bluuebunny/crossref_metadata_2025_split huggingface dataset:
Livestock owners’ anthrax prevention practices and its associated factors in Sekota Zuria district, Northeast Ethiopia
Authors: Seid Kibeb , Shiferaw Atsede Mazengia , Yesuf Nurhusien Nuru , Derso Terefe , Sisay Mekonnen 
Published: February 2020

Abstract
Background
In Ethiopia, the second most prioritized of the zoonotic diseases next to rabies is anthrax. About 50.6% of anthrax cases and 33.3% of deaths of livestock have been reported from Wag-Himra Zone, where appropriate anthrax prevention practices are not implemented by the owners of the animals. Thus, the aim of this study was to determine the extent of appropriate anthrax prevention practices of livestock owners and associated factors in Sekota Zuria district, northwest Ethiopia.

Results
Twenty-five percent (95% CI: 25.2, 26.1%) of the livestock owners implemented appropriate anthrax prevention. Three quarters (74%) of the owners consumed infected meat; more than three quarters (78%) used the skins and hides of animals found dead with anthrax. The odds of appropriate anthrax prevention practices were higher among livestock owners with positive attitude (AOR = 4.16, 95% CI: 2.72, 6.37), who received health education (AOR = 2.00, 95% CI: 1.21, 3.28) and owners who lived in urban areas (AOR = 2.62, 95% CI: 1.43, 4.77) compared to their counterparts. Ability to read and write (AOR = 2.76, 95% CI: 1.74, 4.37), and primary (AOR = 3.6, 95% CI: 1.74, 4.37) or secondary school and above education (AOR = 4.24, 95% CI: 1.61, 11.13) were significantly associated with appropriate anthrax prevention practices.

Conclusion
In Sekota Zuria district, only one quarter of the livestock owners were aware of appropriate anthrax prevention practices. Thus, implementing effective health education and creating positive attitude are vital to improve anthrax prevention practices in the area.
Phenotypic antimicrobial resistance in Escherichia coli strains isolated from swine husbandries in North Western Germany – temporal patterns in samples from laboratory practice from 2006 to 2017
Authors: Moennighoff C. , Thomas N. , Nienhaus F. , Hartmann M. , Menrath A. , Merkel J. , Detlefsen H. , Kreienbrock L. , Hennig-Pauka I. 
Published: February 2020

Abstract
Background
Since 2011, antibiotic usage has decreased continuously in livestock in Germany. Whether this is accompanied by a reduction in bacterial antimicrobial resistance has not been proven so far. In this study 3054 Escherichia coli (E. coli) isolates from pigs which had suffered from disease on 2161 farms in North Western Germany were evaluated retrospectively from 2006 to 2017 for trends in their antimicrobial resistance pattern. Data were substantially related to the “pre-reduction period” and were therefore suggested as a basis for this task.
Minimal inhibitory concentrations for selected antimicrobial substances were evaluated for E. coli strains isolated from different organs of diseased swine sampled for routine diagnostic. In total, 81% of E. coli were isolated from faeces or the gastrointestinal tract, 11% from the genito-urinary tract and 8% from other organs. Susceptibility testing and classification of isolates in accordance with clinical cut-offs followed the Clinical and Laboratory Standards Institute (CLSI). If no clinical cut-offs were available for the respective combination of species, substance and organ, other published clinical cut-offs were used.

Results
Differences in susceptibility patterns between isolates from the gastrointestinal and genito-urinary tract were found for most substances. Isolates from the genito-urinary tract were less frequently resistant to ampicillin, apramycin, colistin, neomycin, spectinomycin and tetracycline and more frequently resistant to enrofloxacin and florfenicol.
A multifactorial logistic regression model revealed time-dependent decreases in frequency of resistant isolates for neomycin, spectinomycin and tetracycline. For colistin, the highest percentage of resistant isolates with 16.0% was found in 2015 followed by a decrease to the level of 2009–2010 in 2017. A decrease in frequencies of ampicillin-resistant isolates was dependent on the age-group and time period. Irrespective of the year, less than 15% E. coli isolates were resistant to apramycin, cephalosporins, colistin, enrofloxacin, florfenicol, gentamicin and neomycin.

