bluuebunny/crossref_metadata_2025_split huggingface dataset:
An octavalent vaccine provides pregnant gilts protection against a highly virulent porcine parvovirus strain
Authors: van den Born Erwin , van den Elzen Paul P. M. , van Kilsdonk Emma , Hoeijmakers Mathieu J. H. , Segers Ruud P. A. M. 
Published: February 2020

Abstract
Background
Porcilis® Ery+Parvo+Lepto is an octavalent inactivated ready-to-use vaccine that contains Erysipelothrix rhusiopathiae (Ery), porcine parvovirus (PPV), and six serogroups of Leptospira (Lepto). The efficacy of Porcilis® Ery + Parvo+Lepto against reproductive problems associated with porcine parvovirus (PPV) infection was evaluated in pregnant gilts. For this, a group of ninegilts was vaccinated twice (at 5 and 6 months old) with Porcilis® Ery + Parvo+Lepto (Group 1), while a group of eight gilts was included as unvaccinated controls (Group 2). All pigs were artificially inseminated 4 weeks after the second vaccination. They were challenged during early gestation with PPV-27a, a virulent cluster D strain, and euthanized to collect their offspring by hysterectomy around day 90 in pregnancy. Antibody responses against PPV in gilts were measured, and the presence of PPV in progeny was also determined.

Results
No clinical signs were observed after vaccination. After PPV challenge, all foetuses from the vaccinated gilts were alive (132/132), while in the unvaccinated group only 41% were alive (46/112), 19.6% were dead and 39.4% of the offspring (44/112) were mummified. PPV could be detected by qPCR in 14% of the progeny from vaccinated gilts at an average of 4.7 log10/ml, whereas this was significantly higher in the control group, where 90% of the progeny were PPV positive, with titres of 9.8 log10/ml on average.

Conclusions
The present study demonstrates that vaccination of gilts with Porcilis® Ery + Parvo+Lepto was safe and induced an immune response sufficient to protect progeny against PPV by reducing transplacental infection.
Resistance of the respiratory system measured with forced oscillation technique (FOT) correlates with bronchial thermoplasty response
Authors: Goorsenberg Annika W. M. , d’Hooghe Julia N. S. , Slats Annelies M. , van den Aardweg Joost G. , Annema Jouke T. , Bonta Peter I. 
Published: February 2020

Abstract
Background
Bronchial Thermoplasty (BT) is an endoscopic treatment for severe asthma using radiofrequency energy to target airway remodeling including smooth muscle. The correlation of pulmonary function tests and BT response are largely unknown. Forced Oscillation Technique (FOT) is an effort-independent technique to assess respiratory resistance (Rrs) by using pressure oscillations including small airways.

Aim
To investigate the effect of BT on pulmonary function, assessed by spirometry, bodyplethysmography and FOT and explore associations between pulmonary function parameters and BT treatment response.

Methods
Severe asthma patients recruited to the TASMA trial were analyzed in this observational cohort study. Spirometry, bodyplethysmography and FOT measurements were performed before and 6 months after BT. Asthma questionnaires (AQLQ/ACQ-6) were used to assess treatment response.

Results
Twenty-four patients were analyzed. AQLQ and ACQ improved significantly 6 months after BT (AQLQ 4.15 (±0.96) to 4.90 (±1.14) and ACQ 2.64 (±0.60) to 2.11 (±1.04), p = 0.004 and p = 0.02 respectively). Pulmonary function parameters remained stable. Improvement in FEV1 correlated with AQLQ change (r = 0.45 p = 0.03). Lower respiratory resistance (Rrs) at baseline (both 5 Hz and 19 Hz) significantly correlated to AQLQ improvement (r = − 0.52 and r = − 0.53 respectively, p = 0.01 (both)). Borderline significant correlations with ACQ improvement were found (r = 0.30 p = 0.16 for 5 Hz and r = 0.41 p = 0.05 for 19 Hz).

Conclusion
Pulmonary function remained stable after BT. Improvement in FEV1 correlated with asthma questionnaires improvement including AQLQ. Lower FOT-measured respiratory resistance at baseline was associated with favorable BT response, which might reflect targeting of larger airways with BT.

