bluuebunny/crossref_metadata_2025_split huggingface dataset:
Findings and measures to eradicate methicillin resistant Staphylococcus aureus clonal complex 7 spa-type t091 in two Norwegian pig farms: a case report
Authors: Karlsen Odd Magne , Sandbu Kari , Grøntvedt Carl Andreas 
Published: December 2020

Abstract
BackgroundThe Norwegian LA-MRSA surveillance and control strategy in pig farms has been largely successful in preventing the establishment of MRSA in the pig population by identifying MRSA positive pig herds and eradicating MRSA from these. It can, however, be challenging to determine whether a particular type of MRSA is livestock-associated, particularly in cases where there is little evidence available to aid in classification.Case presentationIn two Norwegian pig farms linked by trade of live pigs, MRSA CC7 t091 was found in samples from pigs and their environment. Longitudinal sampling, with a time interval of 25 days, in one farm demonstrated an increase in samples positive for MRSA CC7 t091, supporting a classification of the finding as livestock associated. Measures to eradicate MRSA from both farms were imposed by the National Food Safety Authority. Different measures of MRSA sanitation were applied in the two farms, and MRSA was successfully eradicated from both farms.ConclusionsA high-cost, labor intensive and a lower-cost, less labor intensive MRSA eradication protocol, both including total depopulation and repopulation were successful in eradicating MRSA CC7 t091 from two case farms.
Five Long Non-Coding RNAs Establish a Prognostic Nomogram and Construct a Competing Endogenous RNA Network in the Progression of Non-Small Cell Lung Cancer
Authors: Ren Kaiming , Yu Yong 
Published: December 2020

Abstract
Background: Accumulating evidence has revealed that long non-coding RNAs (lncRNAs) play vital roles in the progression of non-small cell lung cancer (NSCLC). But the relationship between lncRNAs and survival outcome of NSCLC remains to be explored. Therefore, we attempt to figure out their survival roles and molecular connection in NSCLC.Methods: By analyzing the transcriptome profiling of NSCLC from TCGA databases, we divided patients into three groups, and identified differentially expressed lncRNAs (DELs) of each group. Next, we explored the prognostic roles of common DELs by univariate and multivariate Cox analysis, LASSON, and Kaplan-Meier analysis. Additionally, we assessed and compared the prognostic accuracy of 5 lncRNAs through ROC curves and AUC values. Ultimately, we detected their potential function by enrichment analysis and molecular connection through establishing a ceRNA network.Results: 197 common DELs were spotted. And we successfully screened out 5 lncRNAs related to the patient's survival, including LINC01833, AC112206.2, FAM83A-AS1, BANCR, and HOTAIR. Combing with age and AJCC stage, we constructed a nomogram that prognostic prediction was superior to the traditional parameters. Furthermore, 275 qualified mRNAs related to 5 lncRNAs were spotted. Functional analysis indicates that these lncRNAs act key roles in the progression of NSCLC, such as P53 and cell cycle signaling pathway. And ceRNA network also suggests that these lncRNAs are tightly connected with tumor progression.Conclusions: A nomogram and ceRNA network based on 5 lncRNAs indicate that there can effectively predict the overall survival of NSCLC and potentially serve as a therapeutic guide for NSCLC.
DLK1-DIO3 Region as a Source of Candidate Tumor Suppressor miRNAs in Papil- Lary Thyroid Carcinoma
Authors: Marson Leonardo Augusto , Alves Letícia Ferreira , Sielski Micheli Severo , Vicente Cristina Pontes , Kimura Edna Teruko , Geraldo Murilo Vieira 
Published: December 2020