Conclusion
An overall time-dependent decrease in the percentage of resistant E. coli isolates was found for some substances. These data from diseased animals indicate an impact of a general reduction in antibiotic usage on development of bacterial antimicrobial resistance in the field and can support the decision-making of swine practitioners for treatment options in swine.
Gene therapy-emulating small molecule treatments in cystic fibrosis airway epithelial cells and patients
Authors: Yang Q. , Soltis A. R. , Sukumar G. , Zhang X. , Caohuy H. , Freedy J. , Dalgard C. L. , Wilkerson M. D. , Pollard H. B. , Pollard B. S. 
Published: February 2020

AbstractBackgroundSeveral small molecule corrector and potentiator drugs have recently been licensed for Cystic Fibrosis (CF) therapy. However, other aspects of the disease, especially inflammation, are less effectively treated by these drugs. We hypothesized that small molecule drugs could function either alone or as an adjuvant to licensed therapies to treat these aspects of the disease, perhaps emulating the effects of gene therapy in CF cells. The cardiac glycoside digitoxin, which has been shown to inhibit TNFα/NFκB signaling in CF lung epithelial cells, may serve as such a therapy.MethodsIB3–1 CF lung epithelial cells were treated with different Vertex (VX) drugs, digitoxin, and various drug mixtures, and ELISA assays were used to assess suppression of baseline and TNFα-activated secretion of cytokines and chemokines. Transcriptional responses to these drugs were assessed by RNA-seq and compared with gene expression in AAV-[wildtype]CFTR-treated IB3–1 (S9) cells. We also compared in vitro gene expression signatures with in vivo data from biopsied nasal epithelial cells from digitoxin-treated CF patients.ResultsCF cells exposed to digitoxin exhibited significant suppression of both TNFα/NFκB signaling and downstream secretion of IL-8, IL-6 and GM-CSF, with or without co-treatment with VX drugs. No evidence of drug-drug interference was observed. RNA-seq analysis showed that gene therapy-treated CF lung cells induced changes in 3134 genes. Among these, 32.6% were altered by digitoxin treatment in the same direction. Shared functional gene ontology themes for genes suppressed by both digitoxin and gene therapy included inflammation (84 gene signature), and cell-cell interactions and fibrosis (49 gene signature), while genes elevated by both were enriched for epithelial differentiation (82 gene signature). A new analysis of mRNA data from digitoxin-treated CF patients showed consistent trends in expression for genes in these signatures.ConclusionsAdjuvant gene therapy-emulating activities of digitoxin may contribute to enhancing the efficacy of currently licensed correctors and potentiators in CF patients.
6′-O-galloylpaeoniflorin regulates proliferation and metastasis of non-small cell lung cancer through AMPK/miR-299-5p/ATF2 axis
Authors: Gao Jinying , Song Lei , Xia Huan , Peng Liping , Wen Zhongmei 
Published: February 2020

Abstract
Background
Recent studies have shown 6'-O-galloylpaeoniflorin (GPF), a nature product extracted from the roots of paeoniflorin exerts anti-oxidant and anti-inflammatory activities. However, the effects of GPF on the proliferation and invasion in non-small cell lung cancer (NSCLC) cells have not been clarified.

Methods
MTT assay was performed to determine the cytotoxicity of GPF treatment on NSCLC cells. Colony formation assay, cell scratch test and transwell assay were performed to determine the proliferation and invasion of NSCLC cells in vitro, respectively. An A549 cell xenograft mouse model was performed to confirm the growth of NSCLC cells in vivo. Western blotting was used to measure the levels of activating transcription factor 2 (ATF2), AMP-activated protein kinase (AMPK) and phosph-AMPK (p-AMPK). Luciferase assay was used to validate the binding of miR-299-5p on the 3' untranslated region (UTR) of ATF2.

Results
Administration of GPF (50 or 100 μM) was significantly cytotoxic to A549 cells and H1299 cells, as well as inhibited the clonality, invasion and metastasis of NSCLC cells in vitro. GPF treatment also inhibited the tumor growth of NSCLC cell mouse xenografts in vivo. Exotic expression of miR-299-5p significantly inhibited the growth of NSCLC cells in vitro and in vivo. Downregulation of miR-299-5p expression attenuated the inhibition of the proliferation and metastasis of non-small cell lung cancer cells by GPF treatment. miR-299-5p significantly decreased ATF2 mRNA and protein levels in A549 cells (p < 0.05). Overexpression of ATF2 blocked the inhibitory effect of miR-299-5p on the proliferation and invasiveness of A549 cells.