Trial registration
ClinicalTrials.gov Identifier: NCT02225392; Registered 26 August 2014.
A comprehensive analysis of the animal carcinogenicity data for glyphosate from chronic exposure rodent carcinogenicity studies
Authors: Portier Christopher J. 
Published: February 2020

AbstractSince the introduction of glyphosate-tolerant genetically-modified plants, the global use of glyphosate has increased dramatically making it the most widely used pesticide on the planet. There is considerable controversy concerning the carcinogenicity of glyphosate with scientists and regulatory authorities involved in the review of glyphosate having markedly different opinions. One key aspect of these opinions is the degree to which glyphosate causes cancer in laboratory animals after lifetime exposure. In this review, twenty-one chronic exposure animal carcinogenicity studies of glyphosate are identified from regulatory documents and reviews; 13 studies are of sufficient quality and detail to be reanalyzed in this review using trend tests, historical control tests and pooled analyses. The analyses identify 37 significant tumor findings in these studies and demonstrate consistency across studies in the same sex/species/strain for many of these tumors. Considering analyses of the individual studies, the consistency of the data across studies, the pooled analyses, the historical control data, non-neoplastic lesions, mechanistic evidence and the associated scientific literature, the tumor increases seen in this review are categorized as to the strength of the evidence that glyphosate causes these cancers. The strongest evidence shows that glyphosate causes hemangiosarcomas, kidney tumors and malignant lymphomas in male CD-1 mice, hemangiomas and malignant lymphomas in female CD-1 mice, hemangiomas in female Swiss albino mice, kidney adenomas, liver adenomas, skin keratoacanthomas and skin basal cell tumors in male Sprague-Dawley rats, adrenal cortical carcinomas in female Sprague-Dawley rats and hepatocellular adenomas and skin keratocanthomas in male Wistar rats.
Unmasking Retinitis Pigmentosa complex cases by a whole genome sequencing algorithm based on open-access tools: hidden recessive inheritance and potential oligogenic variants
Authors: González-del Pozo María , Fernández-Suárez Elena , Martín-Sánchez Marta , Bravo-Gil Nereida , Méndez-Vidal Cristina , Rodríguez-de la Rúa Enrique , Borrego Salud , Antiñolo Guillermo 
Published: February 2020

AbstractBackgroundRetinitis Pigmentosa (RP) is a clinically and genetically heterogeneous disorder that results in inherited blindness. Despite the large number of genes identified, only ~ 60% of cases receive a genetic diagnosis using targeted-sequencing. The aim of this study was to design a whole genome sequencing (WGS) based approach to increase the diagnostic yield of complex Retinitis Pigmentosa cases.MethodsWGS was conducted in three family members, belonging to one large apparent autosomal dominant RP family that remained unsolved by previous studies, using Illumina TruSeq library preparation kit and Illumina HiSeq X platform. Variant annotation, filtering and prioritization were performed using a number of open-access tools and public databases. Sanger sequencing of candidate variants was conducted in the extended family members.ResultsWe have developed and optimized an algorithm, based on the combination of different open-access tools, for variant prioritization of WGS data which allowed us to reduce significantly the number of likely causative variants pending to be manually assessed and segregated. Following this algorithm, four heterozygous variants in one autosomal recessive gene (USH2A) were identified, segregating in pairs in the affected members. Additionally, two pathogenic alleles inADGRV1andPDZD7could be contributing to the phenotype in one patient.ConclusionsThe optimization of a diagnostic algorithm for WGS data analysis, accompanied by a hypothesis-free approach, have allowed us to unmask the genetic cause of the disease in one large RP family, as well as to reassign its inheritance pattern which implies differences in the clinical management of these cases. These results contribute to increasing the number of cases with apparently dominant inheritance that carry causal mutations in recessive genes, as well as the possible involvement of various genes in the pathogenesis of RP in one patient. Moreover, our WGS-analysis approach, based on open-access tools, can easily be implemented by other researchers and clinicians to improve the diagnostic yield of additional patients with inherited retinal dystrophies.
Identification of key genes controlling breast cancer stem cell characteristics via stemness indices analysis
Authors: Pei Jianying , Wang Yanxia , Li Yan 
Published: February 2020

Abstract
Background
With the gradual unveiling of tumour heterogeneity, cancer stem cells (CSCs) are now being considered the initial component of tumour initiation. However, the mechanisms of the growth and maintenance of breast cancer (BRCA) stem cells are still unknown.

