and IL6 between two groups (p-value < 0.001), but we did not find any significant differences between two groups of patients based on DAS28 (p- value> 0.05).ConclusionThe results of our study showed that there were increased oxidative activities in RA patients in comparison to the control group which indicated the presence of inflammatory process causing cellular damage in the patients group. As a consequence, adding some antioxidant agents to RA treatment might have some advantages for the disease control. Based on our findings, it seems that the oxidative process did not have any effect on the disease severity. We also suggest further observational study to confirm the results.
Relationship between structural and functional changes in glaucomatous eyes: A multifocal electroretinogram study
Authors: Tanaka Hiroki , Ishida Kyoko , Ozawa Kenji , Sawada Akira , Mochizuki Kiyofumi , Yamamoto Tetsuya 
Published: January 2020

Abstract
Background: The association between the structure of the macular region and its function as measured by multifocal electroretinography (mfERG) and the mean thresholds (MT) of the visual field (VF) is not well-understood. Methods: The macular retinal nerve fiber layer (mRNFL) and the ganglion cell and inner plexiform layer (GCIPL) in six regions were measured by optical coherence tomography (OCT). For functional assessment, MT and mfERG scans with parameters of the second-order kernel responses within the central 5°, nasal to temporal amplitudes ratio (N/T), and the multifocal photopic negative response to B-wave ratio (mfPhNR/B) were measured. Forty-one glaucoma patients underwent OCT, mfERG, and MT measurement and 55 healthy subjects underwent mfERG. Results: The mfPhNR/B was significantly smaller ( P < 0.01) and the N/T was significantly larger ( P < 0.01) in glaucoma patients than in normal subjects. In glaucoma patients, the N/T is significantly correlated with the thickness of inferior and inferotemporal GCIPL ( r = -0.317 and -0.360, respectively) and MT of corresponding VF areas ( r = -0.330 and -0.334, respectively) (all P values < 0.05). The mfPhNR/B was significantly correlated with the thickness of mRNFL in the central area ( r = 0.365, P = 0.02) and with the MT of all corresponding VF areas ( r rages between 0.330 and 0.460, all P values < 0.04), except for the inferotemporal area. However, correlation was not observed between the N/T and the mfPhNR/B in any location. Conclusions: Significant differences exist between glaucoma and healthy participants in the N/T and mfPhNR/B. Correlations were observed between two mfERG parameters and OCT parameters or MT in glaucoma patients. Further research should seek to demonstrate whether the N/T and the mfPhNR/B should be applied in a complementary fashion.
Ripasudil alleviated the inflammation of RPE cells by targeting the miR-136-5p/ROCK/NLRP3 pathway
Authors: Gao Zhao , Li Qiang , Zhang Yunda , Li Haiyan , Gao Xiaohong , Yuan Zhigang 
Published: January 2020

Abstract
Introduction Inflammation of RPE cells lead to different kinds of eye diseases and affect the normal function of the retina. Furthermore, higher levels of ROCK1 and ROCK2 induced injury of endothelial cells and many inflammatory diseases of the eyes. Ripasudil which was used for the treatment of glaucoma was one kind of the inhibitor of ROCK1 and ROCK2. But whether the ripasudil could relieved the LPS induced inflammation damage of RPE cells was not clear.Material and methods We used the LPS to stimulate ARPE-19 cells which is the RPE cell line. After that, we detected the levels of ROCK1 and ROCK2 by western-blotting assay after the stimulation of LPS and treatment of ripasudil. Then luciferase reporter assays were used to confirm the targeted effect of miR-136-5p on ROCK1 and ROCK2. At last, the levels of NLRP3, ASC, caspase1, IL-1β and IL-18 were detected with the western-blotting after the knockdown of miR-136-5p.Results The levels of ROCK1, ROCK2 and miR-136-5p in ARPE-19 cells was promoted after the stimulation of LPS. After the treatment of ripasudil, the ROCK1, ROCK2 and miR-136-5p was suppressed. The miR-136-5p targeted and inhibited the expression of ROCK1 and ROCK2. Inflammation related proteins NLRP3, ASC, caspase1, IL-1β and IL-18 was inhibited after the treatment of ripasudil. However, the expression of these proteins was rescued after the knockdown of the miR-136-5p.Conclusion Ripasudil relieved the inflammatory injury of RPE cells by upregulating miR-136-5p and therefore inhibiting the expression of ROCK1, ROCK2, NLRP3, ASC, caspase1, IL-1β and IL-18.
Quality improvement education for medical students: a near-peer pilot study
Authors: McGeorge Elizabeth , Coughlan Charles , Fawcett Martha , Klaber Robert 
Published: January 2020