Conclusions
GPF regulates miR-299-5p/ATF2 axis in A549 cells via the AMPK signalling pathway, thereby inhibiting the proliferation and metastasis of non-small cell lung cancer cells.
Production and characterization of yeasts grown on media composed of spruce-derived sugars and protein hydrolysates from chicken by-products
Authors: Lapeña David , Kosa Gergely , Hansen Line D. , Mydland Liv T. , Passoth Volkmar , Horn Svein J. , Eijsink Vincent G. H. 
Published: February 2020

Abstract
Background
A possible future shortage of feed protein will force mankind to explore alternative protein sources that can replace conventional soymeal or fishmeal. Several large industrial organic side-streams could potentially be upgraded to feed protein using a fermentation process to generate single cell protein. Yeast is the most widely accepted microorganism for production of single cell protein, because of its superior nutritional quality and acceptability among consumers. Here, we have assessed the growth of four different yeasts, Cyberlindnera jadinii, Wickerhamomyces anomalus, Blastobotrys adeninivorans and Thermosacc® Dry (Saccharomyces cerevisiae), on media composed of enzymatically saccharified sulfite-pulped spruce wood and hydrolysates of by-products from chicken, and we have characterized the resulting yeast biomass.

Results
Generally, the yeast grew very well on the spruce- and chicken-based medium, with typical yields amounting to 0.4–0.5 g of cell dry weight and 0.2–0.3 g of protein per g of sugar. B. adeninivorans stood out as the most versatile yeast in terms of nutrient consumption and in this case yields were as high as 0.9 g cells and 0.5 g protein per g of sugar. The next best performing yeast in terms of yield was W. anomalus with up to 0.6 g cells and 0.3 g protein per g sugar. Comparative compositional analyses of the yeasts revealed favorable amino acid profiles that were similar to the profiles of soymeal, and even more so, fish meal, especially for essential amino acids.

Conclusions
The efficient conversion of industrial biomass streams to yeast biomass demonstrated in this study opens new avenues towards better valorization of these streams and development of sustainable feed ingredients. Furthermore, we conclude that production of W. anomalus or B. adeninivorans on this promising renewable medium may be potentially more efficient than production of the well-known feed ingredient C. jadinii. Further research should focus on medium optimization, development of semi-continuous and continues fermentation protocols and exploration of downstream processing methods that are beneficial for the nutritional values of the yeast for animal feed.
Metabolic engineering Saccharomyces cerevisiae for de novo production of the sesquiterpenoid (+)-nootkatone
Authors: Meng Xiangfeng , Liu Hui , Xu Wenqiang , Zhang Weixin , Wang Zheng , Liu Weifeng 
Published: February 2020

AbstractBackground(+)-Nootkatone is a highly valued sesquiterpenoid compound, exhibiting a typical grapefruit aroma and various desired biological activities for use as aromatics and pharmaceuticals. The high commercial demand of (+)-nootkatone is predominately met by chemical synthesis, which entails the use of environmentally harmful reagents. Efficient synthesis of (+)-nootkatone via biotechnological approaches is thus urgently needed to satisfy its industrial demand. However, there are only a limited number of studies that report the de novo synthesis of (+)-nootkatone from simple carbon sources in microbial cell factories, and with relatively low yield.ResultsAs the direct precursor of (+)-nootkatone biosynthesis, (+)-valencene was first produced in large quantities inSaccharomyces cerevisiaeby overexpressing (+)-valencene synthase CnVS ofCallitropsis nootkatensisin combination with various mevalonate pathway (MVA) engineering strategies, including the expression of CnVS and farnesyl diphosphate synthase (ERG20) as a fused protein, overexpression of a truncated form of the rate-limiting enzyme 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase (tHMG1), and downregulating the squalene synthase enzyme (ERG9). These approaches altogether brought the production of (+)-valencene to 217.95 mg/L. Secondly, we addressed the (+)-valencene oxidation by overexpressing theHyoscyamus muticuspremnaspirodiene oxygenase (HPO) variant (V482I/A484I) and cytochrome P450 reductase (ATR1) fromArabidopsis thaliana. However, (+)-valencene was predominantly oxidized to β-nootkatol and only minor amounts of (+)-nootkatone (9.66 mg/L) were produced. We further tackled the oxidation of β-nootkatol to (+)-nootkatone by screening various dehydrogenases. Our results showed that the short-chain dehydrogenase/reductase (SDR) superfamily dehydrogenases ZSD1 ofZingiber zerumbetand ABA2 ofCitrus sinensiswere capable of effectively catalyzing β-nootkatol oxidation to (+)-nootkatone. The yield of (+)-nootkatone increased to 59.78 mg/L and 53.48 mg/L by additional overexpression of ZSD1 and ABA2, respectively.ConclusionWe successfully constructed the (+)-nootaktone biosynthesis pathway inS. cerevisiaeby overexpressing the (+)-valencene synthase CnVS, cytochrome P450 monooxygenase HPO, and SDR family dehydrogenases combined with the MVA pathway engineering, providing a solid basis for the whole-cell production of (+)-nootkatone. The two effective SDR family dehydrogenases tested in this study will serve as valuable enzymatic tools in further optimizing (+)-nootkatone production.
The prognostic value of De Ritis (AST/ALT) ratio in patients after surgery for urothelial carcinoma: a systematic review and meta-analysis
Authors: Hu Xu , Yang Wei-Xiao , Wang Yan , Shao Yan-Xiang , Xiong San-Chao , Li Xiang 
Published: February 2020