Methods
To explore the crucial genes modulating BRCA stemness characteristics, we combined the gene expression value and mRNA expression-based stemness index (mRNAsi) of samples from The Cancer Genome Atlas (TCGA), and the mRNAsi was corrected using the tumour purity (corrected mRNAsi). mRNAsi and corrected mRNAsi were analysed and showed a close relationship with BRCA clinical characteristics, including tumour depth, pathological staging and survival status. Next, weighted gene co-expression network analysis (WGCNA) was applied to distinguish crucial gene modules and key genes. A series of functional analyses and expression validation of key genes were conducted using multiple databases, including Oncomine, Gene Expression Omnibus (GEO) and Gene Expression Profiling Integrative Analysis (GEPIA).

Results
This study found that mRNAsi and corrected mRNAsi scores were higher in BRCA tissues than that in normal tissues, and both of them increased with tumour stage. Higher corrected mRNAsi scores showed worse overall survival outcomes. We screened 3 modules and 32 key genes, and those key genes were found to be strongly correlated with each other. Functional analysis revealed that the key genes were related to cell fate decision events such as the cell cycle, cellular senescence, chromosome segregation and mitotic nuclear division. Among 32 key genes, we identified 12 genes that strongly correlated with BRCA survival.

Conclusions
Thirty-two genes were found to be closely related to BRCA stem cell characteristics; among them, 12 genes showed prognosis-oriented effects in BRCA patients. The most significant signalling pathway related to stemness in BRCA was the cell cycle pathway, which may support new ideas for screening therapeutic targets to inhibit BRCA stem characteristics. These findings may highlight some therapeutic targets for inhibiting BRCA stem cells.
Facilitating ventilator weaning through rib fixation combined with video-assisted thoracoscopic surgery in severe blunt chest injury with acute respiratory failure
Authors: Wu Tung-Ho , Lin Hsing-Lin , Chou Yi-Pin , Huang Fong-Dee , Huang Wen-Yen , Tarng Yih-Wen 
Published: February 2020

Abstract
Background
Severe blunt chest injury sometimes induces acute respiratory failure (ARF), requiring ventilator use. We aimed to evaluate the effect of performing rib fixation with the addition of video-assisted thoracoscopic surgery (VATS) on patients with ARF caused by blunt thoracic injury with ventilator dependence.

Methods
This observational study prospectively enrolled patients with multiple bicortical rib fractures with hemothorax caused by severe blunt chest trauma. All patients received positive pressure mechanical ventilation within 24 h after trauma because of ARF. Some patients who received rib fixation with VATS were enrolled as group 1, and the others who received only VATS were designated as group 2. The length of ventilator use was the primary clinical outcome. Rates of pneumonia and length of hospital stay constituted secondary outcomes.

Results
A total of 61 patients were included in this study. The basic demographic characteristics between the two groups exhibited no statistical differences. All patients received operations within 6 days after trauma. The length of ventilator use was shorter in group 1 (3.19 ± 3.37 days vs. 8.05 ± 8.23, P = 0.002). The rate of pneumonia was higher in group 2 (38.1% vs. 75.0%, P = 0.005). The length of hospital stay was much shorter in group 1 (17.76 ± 8.38 days vs. 24.13 ± 9.80, P = 0.011).

Conclusion
Rib fixation combined with VATS could shorten the length of ventilator use and reduce the pneumonia rate in patients with severe chest blunt injury with ARF. Therefore, this operation could shorten the overall length of hospital stay.
Assembly of hundreds of novel bacterial genomes from the chicken caecum
Authors: Glendinning Laura , Stewart Robert D. , Pallen Mark J. , Watson Kellie A. , Watson Mick 
Published: February 2020

Abstract
Background
Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal.

Results
We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome.

Conclusions
This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.
Add-on effect of kinesiotape in patients with acute lateral ankle sprain: a randomized controlled trial
Authors: Shin Jeong-Cheol , Kim Jae-Hong , Nam Dongwoo , Park Gwang-Cheon , Lee Jeong-Soon 
Published: February 2020

Abstract
Background
Evidence for the add-on effect of kinesiotape (KT) with acupuncture for treating ankle sprains remains insufficient. We assessed the add-on effect of KT on ankle sprains by comparing acupuncture combined with KT (AcuKT) with acupuncture alone in patients with acute lateral ankle sprain (ALAS).