Abstract
Background Quality improvement (QI) is an essential component of modern clinical practice. Front-line professionals offer valuable perspectives on areas for improvement and are motivated to deliver change. In the UK, all junior doctors are expected to participate in QI in order to advance to the next stage of their training. However, UK undergraduates receive no standardized training in QI methodology. This is perpetuated within medical schools by a lack of teaching capacity and competing priorities, and may lead to tokenistic engagement with future QI projects. Methods We describe a near-peer teaching programme designed to introduce students to QI methodology. This programme was conceived and delivered in full by junior doctors and used existing resources to ensure high quality teaching content. 111 fifth-year medical students from the University of Cambridge were taught in interactive, participative workshops that encourage them to develop their own QI change ideas and projects. Core topics included the model for improvement, driver diagrams, stakeholder engagement, measurement for improvement and analysing and presenting data. Students completed surveys before and immediately after this intervention to assess their understanding of and confidence in utilizing QI methodology. Questionnaires were also completed by junior doctor tutors. Results Analysis of questionnaires completed before and immediately after the intervention revealed statistically significant improvements in students’ self-reported understanding of QI (p<0.05) and confidence in applying techniques to their own work (p<0.05). Students expressed a preference for QI teaching delivered by junior doctors, citing a relaxed learning environment and greater relevance to their stage of training. Tutors reported increased confidence in using QI techniques and a greater willingness to engage with QI in future. Conclusions In this single-centre study, near-peer teaching produced significant improvements in students’ self-reported understanding of QI and confidence in applying QI methodology. Near-peer teaching may constitute a sustainable means of teaching essential QI skills at undergraduate level. Future work must evaluate objective measures of student engagement with and competence in conducting QI.
Diagnostic biomarker candidates for pulpitis revealed by bioinformatics analysis of merged microarray gene expression datasets
Authors: Chen Ming , Zeng Junkai , Yang Yeqing , Wu Buling 
Published: January 2020

Abstract
Background Pulpitis is known as an inflammatory disease classified by the level of inflammation. The existed traditional methods of evaluating status of dental pulp tissue in clinical practice still have some shortages and limitations. Immediate and accurate diagnosis of pulpitis is essential to the choice of treatment. Through integrating different datasets from Gene Expression Omnibus (GEO) database, we analyzed the merged expression matrix of pulpitis, aiming to identified biological pathways and diagnostic biomarker of pulpitis.Methods By integrating two datasets (GSE77459 and GSE92681) in GEO database using sva and limma packages, differentially expressed genes (DEGs) of pulpitis were identified. Then DEGs were used to analyze biological pathways of dental pulp inflammation with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and the Gene Set Enrichment Analysis (GSEA). Protein–protein interaction (PPI) networks and modules were constructed to identify hub genes with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape.Results A total of 472 DEGs consisting of 396 upregulated and 76 downregulated genes were found in pulpitis tissue. DEGs in GO analysis were enriched in biological processes about inflammation and in KEGG pathway analysis were cytokine-cytokine receptor interaction, chemokine signaling pathway and NF-κB signaling pathway. GSEA results provided further functional annotations including complement system, IL6/JAK/STAT3 signaling pathway and inflammatory response pathways. According to the degrees of nodes in PPI network, 10 hub genes were obtained and 8 diagnostic biomarker candidates were screened, including PTPRC, CD86, CCL2, IL6, TLR8, MMP9, CXCL8 and ICAM1.
Evaluation of 24 protocols for the production of platelet-rich fibrin
Authors: Miron Richard J , Chai Jihua , Fujioka-Kobayashi Masako , Sculean Anton , Zhang Yufeng 
Published: January 2020

