bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computer-assisted textual analysis of free-text comments in the Swiss Cancer Patient Experiences (SCAPE) survey
Authors: Arditi Chantal , Walther Diana , Gilles Ingrid , Lesage Saphir , Griesser Anne-Claude , Bienvenu Christine , Eicher Manuela , Peytremann-Bridevaux Isabelle 
Published: November 2020

Abstract

Background
Patient experience surveys are increasingly conducted in cancer care as they provide important results to consider in future development of cancer care and health policymaking. These surveys usually include closed-ended questions (patient-reported experience measures (PREMs)) and space for free-text comments, but published results are mostly based on PREMs. We aimed to identify the underlying themes of patients’ experiences as shared in their own words in the Swiss Cancer Patient Experiences (SCAPE) survey and compare these themes with those assessed with PREMs to investigate how the textual analysis of free-text comments contributes to the understanding of patients’ experiences of care.

Methods
SCAPE is a multicenter cross-sectional survey that was conducted between October 2018 and March 2019 in French-speaking parts of Switzerland. Patients were invited to rate their care in 65 closed-ended questions (PREMs) and to add free-text comments regarding their cancer-related experiences at the end of the survey. We conducted computer-assisted textual analysis using the IRaMuTeQ software on the comments provided by 31% (n = 844) of SCAPE survey respondents (n = 2755).

Results
We identified five main thematic classes, two of which consisting of a detailed description of ‘cancer care pathways’. The remaining three classes were related to ‘medical care’, ‘gratitude and praise’, and the way patients lived with cancer (‘cancer and me’). Further analysis of this last class showed that patients’ comments related to the following themes: ‘initial shock’, ‘loneliness’, ‘understanding and acceptance’, ‘cancer repercussions’, and ‘information and communication’. While closed-ended questions related mainly to factual aspects of experiences of care, free-text comments related primarily to the personal and emotional experiences and consequences of having cancer and receiving care.

Conclusions
A computer-assisted textual analysis of free-text in our patient survey allowed a time-efficient classification of free-text data that provided insights on the personal experience of living with cancer and additional information on patient experiences that had not been collected with the closed-ended questions, underlining the importance of offering space for comments. Such results can be useful to inform questionnaire development, provide feedback to professional teams, and guide patient-centered initiatives to improve the quality and safety of cancer care.
Development and evaluation of duplex TaqMan real-time PCR assay for detection and differentiation of wide-type and MGF505-2R gene-deleted African swine fever viruses
Authors: Guo Zhenhua , Li Kunpeng , Qiao Songlin , Chen Xin-xin , Deng Ruiguang , Zhang Gaiping 
Published: November 2020

Abstract

Background
African swine fever (ASF) is the most important disease to the pigs and cause serious economic losses to the countries with large-scale swine production. Vaccines are recognized as the most useful tool to prevent and control ASF virus (ASFV) infection. Currently, the MGF505 and MGF360 gene-deleted ASFVs or combined with CD2v deletion were confirmed to be the most promising vaccine candidates. Thus, it is essential to develop a diagnosis method to discriminate wide-type strain from the vaccines used.

Results
In this study, we established a duplex TaqMan real-time PCR based on the B646L gene and MGF505-2R gene. The sequence alignment showed that the targeted regions of primers and probes are highly conserved in the genotype II ASFVs. The duplex real-time assay can specifically detect B646L and MGF505-2R gene single or simultaneously without cross-reaction with other porcine viruses tested. The limit of detection was 5.8 copies and 3.0 copies for the standard plasmids containing B646L and MGF505-2R genes, respectively. Clinical samples were tested in parallel by duplex real-time PCR and a commercial ASFV detection kit. The detection results of these two assays against B646L gene were well consistent.

