bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comprehensive Performance Analysis of Apache Hadoop and Apache Spark for Large Scale Data Sets Using HiBench
Authors: Ahmed Nasim , Barczak Andre L. C. , Susnjak Teo , Rashid Mohammad 
Published: August 2020

Abstract
In recent times Big Data analytics has got tremendous attention and it involves storing, processing, and analysing large scale datasets. The advent of distributed computing frameworks such as Hadoop and Spark offers an efficient solution to analyse vast amounts of data. Due to the availability of an application program ming interface (API) and its performance, Spark become very popular, even more popular than the MapReduce framework. Both these frameworks have more than 150 parameters and the combination of these parameters have a huge impact on cluster performance. The system default parameters help the system administrator to deploy their system applications without much effort, and they can measure their specific cluster performance with factory-set parameters. However, an open question remains: can new parameter selection improve cluster performance? In this regard, our study investigates the most impacting parameters such as input splits and shuffling, in order to compare the performance between Hadoop and Spark, using a specific cluster implemented in our department. We used a trial-and-error approach for tuning these parameters based on a large number of experiments. In order to evaluate the frameworks comparison and analysis, we select two work- loads: WordCount and TeraSort. The performance metrics are carried out based on three criteria, namely execution time, throughput, and speedup. Our experimental results revealed that both system performances heavily depends on input data size and correct parameter selection. The analysis results found, unsurprisingly, that Spark has better performance as compared to Hadoop, achieving up to 2 times speedup in WordCount workload and up to 14 times in TeraSort workloads when default parameters are replaced. Finally, we conclude that the system performance depends on different parameters configuration alternatives, and they depend on the data size.
Circadian Clock Protein PERIOD2 Suppresses the PI3K/Akt Pathway and Promotes Cisplatin Sensitivity in Ovarian Cancer
Authors: Wang Zhaoxia , Li Fengyan , Wei Meiyan , Zhang Sanyuan , Wang Tong 
Published: August 2020

Abstract
Background Circadian clock protein PERIOD2 (PER2) acts as a tumor suppressor in cancer; however, little is known about its involvement in chemosensitivity. Methods This study aimed to investigate the role and underlying mechanisms of PER2 in ovarian cancer sensitivity to cisplatin. Overexpression and knockdown of PER2 were performed to explore its role in ovarian cancer cell sensitivity to cisplatin both in vitro and in vivo. The protein levels of PI3K, AKT, caspase 3, E-cadherin, and other drug resistance-related molecules were determined in parental SKOV3 and SKOV3/DDP cells as well as in xenograft tumor tissues. Results Compared with parental cells, SKOV3/DDP cells had dramatically decreased PER2 expression, possibly due to hypermethylation in the PER2 promoter. PER2 overexpression significantly inhibited proliferation while promoting cisplatin-induced apoptosis in SKOV3 and SKOV3/DDP cells. In agreement, PER2-overexpressing SKOV3/DPP cells yielded significantly reduced tumor mass in cisplatin-treated mice compared with control cells. Mechanistically, PER2 overexpression remarkably reduced the protein amounts of PI3K, AKT, and MDR1, while increasing those of caspase 3 and E-cadherin in tumor tissues. Knockdown of PER2 exhibited opposite effects. PER2 overexpression also reduced the serum levels of TNF-α and IL-6 in tumor-bearing mice before the initiation of cisplatin treatment. Conclusion This study suggests that loss of PER2 contributes to cisplatin resistance in SKOV3 cells, possibly by activating the PI3K/AKT pathway and EMT, inhibiting apoptosis, and promoting drug efflux and inflammatory responses. Overexpression of PER2 could reverse these alterations and sensitize both parental SKOV3 and SKOV3/DDP cells to cisplatin.
Evaluation of the combined antibiotics exposure using the simulator of human intestinal microbial ecosystem (SHIME)
Authors: Liu Lei , Qi Hongmei , Suo Pengcheng , Lin Huai , Wang Siyi , Zuo Xiaojun 
Published: August 2020