Abstract
Background The aim of this study was to evaluate 24 protocols for the production of platelet rich fibrin (PRF) produced via horizontal centrifugation to better understand cell separation following protocols at various times and speeds.Methods All protocols were compared utilizing a recent method to quantify cells in PRF in 1 mL sequential layers pipetted from the upper layer downwards until all 10 mL were harvested. In total, 960 complete blood counts (CBCs) were investigated. Both solid and liquid-based PRF protocols were investigated following 24 protocols involving 6 relative centrifugal force (RCF) values (100,200,400,700,1000 and 1200g) at 4 centrifugation times (3,5,8 and 12 minutes).Results In general, platelets could more easily accumulate in the upper 4 layers when compared to leukocytes owing to their lower cellular density. Protocol time seemed to have a greater impact on the final cell layer separation when compared to the effect of speed. Protocols of greater than 8 minutes at 400 g led to no leukocyte accumulation in the upper PRF layers (found specifically within the buffy coat). Protocols at or below 200 g were unable to effectively accumulate platelets/leukocytes. The optimal centrifugation speed and time for solid-PRF ranged between 400 -700 g for 8 minutes. It was noted that variability in patient baseline platelet/leukocyte/erythrocyte counts (hematocrit) significantly affected cell layer separation. This finding was more pronounced at lower centrifugation speeds.Conclusions Within the investigated ranges, a protocol of 700 g for 8 minutes presented the highest yield of platelets/leukocytes evenly distributed throughout the upper PRF layers.
Colorimetric LAMP Molecular Method for Immediate Detection of Three Periodontal Pathogens
Authors: Al-Hamdoni Sumaya A.S.M. , Al-Rawi Amera M.M. 
Published: January 2020

Abstract

Background and Purpose: For enhancing the efficiency of diagnostic tools and overcome drawbacks faced in diagnosis attempt, molecular methods have been developed aid accurate and rapid identification of bacterial species particularly those which are difficult to study with. The current study searched to find a more specific and rapid method serves researchers for the identification of periodontal pathogens and overcome disturbances encountered in study such anaerobic fastidious organisms. Methods and Results: Three periodontal pathogens, Porphyromonas gingivalis , Tannerella forsythia and Treponema denticola were characterized and identified by phenotypic features and Loop- Mediated Isothermal Amplification (LAMP) techniques which involved 4 sets of primers targeted to 16SrRNA genes and loop primers and the Colorimetric Master Mix containing Bst DNA polymerase and Phenol Red for the detection of amplicon formation. There was a variance in phenotypic characters of the isolates of the same species. LAMP, as a novel molecular technique was of usefulness value in identifying the target weather as extracted DNA or whole cells in a high specific and very rapid manner within 30 min. by visual reading of the results. Conclusion: It is strongly recommended the use of the novel LAMP method in researches work with periodontal pathogens as its advantages make it superior to other molecular techniques in respects of a higher specificity, rapidity, sensitivity and overcome DNA extraction step and special equipment in that it can be used at chair- side identification.
The effect of nicotinamide adenine dinucleotide phosphate oxidase 4 on migration and invasion of fibroblast-like synoviocytes in rheumatoid arthritis
Authors: Lee Ha-Reum , Yoo Su-Jin , Kim Jinhyun , Yoo In Seol , Park Chan Keol , Kang Seong Wook 
Published: January 2020

Abstract
Background: Reactive oxygen species (ROS) regulate the migration and invasion of fibroblast-like synoviocytes (FLS), which are key effector cells in rheumatoid arthritis (RA) pathogenesis. Nicotinamide adenine dinucleotide phosphate oxidase 4 (NOX4) induces ROS generation and consequently, enhances cell migration. Despite the important interrelationship between RA, FLS, and ROS, the effect of NOX4 on RA pathogenesis remains unclear. Methods: FLS isolated from RA (n=5) and osteoarthritis (OA, n=5) patients were stimulated with recombinant interleukin 17 (IL-17; 10 ng/ml) and tumor necrosis factor alpha (TNF-α; 10 ng/ml) for 1 h. Cell migration, invasion, adhesion molecule expression, vascular endothelial growth factor (VEGF) secretion, and ROS expression were examined. The mRNA and protein levels of NOX4 were analyzed by RT-qPCR and western blotting, respectively. The NOX4 inhibitor GLX351322 and NOX4 siRNA were used to inhibit NOX4 to probe the effect of NOX4 on these cellular processes. Results: Migration of RA FLS was increased 2.48-fold after stimulation with IL-17 and TNF-α, while no difference was observed for OA FLS. ROS expression increased in parallel with invasiveness of FLS following cytokine stimulation. When the expression of NOX was examined, NOX4 was significantly increased by 9.73-fold in RA FLS compared to unstimulated FLS. Following NOX4 inhibition, cytokine-induced vascular cell adhesion molecule 1 (VCAM1), VEGF, and migration and invasion capacity of RA FLS were markedly decreased to unstimulated levels. Conclusion: NOX4 is a key contributor to cytokine-enhanced migration and invasion via modulation of ROS, VCAM1, and VEGF in RA FLS.