Conclusion
We successfully developed and evaluated a duplex TaqMan real-time PCR method which can effectively distinguish the wide type and MGF505 gene-deleted ASFVs. It would be a useful tool for the clinical diagnosis and control of ASF.
The association between SAα2,3Gal occurrence frequency and avian influenza viral load in mallards (Anas platyrhynchos) and blue-winged teals (Spatula discors)
Authors: Dolinski Amanda C. , Jankowski Mark D. , Fair Jeanne M. , Owen Jennifer C. 
Published: November 2020

AbstractBackgroundIndividual heterogeneity in pathogen load can affect disease transmission dynamics; therefore, identifying intrinsic factors responsible for variation in pathogen load is necessary for determining which individuals are prone to be most infectious. Because low pathogenic avian influenza viruses (LPAIV) preferentially bind to alpha-2,3 sialic acid receptors (SAα2,3Gal) in the intestines and bursa of Fabricius in wild ducks (AnasandSpatulaspp.), we investigated juvenile mallards (Anas platyrhyncos) and blue-winged teals (Anas discors) orally inoculated with A/northern pintail/California/44221–761/2006 (H5N9) and the virus titer relationship to occurrence frequency of SAα2,3Gal in the intestines and bursa. To test the natural variation of free-ranging duck populations, birds were hatched and raised in captivity from eggs collected from nests of free-ranging birds in North Dakota, USA. Data generated from qPCR were used to quantify virus titers in cloacal swabs, ileum tissue, and bursa of Fabricius tissue, and lectin histochemistry was used to quantify the occurrence frequency of SAα2,3Gal. Linear mixed models were used to analyze infection status, species, and sex-based differences. Multiple linear regression was used to analyze the relationship between virus titer and SAα2,3Gal occurrence frequency.ResultsIn mallards, we found high individual variation in virus titers significantly related to high variation of SAα2,3Gal in the ileum. In contrast to mallards, individual variation in teals was minimal and significant relationships between virus titers and SAα2,3Gal were not determined. Collectively, teals had both higher virus titers and a higher occurrence frequency of SAα2,3Gal compared to mallards, which may indicate a positive association between viral load and SAα2,3Gal. Statistically significant differences were observed between infected and control birds indicating that LPAIV infection may influence the occurrence frequency of SAα2,3Gal, or vice versa, but only in specific tissues.ConclusionsThe results of this study provide quantitative evidence that SAα2,3Gal abundance is related to LPAIV titers; thus, SAα2,3Gal should be considered a potential intrinsic factor influencing variation in LPAIV load.
The association between serum vitamin D and obstructive sleep apnea: an updated meta-analysis
Authors: Li Xiaoyan , He Jie , Yun Jie 
Published: November 2020

Abstract

Background
The objective was to determine whether OSA patients have a low serum vitamin D level by systematic review and meta-analysis.

Methods
This study searched the following electronic bibliographic databases: Embase, Medline, Web of Science, PubMed, VIP, Wanfang, CNKI and SinoMed. All data were searched between January 2000 and August 2020. The quality of the included studies was estimated by two researchers according to the Newcastle–Ottawa Scale and Agency for Healthcare Research and Quality. All qualified studies and statistical analyses were conducted using RevMan 5.2.

Results
Twenty-nine eligible studies compromising 6717 participants met the inclusion criteria of the meta-analysis. The results revealed that the serum 25(OH)D level was significantly lower in OSA patients than the controls. According to the severity of the disease, subgroup analysis was performed; the results demonstrated that the serum 25(OH)D level was not decreased in mild OSA patients compared with the controls, while the serum 25(OH)D level in moderate and severe OSA patients was lower than that in the controls. Furthermore, based on ethnicity, BMI, PSG type, study quality and latitude, the subjects were divided into different subgroups for meta-analysis. The results revealed that the serum 25(OH)D level in all OSA subgroups was decreased compared with that in the control group.