Abstract
Background: Antibiotics are emerging toxic contaminant that have potential public health risk worldwide, which also would cause human intestinal microbial disorder and develop multiple human diseases. However, to date, the combination effects of antibiotics on human intestinal microbiota dysbiosis and related health risk are not fully understood. Moreover, there is limited information on using probiotics or synbiotics for restoration of intestinal microbiome affected by antibiotics. Therefore, this study evaluated the in vitro ability of combined effects of amoxicillin (Amx) and gentamycin (Gen), and the restoration effects of probiotics or synbiotics on ARGs as well as human disease-related pathways in the simulated human gut.Results: This study indicated that the combination exposure of Amx and Gen was confirmed to promote the increase of most ARGs and the disease-related pathways, which may be better restored by probiotics treatment. The results of the alpha diversity of the combined antibiotics exposure or the recovery microbial community showed no difference from the control. However, the beta diversity results indicated their differences, and the ascending colon sample recovered better under natural condition while the descending colon sample recovered better after probiotics treatment. Combination effects on the genetic level might attribute to microbiota shift, which were explained well by the phenomenon that Escherichia/Shigella was positively associated with the ARGs, and Klebsiella and Escherichia/Shigella were positively related to the human disease-related pathways.Conclusion: These results might be valuable to direct the future work and opened up new perspectives to address the direct effects of combine antibiotics on the intestinal microbiota and find a promising strategy to restore the antibiotics associated dysbiosis of gut microbiota.
Evaluation of Clinical Practice Settings for Baccalaureate Nursing Students’ Development of Clinical Judgment
Authors: Galante Christine 
Published: August 2020

Abstract
Background: Recipients of health care in the 21st century demand excellent patient-centered care and outcomes. Leaders of health care organizations, as well as political and national organizations, have focused their attention to the readiness of newly graduated baccalaureate of science in nursing prepared nurses to care for patients. Bridging the gap from nursing science theory to professional practice remains a challenge for nursing programs. The purpose of this study was to evaluate the impact of the clinical learning practice settings on the individual student’s development of clinical judgment skills. Methods: This quantitative comparative pilot study evaluated the unlicensed BSN student’s ability to demonstrate safe and effective patient care before and after exposure to a clinical learning setting. This project involved applying a progressive simulation experience with a quantitative pretest (prior to clinical exposure) and posttest (after clinical exposure) to determine the impact of two nursing clinical learning models, a traditional clinical model and a dedicated education model, on individual students’ development of clinical judgment. Data was analyzed using SPSS version 24. Results: Students in the dedicated education clinical learning model demonstrated statistically significant change in the pre- and post-test scores improvement in their clinical judgment competency. Conclusions: Although both clinical models provided evidence in support of student development of the professional competency of clinical judgment, there is a need to continue to evaluate the long-term impact of this model on student learning outcomes.
The Molecular Mechanism of Targeting the NF-κB Signaling Pathway to Modulate Mycoplasma Ovipneumoniae Infection in Sheep Based on Transcriptome Sequencing
Authors: Zhu Mengting , Liang Yanping , Wu Pei , Nan Ying , Zhang Hongmei , Zhao Zongsheng 
Published: August 2020

Abstract
Background: MicroRNAs (miRNAs) play a key role in Mannan-binding lectin (MBL)-mediated resistance to Mycoplasma ovipneumoniae (MO) pneumonia (MP), by regulating the translation of mRNAs of target genes, thereby regulating the immune response. Sheep with different MBL genotypes have different plasma MBL levels, and show varied resistance to MP. Results: Using previously constructed high-throughput sequencing and transcriptome databases, miRNA-mRNA joint analysis showed that miR-509-5p is differentially expressed. miR-509-5p target genes were predicted using bioinformatic analysis, among which TRAF6 was selected. A TRAF6 dual luciferase reporter vector was co-transfected into 293T cells and sheep respiratory mucosal epithelial cells to detect and analyze changes in luciferase activity. qRT-PCR was used to analyze the effect of miR-509-5p on the expression and regulation of TRAF6 and other genes related to the NF-κB signaling pathway. miR-509-5p mimic and miR-509-5p mimic NC were transfected into susceptible sheep respiratory mucosal epithelial cells, for MO challenge infection experiments. The expression levels of cytokines, TRAF6 and other related genes in the NF-κB pathway were analyzed by ELISA and qRT-PCR. Conclusion: The results proved that miR-509-5p targets TRAF6 to affect the expression of downstream genes and cytokines, which negatively regulates the NF-κB pathway, thereby affecting the inflammatory response.
Wandering minds, sleepy brains: lapses of attention and local sleep in wakefulness
Authors: Andrillon Thomas , Burns Angus , Mackay Teigane , Windt Jennifer , Tsuchiya Naotsugu 
Published: August 2020