Abstract
Background: DLK1-DIO3 genomic region comprises one of the largest microRNA (miRNAs) clusters in human genome. In previous studies we showed the downregulation of several miRNAs from the genomic region in papillary thyroid carcinoma (PTC). Due to the large number of miRNAs within this region the individual contribution of these molecules to PTC development and progression remains unclear. Methods: We used different computational resources to clarify the contribution of DLK1-DIO3-derived miRNAs to PTC. Results: Our analysis suggests that 12 miRNAs from this region cooperate to modulate distinct cancer-relevant biological processes, potentially responding for most of the impact of DLK1-DIO3-derived miRNAs to PTC development and progression. The overexpression of miR-485-5p in two PTC cell lines decreased proliferation and migration, confirming the biological relevance of in silico data. Conclusion: Our results shed light on the role of DLK1-DIO3 region, harboring several tumor suppressor miRNAs in thyroid cancer and open perspectives for the functional exploration of these miRNAs as therapeutic targets for PTC.
Calcium- and iron-chelating activity and functional properties of salmon by-product proteolysate
Authors: Vo Tam Dinh Le , Vo Bao Chi , Tran Linh Thi Thuy , Nguyen Linh Vy Truc , Nguyen Phuong Thanh , Le Duy Thanh , Tran Minh Cao , Bui Phong Thanh 
Published: December 2020

Abstract
In this study, calcium- and iron-binding proteolysate were generated using salmon by-product. It was shown by the result that under the hydrolysis condition including Neutrase, 45 oC, pH 7, E:S proportion of 70 U/g protein and 8 h of hydrolysis, the proteolysate reached the peaks of CaBC and IBC of 220.8 ± 3.1 mgCa2+/g protein and 232.3 ± 4.7 µgFe2+/g protein, respectively. In pH from 3–8, after heating at 63 °C for 30 min or 93 °C for 30 s (i) its solubility was over 85% and remained over 65%; (ii) FCs and FSs were 1.4–4.7 and 1.8–12.8 times lower than those of albumin; (iii) EAIs and ESIs were 1.1–2.7 and 4.1–11.1 folds less than those of sodium caseinate, respectively; (iv) WHC and OHC reached 2.00 ± 0.09 mL water/g proteolysate powder and 6.47 ± 0.25 mL oil/g proteolysate powder, respectively. Moreover, the < 1 kDa fraction displayed the highest CaBC and IBC. In conclusion, the proteolysate/peptides could be utilized in either easing micronutrient deficiency or preparation of functional peptides.
LIPUS&nbsp;Setting and Combined Effect With Therapeutic Exercise for Knee Osteoarthritis: A Systematic Review
Authors: Kitano Masashi , Okawa Yuse , Kawahata Hirohisa , Kudo Shintarou 
Published: December 2020

Abstract
[PURPOSE] Knee osteoarthritis (OA) is a chronic progressive disorder characterized by pain and decreased joint function. In the conservative treatment for the knee OA, the physiotherapy is known to be a common intervention. Recently, low-intensity pulsed ultrasound therapy (LIPUS) which has an effect on knee pain of knee OA has been used with therapeutic exercise. However, the combined effect of LIPUS with therapeutic exercise did not have enough evidence.This study was conducted to assess both setting off the LIPUS and combined effect of the therapeutic exercise in the Knee OA.[METHODS] PubMed, PEDro, CENTRAL were searched for RCTs on published before September 2019. The irradiation intensity, irradiation site, and treatment period of LIPUS were examined. Meta-analysis was performed to analyze the short and long term combined effect which was LIPUS with therapeutic exercise on the VAS score. Statistical calculations of both LIPUS with therapeutic exercise group and only therapeutic exercise group were compared from detailed data of the all eligible studies [RESULTS] Seven RCTs were eligible. Both irradiation intensity and site were varied. Three RCTs were included in the meta-analysis, involving a total of 210 knees. There was no significant improvement in pain in the LIPUS with therapeutic exercise (LIPUS) group compared with the therapeutic exercise group in short-term (MD; -6.86, 95% CI; -18.70 to 4.99 , I2 = 74%, heterogeneity: P = 0.02) and long-term (MD; -16.01 95% CI; -32.03 to 0.01, I2 = 82%, heterogeneity: P = 0.004) effects.[CONCLUSIONS]We did not find consistent evidence of the effects of combined to LIPUS and therapeutic exercise for Knee OA. Because, selected trials were varied in intensity and irradiation site and treatment durations, which might contribute to the existence of heterogeneity. Furthermore, there were few RCTs that resulted in knee joint function.The LIPUS combined therapeutic exercise found no significant decrease the knee pain than therapeutic exercise. Therefore, RCTs were recommended by well-designed intensity and irradiation site.
Protocol for a Meta-narrative Review on Research Paradigms Addressing the Urban Built Environment and Human Health
Authors: Kim Jinhee , Harris-Roxas Ben , de Leeuw Evelyne , Lilley David , Crimeen Alana , Sainsbury Peter 
Published: December 2020