Conclusions
The present meta-analysis shows that the serum vitamin D level was different between OSA patients and healthy people. OSA patients could have a low serum vitamin D level.
Construction and description of a constitutive plipastatin mono-producing Bacillus subtilis
Authors: Vahidinasab Maliheh , Lilge Lars , Reinfurt Aline , Pfannstiel Jens , Henkel Marius , Morabbi Heravi Kambiz , Hausmann Rudolf 
Published: November 2020

AbstractBackgroundPlipastatin is a potentBacillusantimicrobial lipopeptide with the prospect to replace conventional antifungal chemicals for controlling plant pathogens. However, the application of this lipopeptide has so far been investigated in a few cases, principally because of the yield in low concentration and unknown regulation of biosynthesis pathways.B. subtilissynthesizes plipastatin by a non-ribosomal peptide synthetase encoded by theppsABCDEoperon. In this study,B. subtilis3NA (a non-sporulation strain) was engineered to gain more insights about plipastatin mono-production.ResultsThe 4-phosphopantetheinyl transferase Sfp posttranslationally converts non-ribosomal peptide synthetases from inactive apoforms into their active holoforms. In case of 3NA strain,sfpgene is inactive. Accordingly, the first step was an integration of a repairedsfpversion in 3NA to construct strain BMV9. Subsequently, plipastatin production was doubled after integration of a fully expresseddegQversion fromB. subtilisDSM10Tstrain (strain BMV10), ensuring stimulation of DegU-P regulatory pathway that positively controls theppsABSDEoperon. Moreover, markerless substitution of the comparably weak native plipastatin promoter (Ppps) against the strong constitutive promoter Pvegled to approximately fivefold enhancement of plipastatin production in BMV11 compared to BMV9. Intriguingly, combination of both repaireddegQexpression and promoter exchange (Ppps::Pveg) did not increase the plipastatin yield. Afterwards, deletion of surfactin (srfAA-AD) operon by the retaining the regulatorycomSwhich is located withinsrfABand is involved in natural competence development, resulted in the loss of plipastatin production in BMV9 and significantly decreased the plipastatin production of BMV11. We also observed that supplementation of ornithine as a precursor for plipastatin formation caused higher production of plipastatin in mono-producer strains, albeit with a modified pattern of plipastatin composition.ConclusionsThis study provides evidence thatdegQstimulates the native plipastatin production. Moreover, a full plipastatin production requires surfactin synthetase or some of its components. Furthermore, as another conclusion of this study, results point towards ornithine provision being an indispensable constituent for a plipastatin mono-producerB. subtilisstrain. Therefore, targeting the ornithine metabolic flux might be a promising strategy to further investigate and enhance plipastatin production byB. subtilisplipastatin mono-producer strains.
An automated oxystat fermentation regime for microoxic cultivation of Magnetospirillum gryphiswaldense
Authors: Riese Cornelius N. , Uebe René , Rosenfeldt Sabine , Schenk Anna S. , Jérôme Valérie , Freitag Ruth , Schüler Dirk 
Published: November 2020

Abstract

Background
Magnetosomes produced by magnetotactic bacteria represent magnetic nanoparticles with unprecedented characteristics. However, their use in many biotechnological applications has so far been hampered by their challenging bioproduction at larger scales.

Results
Here, we developed an oxystat batch fermentation regime for microoxic cultivation of Magnetospirillum gryphiswaldense in a 3 L bioreactor. An automated cascade regulation enabled highly reproducible growth over a wide range of precisely controlled oxygen concentrations (1–95% of air saturation). In addition, consumption of lactate as the carbon source and nitrate as alternative electron acceptor were monitored during cultivation. While nitrate became growth limiting during anaerobic growth, lactate was the growth limiting factor during microoxic cultivation. Analysis of microoxic magnetosome biomineralization by cellular iron content, magnetic response, transmission electron microscopy and small-angle X-ray scattering revealed magnetosomal magnetite crystals were highly uniform in size and shape.

Conclusion
The fermentation regime established in this study facilitates stable oxygen control during culturing of Magnetospirillum gryphiswaldense. Further scale-up seems feasible by combining the stable oxygen control with feeding strategies employed in previous studies. Results of this study will facilitate the highly reproducible laboratory-scale bioproduction of magnetosomes for a diverse range of future applications in the fields of biotechnology and biomedicine.
Integrative in silico and in vitro transcriptomics analysis revealed new lncRNAs related to intrinsic apoptotic genes in colorectal cancer
Authors: Akbari Fatemeh , Peymani Maryam , Salehzadeh Ali , Ghaedi Kamran 
Published: November 2020