Abstract
Background
Recently, the De Ritis (AST/ALT) ratio has been considered as a prognostic biomarker for various malignancies. We conducted this systematic review and meta-analysis to explore the prognostic value of preoperative De Ritis ratio in patients after surgery for urothelial carcinoma.

Methods
We searched the online database Embase, PubMed and Cochrane Library up to October 2019. The hazard ratio (HR) and 95% confidence interval (CI) were extracted from the studies.

Results
A total of 8 studies incorporating 3949 patients were included in the quantitative synthesis. We observed that elevated preoperative De Ritis ratio is associated with inferior OS (HR = 1.97; 95% CI 1.70–2.28; P < 0.001), CSS (HR = 2.40; 95% CI 2.02–2.86; P < 0.001), RFS (HR = 1.31; 95% CI 1.11–1.54; P = 0.001), PFS (HR = 2.07; 95% CI 1.68–2.56; P < 0.001) and MFS (HR = 2.39; 95% CI 1.16–4.91; P = 0.018). Stratified by diseases, the elevated De Ritis ratio also served as an unfavorable factor.

Conclusion
The elevated preoperative De Ritis ratio is an unfavorable factor for patients with urothelial carcinoma. In patients with BC and UTUC, the elevated preoperative De Ritis ratio is also associated with poor prognosis. But De Ritis ratio must be validated in large, independent cohorts before it can be applied widely.
The effect of vitamin D supplementation on hemoglobin concentration: a systematic review and meta-analysis
Authors: Arabi Seyed Mostafa , Ranjbar Golnaz , Bahrami Leila Sadat , Vafa Mohammadreza , Norouzy Abdolreza 
Published: February 2020

AbstractAimsThe purpose of this review was to investigate the effect of vitamin D supplements on hemoglobin concentration in subjects aged 17.5–68 years old; using randomized controlled trials (RCTs).MethodsRelevant RCT studies were identified from January 2000 to January 2019 by using MeSH terms in PubMed, Embase, Cochrane Library, Clinical trials, Scopus databases and gray literature. The studies were reviewed systematically, and quality assessments were evaluated by the guidelines of the Cochrane risk of bias. The effect of vitamin D supplements (n = 14) on hemoglobin concentration was considered as primary outcome, while its effects on the levels of ferritin, transferrin saturation and iron status were derived as secondary outcomes. In total, 1385 subjects with age range of 17.5 to 68 years old were examined for 3 h to 6 months; Mean (standard deviation) or median interquartile changes in the hemoglobin concentration in each treatment group was recorded for meta-analysis.ResultsFourteen RCTs met the inclusion criteria. Current study findings propose that vitamin D supplementation leads to a non-significant reduction in hemoglobin levels in subjects (17.5–68 years old) [std. mean difference (SMD): 0.01; 95% CI: − 0.28, 0.29;P = 0.95], also it has no significant effect on ferritin concentrations [std. mean difference (SMD): -0.01; 95% CI: [− 0.20, 0.18;P = 0.91]. However, vitamin D supplementation demonstrated positive effects on transferrin saturation [mean difference (MD): 1.54; 95% CI: 0.31, 2.76;P = 0.01] and iron status [std. mean difference (SMD): 0.24; 95% CI: − 0.09, 0.39;P = 0.002].ConclusionCurrent review concluded that supplementation with vitamin D had no significant effect on hemoglobin and ferritin levels while positive effects on transferrin saturation and iron status were observed. Further clinical studies are required to determine the actual effect of this intervention on hemoglobin levels.
Gut metabolomics profiling of non-small cell lung cancer (NSCLC) patients under immunotherapy treatment
Authors: Botticelli Andrea , Vernocchi Pamela , Marini Federico , Quagliariello Andrea , Cerbelli Bruna , Reddel Sofia , Del Chierico Federica , Di Pietro Francesca , Giusti Raffaele , Tomassini Alberta , Giampaoli Ottavia , Miccheli Alfredo , Zizzari Ilaria Grazia , Nuti Marianna , Putignani Lorenza , Marchetti Paolo 
Published: February 2020

Abstract
Background
Despite the efficacy of immune checkpoint inhibitors (ICIs) only the 20–30% of treated patients present long term benefits. The metabolic changes occurring in the gut microbiota metabolome are herein proposed as a factor potentially influencing the response to immunotherapy.