Abstract
BackgroundUrban health is a field of research and practice that has attracted the interest of various disciplines. While it is encouraged for diverse disciplines to contribute to a multidisciplinary field of study such as urban health, this often results in tensions, conflicts or competition between the different traditions that stem from different epistemological backgrounds.This meta-narrative review aims to identify and describe the multiple paradigms and articulate the underlying epistemological, ontological, methodological and aetiological differences in their approaches. Articulating the paradigms not only contributes to the advancement of research, but also provides a framework for understanding the different policy beliefs and ideas policy actors hold and apply in the policy process.MethodsWe apply the meta-narrative method to systematic literature review which includes the following six iterative phases. The planning phase includes the finalisation of the review protocol and assembly of review team. The search phase includes a comprehensive literature search in key databases and a double-sided systematic snowballing method. Bibliometric analyses of this literature will be used to triangulate the mapping of the paradigms. The mapping phase includes identifying the dominant paradigms and landmark publications through agreement with the review team. In the appraisal phase, the literature will be assessed by their respective quality standards, followed by data extraction to identify the individual narratives in the conceptual, theoretical, methodological and instrumental dimensions of each paradigm. The synthesis phase will review the data to compare and contrast and identify the overarching meta-narratives. The recommendation phase will include dissemination of the findings from the review. DiscussionThe meta-narrative review will reveal the how the different paradigms conceptualise, frame and prioritise urban health issues, their preferred methodologies to study the phenomenon, and the nature of the solutions to improve human health. This review will assist researchers and practitioners in understanding and interpreting evidence produced by other traditions that study urban health. Through this, urban health researchers and practitioners will be able to seek coherence in understanding, explaining and exploring the urban health phenomenon.Systematic review registrationPROSPERO CRD42020192992
Comparison of Microbiota in the Upper Versus Lower Respiratory Tract in Children During Health and Respiratory Disease: a Protocol for a Systematic Review
Authors: Rao Richa , Mathew Joseph L. 
Published: December 2020

Abstract
Background: Several species of organisms reside in the upper airways of healthy infants and children. In most cases they do no harm to the host despite being potentially pathogenic. In contrast, the lung in healthy people was considered to be a sterile environment, but sophisticated techniques have recently demonstrated colonization by a complex population of microorganisms in healthy adults. It is unclear if a similar situation happens in healthy children. In children with respiratory disease, several micro-organisms can be recovered from the upper as well as lower respiratory tracts. However, the correlation between organisms recovered from the two sites is unclear. This systematic review is designed to explore the microbial composition of the respiratory system in apparently healthy asymptomatic children, comparing the organisms identified in the upper airways versus the lungs. We also intend to compare the site-specific prevalence and pattern of organisms in healthy children versus those with various respiratory diseases. We will also compare the organism identified in the upper airway versus the lungs in children with respiratory disease.Methods: We will search the following electronic databases: Medline, Embase and the Cochrane Library. Reference list of relevant studies will be examined for links to potential related articles. Two reviewers will independently determine study eligibility. The methodological quality of the observational included studies will be scored using the Newcastle Ottawa Scale tool for assessing risk of bias. We will extract data from included studies and perform meta-analysis where feasible.Results: The search strategy will be refined and the literature search will take place independently by two authors. Final stage will include analyses and writing.Discussion: Through the publication of this protocol, readers will be able to assess the research question and methods presented in this protocol. Upon publication of the review, readers will be able to assess whether the review was conducted according to pre-defined plan. Researchers will be aware that the review is underway, thereby avoid duplication, and be able to use it as a basis for planning similar reviews.PROSPERO registration number: CRD42020202115
Antegrade or Retrograde Approach for the Management of Tandem Occlusions in Acute Ischemic Stroke: Protocol for a Systematic Review and Meta-Analysis
Authors: Zhang Xiao , Bai Xuesong , Wang Xue , Yang Wuyang , Wang Jie , Wang Tao , Xu Ran , Qian Xia , Wang Yan , Yang Kun , Feng Yao , Ma Yan , Chen Yanfei , Jiao Liqun 
Published: December 2020