AbstractBackgroundPathogenesis of colorectal cancer (CRC) is connected to deregulation of apoptosis while the effect of lncRNAs, as critical regulatory molecules, on this pathway is not clear well. The present study aimed to identify differential expression of genes and their related lncRNAs which are significantly associated with intrinsic apoptotic pathway in CRC.MethodsThe connection between CRC and apoptosis was investigated by literature reviews and the genes were enriched by using Enrichr. At the next step, differential expression of enriched genes were evaluated between normal and tumor populations in data sets and were downloaded from GEO. Then, meta-analysis and probe re-annotation were performed. For lncRNAs selection through the highest expression correlation with each of candidate genes, mRNA-lncRNA interaction of screened genes and all of lncRNAs were visualized using Cytoscape. Identified differential expression genes and lncRNAs were validated using TCGA-COAD and the obtained data were confirmed by in vitro studies in the presence of Ag@Glu-TSC nanoparticle as an apoptotic inducer. Cytotoxicity and apoptosis induction effect of Ag@Glu-TSC on Caco-2 cells was determined via MTT and Annexin V/PI, respectively. The expression of genes and lncRNAs were assayed in presence of mentioned nanoparticle. Finally, the expression level of desired genes and lncRNAs were proven in CRC tissues compared to adjacent normal tissues.ResultsAfter detection of 48 genes associated with intrinsic apoptosis in CRC according to literature, Enrichr screened 12 common genes involved in this pathway. Among them, 6 genes includingBCL2,BCL2L11,BAD,CASP7,CASP9, andCYCSexpression reduced in tumor tissue compared to normal according to meta-analysis studies and RNA-seq TCGA data. Afterwards, association of 8 lncRNAs comprisingCDKN2B-AS1,LOC102724156,HAGLR,ABCC13,LOC101929340,LINC00675,FAM120AOS,PDCD4-AS1with more than 5 candidate genes were identified. In vitro studies revealed that four selected lncRNAs including,CDKN2B-AS1,LOC102724156,HAGLRandFAM120AOSwere significantly increased in the presence of in optimum concentration of Ag@Glu/TSC and decreased in tumor tissues versus adjacent normal tissues.ConclusionThis study developed a new data mining method to screen differentially expressed lncRNAs which are involved in regulation of intrinsic apoptosis pathway in CRC quickly using published gene expression profiling microarrays. Moreover, we could validate a number of these regulators in the cellular and laboratory disease models.
Identification of RASSF1A promoter hypermethylation as a biomarker for hepatocellular carcinoma
Authors: Xu Gang , Zhou Xiaoxiang , Xing Jiali , Xiao Yao , Jin Bao , Sun Lejia , Yang Huayu , Du Shunda , Xu Haifeng , Mao Yilei 
Published: November 2020

Abstract

Background
RAS association domain family protein 1A (RASSF1A) promoter hypermethylation is suggested to be linked to hepatocellular carcinoma (HCC), but the results remained controversial.

Methods
We evaluated how RASSF1A promoter hypermethylation affects HCC risk and its clinicopathological characteristics through meta-analysis. Data on DNA methylation in HCC and relevant clinical data were also collected based on The Cancer Genome Atlas (TCGA) database to investigate the prognostic role of RASSF1A promoter hypermethylation in HCC.

Results
Forty-four articles involving 4777 individuals were enrolled in the pooled analyses. The RASSF1A promoter methylation rate was notably higher in the HCC cases than the non-tumor cases and healthy individuals, and was significantly related to hepatitis B virus (HBV) infection-positivity and large tumor size. Kaplan–Meier survival analysis revealed that HCC cases with RASSF1A promoter hypermethylation had worse outcomes. Receiver operating characteristic curves confirmed that RASSF1A promoter methylation may be a marker of HCC-related prognoses.