Methods
The metabolomic profiling of gut microbiota was characterized in 11 patients affected by non-small cell lung cancer (NSCLC) treated with nivolumab in second-line treatment with anti-PD-1 nivolumab. The metabolomics analyses were performed by GC–MS/SPME and 1H-NMR in order to detect volatile and non-volatile metabolites. Metabolomic data were processed by statistical profiling and chemometric analyses.

Results
Four out of 11 patients (36%) presented early progression, while the remaining 7 out of 11 (64%) presented disease progression after 12 months. 2-Pentanone (ketone) and tridecane (alkane) were significantly associated with early progression, and on the contrary short chain fatty acids (SCFAs) (i.e., propionate, butyrate), lysine and nicotinic acid were significantly associated with long-term beneficial effects.

Conclusions
Our preliminary data suggest a significant role of gut microbiota metabolic pathways in affecting response to immunotherapy. The metabolic approach could be a promising strategy to contribute to the personalized management of cancer patients by the identification of microbiota-linked “indicators” of early progressor and long responder patients.
Automated quantification of Epstein-Barr virus in whole blood for post-transplant lymphoproliferative disorders monitoring
Authors: Salmona Maud , Stefic Karl , Mahjoub Nadia , de Fontbrune Flore Sicre , Maylin Sarah , Simon François , Scieux Catherine , Socié Gérard , Mazeron Marie-Christine , LeGoff Jérôme 
Published: February 2020

Abstract
Background
Standardized and sensitive assays for Epstein Barr Virus (EBV) are needed to define universal cutoff for treatment initiation in allogeneic hematopoietic stem cells transplant recipients. In a context of accreditation and the availability of EBV international standard, we evaluated the Abbott RealTime EBV (RT) assay for EBV quantification in whole blood.

Methods
The RT assay was compared on 282 prospective clinical samples with the Artus EBV PCR Kit V1 assay (V1) and we analyzed the kinetics of EBV load in 11 patients receiving rituximab treatment.

Results
The estimated limit of detection was 88 IU/mL. The assay was linear (r2 = 0.9974) in the range of all samples tested (100 to 1,000,000 IU/mL). Intra-assay coefficients of variation (CV) ranged between 0.35 and 1.35%, and inter-assay CV between 3.40 and 4.5%. On samples above the limit of quantification, the two assays were strongly correlated. EBV RT values were on average 0.30 log10 IU/mL lower than those measured with the V1 assay. In patients treated with rituximab, the RT assay remained positive in 5 patients at the time it dropped below undetectable levels with the V1 assay.

Conclusions
In conclusion, the RT assay is a reliable assay for EBV load in whole blood. Its sensitivity will enable to estimate the kinetics of EBV load and the impact of treatments to control EBV reactivations.
lncRNA GAS8-AS1 downregulates lncRNA UCA1 to inhibit osteosarcoma cell migration and invasion
Authors: Zha Zhuqing , Han Qingmin , Liu Wenjing , Huo Shaochuan 
Published: February 2020

Abstract
Background
Osteosarcoma (OS) is the most common type of primary bone tumor that mainly affects adolescents and young adults. The present study explored the role of lncRNA GAS8-AS1 in OS.

Methods
A total of 48 OS patients were selected from the 82 OS patients admitted by Luoyang Orthopedic Hospital of Henan Province between May 2010 and May 2013. Transient cell transfections, Transwell cell migration and invasion assay, RT-qPCR, and patient follow-up were carried out during the research.

Results
The results showed that GAS8-AS1 was downregulated, while UCA1 was upregulate in cancer tissues in comparison to adjacent non-cancer tissues of OS patients. GAS8-AS1 was not affected by clinical stage. Follow-up study showed that downregulated GAS8-AS1 in cancer tissues was closely correlated with poor survival. GAS8-AS1 and UCA1 were inversely correlated in cancer tissues. Overexpression of UCA1 failed to affect the expression of GAS8-AS1, while overexpression of GAS8-AS1 led to downregulated expression of UCA1 in OS cells, while the molecular mediators between these two lncRNAs are unknown. Overexpression of GAS8-AS1 did not affect OS cell proliferation but significantly inhibited cancer cell migration and invasion. Overexpression of UCA1 promoted the migration and invasion of OS cells and attenuated the effects of overexpressing GAS8-AS1.

Conclusions
Therefore, GAS8-AS1 may inhibit OS cell migration and invasion by downregulating oncogenic UCA1.