Abstract
BackgroundAcute ischemic stroke (AIS) is a major contributor to global morbidity and mortality, and mechanical thrombectomy (MT) is an effective treatment for AIS. AIS caused by tandem intracranial and extracranial occlusions are not rare. Evidence for optimal MT strategy regarding order of treatment, including antegrade (extracranial first) or retrograde (intracranial first) approach is lacking. Therefore, a systematic review and meta-analysis is necessary to compare the two approaches for optimal management of tandem lesions in AIS.MethodsThis study will be performed with accordance to the PRISMA statement. Major databases including PubMed, Web of Science, Embase, and the Cochrane Library will be used for literature search. Randomized controlled trials and high-quality observational studies will be included. Risk of bias will be assessed using the Cochrane Collaboration criteria or Newcastle–Ottawa Scale according to type of study. Two reviewers will independently screen for eligible studies and perform data extraction. The primary outcomes are successful recanalization at post-intervention, and favorable outcome at 3-month follow-up. Secondary outcomes include duration of onset to arrival, onset to puncture, onset to recanalization, intracerebral hemorrhage, procedure and device related complications and mortality at 3-month follow-up. We will assess heterogeneity using the I2 statistic. Subgroup and sensitivity analyses will be performed to explore the sources of heterogeneity. Specific results will be described in narrative form when insufficient suitable studies are available for meta-analysis.DiscussionThis study will provide a reliable evidence base for antegrade or retrograde approach for the management of tandem lesions in AIS by synthesizing evidence from current pieces of literature comparing the two approaches, and also will provide updated clinical evidence of strategy selection and decision-making for this special group of patients. PROSPERO registration numberCRD42020199093
Uev1A Promotes Breast Cancer Cell Migration and EMT by Up-Regulating CT45A Expression via the AKT Pathway
Authors: Niu Tong , Wu Zhaojia , Xiao Wei 
Published: December 2020

Abstract
IntroductionUEV1A encodes a ubiquitin-E2 variant closely associated with tumorigenesis and metastasis, but its underlying mechanism in promoting tumorigenesis remain to be investigated. MethodsIn this study, we experimentally manipulated UEV1A and CT45A gene expression and monitored their effects on cancer-related gene expression, cell migration and the signal transduction cascade.ResultsIt was found that UEV1A overexpression induces CT45A family gene expression in breast cancer cells. Indeed, ectopic expression of UEV1A is sufficient to induce CT45A and its downstream genes involved in tumorigenesis, epithelial-mesenchymal transition (EMT), stemness and metastasis, and promote cell migration and EMT. Consistently, depletion of CT45A abolishes the above effects, indicating that CT45A is a critical downstream effector of Uev1A. The Uev1A-induced cell migration and EMT is dependent on AKT signaling but independent of NF-κB signaling, indicating that CT45A acts downstream of the AKT pathway. ConclusionsBased on previous reports and observations in this study, we propose that the Ubc13-Uev1A complex activates AKT through K63-linked polyubiquitination, which leads to enhanced CT45A expression, stimulated cell migration and EMT. Since similar effects were also observed in a colorectal cancer cell line, we propose that the Ubc13/Uev1A-AKT-CT45A axis promotes tumorigenesis and metastasis in a broad range of tissues.
Fabrication of Ordered Micro/Nanostructures Using Probe-Based Force-Controlled Micromachining System
Authors: Geng Yanquan , Wang Yuzhang , Cai Jianxiong , Zhang Jingran , Yan Yongda 
Published: December 2020