Methods
This study was a multicenter, randomized controlled clinical trial that included a per-protocol analysis of the add-on effect of KT on ALAS. The randomization was software based and only the assessors were blinded. Sixty participants (20 each from three centers) with grade I or II ALAS were randomly assigned to acupuncture (n = 30) or AcuKT (n = 30) groups. Both groups received acupuncture treatment once daily, 5 days per week for 1 week. The AcuKT group received additional KT treatment. Visual analog scale (VAS) scores for pain and the Foot and Ankle Outcome Score (FAOS) were obtained, and edema measurements were performed at baseline (week 0), at the end of the intervention (week 1), and at 4 weeks after intervention (week 5). The European Quality of Life Five Dimension-Five Level Scale (EQ-5D-5 L) measurements were conducted at week 0, week 1, week 5, and week 26 after the intervention. The number of recurrent ankle sprains was determined at 4, 8, 12 and 26 weeks after the intervention.

Results
Fifty-six patients with ALAS completed the trial (AcuKT group, n = 27; acupuncture group, n = 29). There were significant changes in visual analog scale score (AcuKT, P < 0.001; acupuncture, P < 0.001), the FAOS (AcuKT, P < 0.001; acupuncture, P < 0.001), and EQ-5D-5 L measurements (AcuKT, P < 0.001; acupuncture, P < 0.001) within both groups. There were no significant differences between groups in terms of any outcome or in a subanalysis based on symptom severity.

Conclusions
These results indicate that AcuKT did not show a positive add-on effect of KT with acupuncture in terms of pain reduction, edema, recovery of function, activities of daily living, quality of life or relapse of ALAS.

Trial registration
Clinical Research Information Service (cris.nih.go.kr), KCT0002257. Registered on 27 February 2017.
High anti-Ascaris seroprevalence in fattening pigs in Sichuan, China, calls for improved management strategies
Authors: Zheng Youle , Xie Yue , Geldhof Peter , Vlaminck Johnny , Ma Guangxu , Gasser Robin B. , Wang Tao 
Published: February 2020

Abstract
Background
Ascariasis, caused by Ascaris suum, is an important soil-transmitted parasitic disease of pigs worldwide. It leads to significant economic losses in the pork industry, as a consequence of low feed conversion efficiency in pigs and liver condemnation at slaughter. Despite ascariasis still being widespread on pig farms in many developing and the industrialised countries, there are surprisingly limited data on porcine ascariasis in China, where nearly half of the world’s total pork is produced.

Methods
In the present study, using the recently developed A. suum-haemoglobin (As-Hb) antigen-based serological test, we screened 512 individual serum samples from fattening pigs from 13 farms across seven distinct locations of Sichuan Province in China for anti-Ascaris antibody.

Results
The prevalence of anti-Ascaris antibody ranged from 0% to 100% on the distinct farms, with the mean (overall) seroprevalence being > 60%. There was no significant difference in seroprevalence between the intensive and extensive farms.

Conclusions
To our knowledge, this is the first study to measure anti-Ascaris seroprevalence in China. The results of this ‘snapshot’ investigation indicate that Ascaris infection in commercial pig farms in Sichuan Province is seriously underestimated, encouraging future, large-scale serological studies to assess the distribution and extent of Ascaris exposure and infection in various regions of China and the world.
Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish
Authors: den Broeder Marjo J. , Ballangby Jarle , Kamminga Leonie M. , Aleström Peter , Legler Juliette , Lindeman Leif C. , Kamstra Jorke H. 
Published: February 2020

Abstract
Background
Recent studies indicate that exposure to environmental chemicals may increase susceptibility to developing metabolic diseases. This susceptibility may in part be caused by changes to the epigenetic landscape which consequently affect gene expression and lead to changes in lipid metabolism. The epigenetic modifier enhancer of zeste 2 (Ezh2) is a histone H3K27 methyltransferase implicated to play a role in lipid metabolism and adipogenesis. In this study, we used the zebrafish (Danio rerio) to investigate the role of Ezh2 on lipid metabolism and chromatin status following developmental exposure to the Ezh1/2 inhibitor PF-06726304 acetate. We used the environmental chemical tributyltin (TBT) as a positive control, as this chemical is known to act on lipid metabolism via EZH-mediated pathways in mammals.