Abstract
Attentional lapses are ubiquitous and can negatively impact performance. They correlate with mind wandering, or thoughts that are unrelated to ongoing tasks and environmental demands. In other cases, the stream of consciousness itself comes to a halt and the mind goes blank. What happens in the brain that leads to these mental states? To understand the neural mechanisms underlying attentional lapses, we cross-analyzed the behavior, subjective experience and neural activity of healthy participants performing a task. Random interruptions prompted participants to indicate whether they were task-focused, mind-wandering or mind-blanking. High-density electroencephalography revealed the occurrence of spatially and temporally localized sleep-like patterns of neural activity. This “local sleep” accompanied behavioral markers of lapses and preceded reports of mind wandering and mind blanking. Furthermore, the location of local sleep distinguished sluggish versus impulsive behaviors, mind wandering versus mind blanking. Despite contrasting cognitive profiles, attentional lapses could share a common physiological origin: the appearance of local islets of sleep within the awake brain.
Mesenchymal stem cell-derived exosome miR-21-3p prevents renal fibrosis
Authors: Li Zongying , Cao Shuyi 
Published: August 2020

Abstract
Background: Renal fibrosis is the pathological result of excessive deposition of extracellular matrix (ECM) in the process of chronic kidney disease, but its mechanism is not clear. Mesenchymal stem cells (MSCs) exerts its therapeutic effect mainly through paracrine effects, such as exosome, to change the cellular microenvironment. Here, we explore the function of exosome derived MSCs in renal fibrosis.Methods: UUO model was constructed to simulate renal fibrosis in mice. Heat map and RT-PCR were used to explore the differential expression of miRNAs. RT-PCR and western blot were performed to detect the expression levels of fibrosis-associated genes and proteins in vivo and vitro. Transmission electron microscope and particle size detection were used to confirm the exosome construct. Then we forced expression of miR-21-3p in MSCs and isolated the exosomes. Then the fibrosis-associated genes and proteins were explored after exosomes injection.Results: In this study, we observed that exogenous miR-21-3p, interacted with smad2, the downstream target of miR-21-3p, which prevented renal fibrosis in UUO mice, and alleviate fibrosis in TGF-β1-induced renal tubular epithelium cells (HK-2). The extractive exosome-miR-21-3p treatment blocked renal fibrosis in UUO mice and alleviated fibrosis in TGF-β1-induced HK-2 cells and renal fibrosis mice. Conclusion: Taken together, Overexpression of miR-21-3p prevented CKD-induced renal fibrosis via exosome-mediated miR-21-3p transfer. These results suggest possible therapeutic strategies for using exosome delivery of miR-21-3p to treat complications of CKD.
Population Genetic Analysis of Plasmodium Falciparum Circumsporozoite Protein in Two Distinct Ecological Regions in Ghana
Authors: Amegashie Elikplim A , Amenga-Etego Lucas , Adobor Courage , Ogoti Peter , Mbogo Kevin , Amambua-Ngwa Alfred , Ghansah Anita 
Published: August 2020