Abstract
This paper presents a probe-based force-controlled nanoindentation method to fabricate ordered micro/nanostructures. Both the experimental and finite element simulation approaches are employed to investigate the influence of the interval between the adjacent indentations and the rotation angle of the probe on the formed micro/nanostructures. The non-contacting part between indenter and the sample material and the height of the material pile-up are two competing factors to determine the depth relationship between the adjacent indentations. For the one array indentations, nanostructures with good depth consistency and periodicity can be formed after the depth of the indentation becoming stable, and the variation of the rotation angle results in the large difference between the morphology of the formed nanostructures at the bottom of the one array indentation. In addition, for the indentation arrays, the nanostructures with good consistency and periodicity of the shape and depth can be generated with the spacing greater than 1 μm. Finally, Raman tests are also carried out based on the obtained ordered micro/nanostructures with Rhodamine probe molecule. The indentations arrays with a smaller spacing lead to better the enhancement effect of the substrate, which has the potential applications in the fields of biological or chemical molecular detection.
Weighted Gene Co-expression Network Analysis Identifies Specific Modules and Hub Genes Related to Alzheimer's Disease
Authors: Yang Kang , Deng Bin , Xie Liju , Bo Dandan , Mao Jingsong , Song Yabin 
Published: December 2020

Abstract
Background: Alzheimer's disease (AD) is the most common cause of dementia. We used Weighted gene co-expression network (WGCNA) to construct a gene co-expression network to analyze AD-related genes and find biomarkers of AD. An AD RNA chip expression data was downloaded from NCBI's GEO database. The construction of the gene co-expression network was completed by the WGCNA package of R software. Functional annotation of genes was performed by gene ontology and Kyoto Encyclopedia Gene and Genomic pathway analysis.Results: We used WGCNA to construct a co-expression network of 2713 differential expression genes in 56 AD patients and 44 healthy controls, and finally identified 7 gene modules, ranging in size from 32 to 1619. Correlation analysis of gene modules and disease showed that the turquoise module and the brown module were significantly associated with age. The turquoise module has obvious biological significance. The hub gene in this module is ATL1, which is involved in synaptic signaling and MAPK signaling pathways. The hub gene in the Brown module is CIRBP, which may be related to the regeneration of synapses.Conclusions: This study used WGCNA, an efficient system biology algorithm, to analyze the hub genes related to AD for the first time and provide a new direction for the future research of AD.
A One Health Approach to Studying the Differences in the Evolutionary Dynamics of MERS and SARS Coronaviruses
Authors: Zhang Xu , Sabir Jamal S. M. , Shen Xuejuan , Pu Zhiqing , Hajrah Nahid H. , Ahmed Mohamed M. M. , Luo Tingting , Sabir Meshaal J. , Al-Zogabi Onaizan Godian , Pan Junbin , Irwin David M. , Shen Yongyi 
Published: December 2020

Abstract
BackgroundSARS-CoV and MERS-CoV are two coronaviruses that received great attention due to their high pathogenicity and mortality rates in human populations. While SARS was controlled, MERS continues to be a global public health concern. To examine differences in the epidemic patterns of these two viruses, we collected all available sequences to compare the different evolutionary characteristics of SARS-CoV and MERS-CoV. Notably, almost all of the human infection cases occurred in the Middle East, and cases that occurred outside of the Middle East involved travelers from this region, while African infections have so far not been reported. It is not clear that genetic differences between Africans and Arabs lead to differences in susceptibility.ResultsIn this study, we compared their evolutionary dynamics to provide a One Health perspective of their different results of disease control. The phylogenetic network of SARS-CoVs showed that human isolates gathered into a “super-spreader” cluster, and were distinct from civet isolates. In contrast, dromedary camel- and human-isolated MERS-CoVs were clustered together. Thus, most clades of MERS-CoV can infect humans, and MERS-CoVs seem easier to spill over from animal-to-human interface. Although MERS-CoVs are endemic to dromedary camels in both the Middle East and Africa, all human infections are linked to the Middle East. The nucleotide sequences of the MERS-CoV receptor gene--dipeptidyl peptidase 4 (DPP4) from 30 Egyptians, 36 Sudanese, and 34 Saudi Arabians showed little difference.ConclusionsOur study reveals the reason why MERS-CoV is not easily controlled. Analysis of genetic differences between Africans and Arabs suggest that human population differences in DPP4 might not be the reason for their different MERS prevalence, raising the possibility that other reasons, such as poorer disease surveillance in Africa, might explain these observations.