Results
Zebrafish embryos (0–5 days post-fertilization, dpf) exposed to non-toxic concentrations of PF-06726304 acetate (5 μM) and TBT (1 nM) exhibited increased lipid accumulation. Changes in chromatin were analyzed by the assay for transposase-accessible chromatin sequencing (ATAC-seq) at 50% epiboly (5.5 hpf). We observed 349 altered chromatin regions, predominantly located at H3K27me3 loci and mostly more open chromatin in the exposed samples. Genes associated to these loci were linked to metabolic pathways. In addition, a selection of genes involved in lipid homeostasis, adipogenesis and genes specifically targeted by PF-06726304 acetate via altered chromatin accessibility were differentially expressed after TBT and PF-06726304 acetate exposure at 5 dpf, but not at 50% epiboly stage. One gene, cebpa, did not show a change in chromatin, but did show a change in gene expression at 5 dpf. Interestingly, underlying H3K27me3 marks were significantly decreased at this locus at 50% epiboly.

Conclusions
Here, we show for the first time the applicability of ATAC-seq as a tool to investigate toxicological responses in zebrafish. Our analysis indicates that Ezh2 inhibition leads to a partial primed state of chromatin linked to metabolic pathways which results in gene expression changes later in development, leading to enhanced lipid accumulation. Although ATAC-seq seems promising, our in-depth assessment of the cebpa locus indicates that we need to consider underlying epigenetic marks as well.
Effect of extremely low-concentration gaseous chlorine dioxide against surface Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii in wet conditions on glass dishes
Authors: Morino Hirofumi , Futatsukame Masafumi , Miura Takanori , Shibata Takashi 
Published: February 2020

Abstract
Objective
Healthcare-associated infections due to Gram-negative bacteria (GNB) are a major cause of mortality and morbidity throughout the world. The purpose of the research described here was to evaluate the possibility of using an extremely low-concentration gaseous chlorine dioxide (ClO2, 0.01 ppmv, 0.028 mg/m3) as a technique to reduce the risk of environmental infection by GNB. In this study we set up an exposure chamber (1 m3) and used three types of GNB, namely Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii.

Results
The extremely low-concentration gaseous ClO2 inactivated E. coli (> 2 log10 reductions, within 2 h), P. aeruginosa (> 4 log10 reductions, within 2 h) and A. baumannii (> 2 log10 reductions, within 3 h) in wet conditions on glass dishes. Treatment of moist environments with extremely low-concentration gaseous ClO2 may help to reduce the risk of environmental infection by GNB without harmful effects.
Determinations of the peroxidative susceptibilities of cod liver oils by a newly-developed 1H NMR-based method: resistance of an antioxidant-fortified product isolated from pre-fermented sources
Authors: Percival B. C. , Zbasnik R. , Schlegel V. , Edgar M. , Zhang J. , Grootveld M. 
Published: February 2020

Abstract
Objective
To explore the molecular composition and antioxidant status of four natural (unrefined) cod liver oil (CLO) products, three of which (Products 1–3) were non-fermented, whilst one (Product 4) was isolated from pre-fermented cod livers, and hence was naturally antioxidant-fortified. Potential antioxidants and aldehyde-scavenging agents were determined by recommended and/or 1H NMR methods; peroxyl radical-specific oxygen radical absorbance capacity (ORAC) values were measured fluorimetrically. The activities of such antioxidants were also investigated by assessing the susceptibilities/resistivities of these CLOs to thermo-oxidation by 1H NMR analysis, which monitored the time-dependent evolution of aldehydic lipid oxidation products at 180 °C.

Results
Product 4 displayed much higher, albeit variable ORAC values (mean ± SEM 91.4 ± 19.5 mmol. trolox equivalents/kg) than those of Products 1–3, an observation arising from significant levels of peroxidation-blocking and/or aldehyde-consuming collagenous polypeptides/peptides, flavonones, biogenic amines, total phenolics, tannins, and ammoniacal agents therein. All of these agents were undetectable in Products 1–3. Quantitative considerations indicated that collagenous gel agents (present at ca. 1.5% (w/w)) were the most powerful Product 4 antioxidants. Significantly lower levels of aldehydes were generated in this product when exposed to thermal-stressing episodes. Results confirmed the enhanced peroxidative resistivity of a pre-fermented, antioxidant-rich natural CLO over those of corresponding non-fermented products. Product 4: Green Pasture Blue Ice™ fermented cod liver oil.