Abstract
BackgroundExtensive genetic diversity in the Plasmodium falciparum circumsporozoite protein (PfCSP) is a major contributing factor to the moderate efficacy of the RTS,S/ASO1 vaccine. Understanding the extent and dynamics of PfCSP genetic diversity in different transmission settings will help to interpret the results of current RTS,S efficacy and Phase IV implementation trials conducted within and between populations in malaria endemic areas such as Ghana. MethodsPfcsp sequences were retrieved from Illumina generated paired-end short-read sequences of 101 and 131 malaria samples from children aged 6-59 months with clinical malaria presenting at health facilities in Cape Coast (on the coastal belt) and Navrongo (Guinea savannah region) respectively in Ghana. The sequences were mapped to the 3D7 reference strain genome to yield high-quality genome-wide coding sequence data. Following data filtering and quality checks to remove missing data, 220 sequences were retained and analyzed for allele frequency spectrum, genetic diversity both within host and between the populations and signatures of selection. Population genetics tools were used to determine the extent and dynamics of Pfcsp diversity in P. falciparum from the two geographically distinct locations in Ghana. ResultsPfcsp was extensively diverse at the two sites with higher transmission site, Navrongo, recording both higher within host and population level diversity. The vaccine strain C-terminal epitope of Pfcsp was found in only 5.9% and 45.7% of the Navrongo and Cape Coast sequences respectively. Amino acid variations ranging between 1 and 6 were observed in the TH2R and TH3R epitope regions of the PfCSP. Tajima’s D was negatively skewed especially for the population from Cape Coast given expected historical population expansion. On the contrary, positive Tajima’s D was observed for the Navrongo P. falciparum population, consistent with balancing selection acting on the immuno-dominant TH2R and TH3R vaccine epitopes. ConclusionThe low frequencies of Pfcsp vaccine haplotype in the populations analyzed calls for additional molecular and immuno-epidemiological studies with temporal and wider geographic sampling in endemic populations targeted for RTS,S application. These results have implications on the efficacy of the vaccine in Ghana and will inform the choice of alleles to include in future multivalent or chimeric vaccines.
Self-perceived Preparedness to Prescribe Antibiotics Among Swiss Medical Students: Results from a Cross-sectional Survey in four Swiss Universities in 2015.
Authors: Ranzani Alice , Catho Gaud , Pulcini Céline , Dyar Oliver J. , Huttner Benedikt D. 
Published: August 2020

Abstract
BackgroundPrevious studies have highlighted that medical students do not feel well prepared to prescribe antimicrobials. The ESCMID Study Group for Antimicrobial stewardshiP (ESGAP) conducted a survey among European medical students to assess self-reported preparedness about prudent antibiotic use and the perceived lack of education. The aim of the present study was to specifically focus on the perceptions of Swiss medical students. MethodsA cross-sectional web-based survey was conducted in 2015 by ESGAP involving sixth-year medical students from Switzerland. The survey investigated self-reported preparedness on diagnosis and treatment of infections, availability and perceived usefulness of different teaching methods and the perceived need for further education on antibiotic use. “Preparedness scores” were created by calculating the percentage of students who felt sufficiently prepared on each topic. ResultsWe received responses from 137 medical students from 4 medical schools (Bern, Geneva, Lausanne and Zurich). The overall estimated response rate was 19%. Overall, 62% of Swiss students reported needing more education on antibiotics or at least on their prudent use. Teaching methods perceived as more useful were discussion of clinical cases (80.2%), clinical rotation in infectious diseases (77.0%) and small group teaching (75.0%), but the latter 2 were reported as unavailable for nearly half of the students (36.5% and 47.5%, respectively). Almost all of the students felt sufficiently prepared to recognize clinical signs of infection (99.3%), to interpret inflammation markers (94.9%) and to have sufficient knowledge of consequences of antibiotic misuse (95.5%). Less than half of them felt prepared to select the right empirical treatment without using guidelines (33.8%), to identify the need for combination therapy (39.7%) or to select the shortest adequate treatment duration (39.3%). ConclusionsMost Swiss final year medical students feel they need more education on antibiotics. Some of the teaching methods perceived as more useful by students seem still insufficiently available in Swiss medical schools. Active and interprofessional teaching activities can be a first step towards more effective education on prudent antibiotic use.
GsLTP, a Non-Specific Lipid Transfer Protein from Glycine soja, Enhances Drought and Salt Stress Tolerance in Transgenic Tobacco
Authors: Fan Jinping , Liu Jingshuang , Cao Lei , Wang Jiayue , Meng Qingxue , Che Daidi 
Published: August 2020

Abstract
Background

Lipid transfer proteins (LTPs) mainly exist in plant cell walls where they make an important impact in the transport of diverse lipophilic compounds. Although the functions of several LTPS in different plant species have been identified, little is known about the biochemical and enzymatic activities of LTP family members in soybeans.
Results