Conclusions
RASSF1A promoter hypermethylation is a promising biomarker for the diagnosis of HCC from tissue and peripheral blood, and is an emerging therapeutic target against HCC.
Molecular epidemiology of Plasmodium falciparum by multiplexed amplicon deep sequencing in Senegal
Authors: Ndiaye Tolla , Sy Mouhamad , Gaye Amy , Siddle Katherine J. , Park Daniel J. , Bei Amy K. , Deme Awa B. , Mbaye Aminata , Dieye Baba , Ndiaye Yaye Die , Ndiaye Ibrahima Mbaye , Diallo Mamadou Alpha , Diongue Khadim , Volkman Sarah K. , Badiane Aida Sadikh , Ndiaye Daouda 
Published: November 2020

AbstractBackgroundMolecular epidemiology can provide important information regarding the genetic diversity and transmission ofPlasmodium falciparum, which can assist in designing and monitoring elimination efforts. However, malaria molecular epidemiology including understanding the genetic diversity of the parasite and performing molecular surveillance of transmission has been poorly documented in Senegal. Next Generation Sequencing (NGS) offers a practical, fast and high-throughput approach to understand malaria population genetics. This study aims to unravel the population structure ofP. falciparumand to estimate the allelic diversity, multiplicity of infection (MOI), and evolutionary patterns of the malaria parasite using the NGS platform.MethodsMultiplex amplicon deep sequencing of merozoite surface protein 1 (PfMSP1) and merozoite surface protein 2 (PfMSP2) in fifty-threeP. falciparumisolates from two epidemiologically different areas in the South and North of Senegal, was carried out.ResultsA total of 76Pfmsp1and 116Pfmsp2clones were identified and 135 different alleles were found, 56 and 79 belonged to thepfmsp1andpfmsp2genes, respectively. K1 and IC3D7 allelic families were most predominant in both sites. The local haplotype diversity (Hd) and nucleotide diversity (π) were higher in the South than in the North for both genes. Forpfmsp1, a high positive Tajima’s D (TD) value was observed in the South (D = 2.0453) while negative TD value was recorded in the North (D = − 1.46045) and F-Statistic (Fst) was 0.19505. Forpfmsp2, non-directional selection was found with a highly positive TD test in both areas and Fst was 0.02111. The mean MOI for both genes was 3.07 and 1.76 for the South and the North, respectively, with a statistically significant difference between areas (p = 0.001).ConclusionThis study revealed a high genetic diversity ofpfmsp1andpfmsp2genes and low genetic differentiation inP. falciparumpopulation in Senegal. The MOI means were significantly different between the Southern and Northern areas. Findings also showed that multiplexed amplicon deep sequencing is a useful technique to investigate genetic diversity and molecular epidemiology ofP. falciparuminfections.
The preoperative and the postoperative neutrophil-to-lymphocyte ratios both predict prognosis in gastric cancer patients
Authors: Kim Eun Young , Song Kyo Young 
Published: November 2020

Abstract

Background
Both the preoperative and postoperative neutrophil-to-lymphocyte ratios (NLRs) have been proposed to predict the long-term prognosis in some cancers, including gastric cancer. The present study investigated the prognostic impact of postoperative NLR, and its preoperative to postoperative changes, in patients with gastric cancer.

Methods
From 2009 to 2012, 1227 consecutive patients who underwent curative surgery for gastric cancer were enrolled in this study. The optimal cut-off value for the postoperative 6-month NLR was 1.7, as determined by receiver operating characteristic curve analysis. Patients were categorized into low- and high-NLR groups based on their postoperative NLR. Four additional groups (low to low, low to high, high to low, and high to high groups) were defined based on the preoperative to postoperative change in the NLR.

Results
The 5-year overall survival (OS) rates of the low- and high-NLR group were 90.7% and 83.0%, respectively (P < 0.001). The differences in OS were significant in stage I and stage III gastric cancer patients (P< 0.001 and 0.012, respectively). Postoperative NLR was an independent prognostic factor for OS (hazard ratio [HR] = 1.556; P = 0.010). The high to high NLR change was a significant predictor of OS (HR = 1.817; P = 0.003).

Conclusions
High preoperative and postoperative NLRs, and especially the persistent elevation of preoperative to postoperative NLR, were significant poor prognostic factors for OS in patients with gastric cancer.