Herein, GsLTP was identified from Glycine soja using soybean gene microarray expression and screened in a salt stress expressed sequence tag (EST) library. The 369 bp open reading frame (ORF) encodes a protein of 122 amino acids, and the cDNA sequence shares similarity with LTP genes in other plants such as soybean (93%) and Vigna (72%). The function of the gene was characterized in transgenic tobacco. Various physiological characteristics under different environmental stresses were investigated. We discovered that over-expression of GsLTP enhanced tolerance to drought and salt stresses.
Conclusions

Our results indicate that GsLTP plays an important role in multiple abiotic signalling pathways, and provide a theoretical basis and practical gene resource for crop breeding.
Effect of ezrin regulation by sperm-borne miR-183 on the formation of microvilli and early development of bovine embryos.
Authors: Zuo Zhenzi , Liu Xu , Wang Zheng , Qiao Fang , Wang Jingyi , Zhang Jingcheng , Zhang Yong , Qing Suzhu , Wang Yongsheng 
Published: August 2020

Abstract
Background: Mature sperm contain both coding and non-coding RNAs, which can be delivered into an oocyte with the sperm at fertilization. Accumulating evidence shows that these sperm-borne RNAs play crucial roles in epigenetic reprogramming, remodeling, embryonic development, and offspring phenotype. MiR-183 is highly expressed in bovine sperm, and can be delivered into oocytes during fertilization. Results: Here we used bioinformatics and luciferase assays to show that the ezrin gene, EZR, is one of the targets of miR-183 in early embryos, while gain- and loss-of-function studies demonstrated their regulatory relationship. Scanning electron microscopy showed that the density of microvilli on the surface of somatic cell nuclear transfer (SCNT) embryos was significantly higher than on in vitro fertilized (IVF) embryos and was significantly reduced by injection of miR-183. EZR-siRNA injected into SCNT embryos had a similar effect. This indicated that a deficiency in sperm-borne miRNA-183 might lead to abnormal changes in microvilli by down-regulating ezrin protein. We used bioinformatics to select the proteins that worked in combination with ezrin to regulate microvilli function. Co-IP mass spectrometry and immunofluorescence identified SLC9A3R1 as the protein functioning in synergy with ezrin in early bovine embryos. Gain-of-function studies showed that miR-183 significantly improved developmental competence of SCNT embryo in terms of cleavage (76.63% vs 64.32%, p<0.05), blastocyst formation (43.75% vs 28.26%, p<0.05), apoptotic index (5.21% vs 12.64%, p<0.05), and the trophoblast ratio (32.65% vs 25.58%, p<0.05) in day 7 blastocysts. Conclusions: In conclusion, the present studies indicated that sperm-borne miR-183 might influence the formation of microvilli and embryo development by regulating expression of EZR mRNA.
Accuracy of Remote Diagnoses Using Intraoral Scans Captured in Approximate True Color: A Validation Study in Teledentistry
Authors: Steinmeier Sabrina Jenny , Wiedemeier Daniel , Hämmerle Christoph HF , Mühlemann Sven 
Published: August 2020

Abstract
Background: Intraoral scans provide three-dimensional images with approximate true colors, representing possible tool in teledentistry for remote screening.Aim: To evaluate the levels of agreement between scorings derived from intraoral scans (IOS) and scorings derived from clinical examinations for assessing dental and periodontal conditions. Material and Methods: The sample included 10 patients in need of a restorative treatment. Following an intraoral scan, a full-mouth dental and periodontal examination was performed and periapical radiographs were taken. The intraoral scans were transmitted from the intraoral scanner to a cloud server. Ten examiners were asked to perform dental and periodontal assessments solely based on the intraoral scans. The scans were presented to the examiners on a tablet computer using the IOS-specific viewer app. Thereafter, the periapical radiographs were added and the examiners asked to do provide a second round of assessments. The remote scoring was compared to the clinical scoring derived from the clinical examination. The time for the remote assessment was recorded. The agreement between remote and clinical scorings was then analyzed descriptively.Results: Conclusion: The remote screening was effective in detecting patients in need for a clinical examination and was time-efficient. Further improvement of the image quality of intraoral scans may allow increasing the accuracy of remote assessments.