bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dysregulation of TNF-α and IFN-γ expression is a common host immune response in a chronically infected mouse model of melioidosis when comparing multiple human strains of Burkholderia pseudomallei
Authors: Amemiya Kei , Dankmeyer Jennifer L. , Bearss Jeremy J. , Zeng Xiankun , Stonier Spencer W. , Soffler Carl , Cote Christopher K. , Welkos Susan L. , Fetterer David P. , Chance Taylor B. , Trevino Sylvia R. , Worsham Patricia L. , Waag David M. 
Published: February 2020

Abstract
Background
Melioidosis is endemic in Southeast Asia and Northern Australia and is caused by the Gram-negative, facultative intracellular pathogen Burkholderia pseudomallei. Diagnosis of melioidosis is often difficult because of the protean clinical presentation of the disease, and it may mimic other diseases, such as tuberculosis. There are many different strains of B. pseudomallei that have been isolated from patients with melioidosis, but it was not clear if they could cause a similar disease in a chronic BALB/c murine model of melioidosis. Hence, we wanted to examine chronically infected mice exposed to different strains of B. pseudomallei to determine if there were differences in the host immune response to the pathogen.

Results
We identified common host immune responses exhibited in chronically infected BALB/c mice, although there was some heterogeneity in the host response in chronically infected mice after exposure to different strains of B. pseudomallei. They all displayed pyogranulomatous lesions in their spleens with a large influx of monocytes/macrophages, NK cells, and neutrophils identified by flow cytometry. Sera from chronically infected mice by ELISA exhibited elevated IgG titers to the pathogen, and we detected by Luminex micro-bead array technology a significant increase in the expression of inflammatory cytokines/chemokines, such as IFN-γ, IL-1α, IL-1β, KC, and MIG. By immunohistochemical and in situ RNA hybridization analysis we found that the increased expression of proinflammatory cytokines (IL-1α, IL-1β, TNF-α, IFN-γ) was confined primarily to the area with the pathogen within pyogranulomatous lesions. We also found that cultured splenocytes from chronically infected mice could express IFN-γ, TNF-α, and MIP-1α ex vivo without the need for additional exogenous stimulation. In addition by flow cytometry, we detected significant amounts of intracellular expression of TNF-α and IFN-γ without a protein transport blocker in monocytes/macrophages, NK cells, and neutrophils but not in CD4+ or CD8+ T cells in splenocytes from chronically infected mice.

Conclusion
Taken together the common features we have identified in chronically infected mice when 10 different human clinical strains of B. pseudomallei were examined could serve as biomarkers when evaluating potential therapeutic agents in mice for the treatment of chronic melioidosis in humans.
Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea
Authors: Zhang Ru-Yi , Zou Bin , Yan Yong-Wei , Jeon Che Ok , Li Meng , Cai Mingwei , Quan Zhe-Xue 
Published: February 2020

Abstract
Background
Amplification of small subunit (SSU) rRNA genes with universal primers is a common method used to assess microbial populations in various environmental samples. However, owing to limitations in coverage of these universal primers, some microorganisms remain unidentified. The present study aimed to establish a method for amplifying nearly full-length SSU rRNA gene sequences of previously unidentified prokaryotes, using newly designed targeted primers via primer evaluation in meta-transcriptomic datasets.

Methods
Primer binding regions of universal primer 8F/Arch21F for bacteria or archaea were used for primer evaluation of SSU rRNA sequences in meta-transcriptomic datasets. Furthermore, targeted forward primers were designed based on SSU rRNA reads from unclassified groups unmatched with the universal primer 8F/Arch21F, and these primers were used to amplify nearly full-length special SSU rRNA gene sequences along with universal reverse primer 1492R. Similarity and phylogenetic analysis were used to confirm their novel status.

Results
Using this method, we identified unclassified SSU rRNA sequences that were not matched with universal primer 8F and Arch21F. A new group within the Asgard superphylum was amplified by the newly designed specific primer based on these unclassified SSU rRNA sequences by using mudflat samples.

Conclusion
We showed that using specific primers designed based on universal primer evaluation from meta-transcriptomic datasets, identification of novel taxonomic groups from a specific environment is possible.
Variation in plastid genomes in the gynodioecious species Silene vulgaris
Authors: Krüger Manuela , Abeyawardana Oushadee A. J. , Juříček Miloslav , Krüger Claudia , Štorchová Helena 
Published: February 2020

AbstractBackgroundGynodioecious species exist in two sexes – male-sterile females and hermaphrodites. Male sterility in higher plants often results from mitonuclear interaction between the CMS (cytoplasmic male sterility) gene(s) encoded by mitochondrial genome and by nuclear-encoded restorer genes. Mitochondrial and nuclear-encoded transcriptomes in females and hermaphrodites are intensively studied, but little is known about sex-specific gene expression in plastids. We have compared plastid transcriptomes between females and hermaphrodites in two haplotypes of a gynodioecious speciesSilene vulgariswith known CMS candidate genes.ResultsWe generated complete plastid genome sequences from five haplotypesS. vulgarisincluding the haplotypes KRA and KOV, for which complete mitochondrial genome sequences were already published. We constructed a phylogenetic tree based on plastid sequences ofS. vulgaris. Whereas lowlandS. vulgarishaplotypes including KRA and KOV clustered together, the accessions from high European mountains diverged early in the phylogram.S. vulgarisbelongs amongSilenespecies with slowly evolving plastid genomes, but we still detected 212 substitutions and 112 indels between two accessions of this species. We estimated elevated Ka/Ks in thendhFgene, which may reflect the adaptation ofS. vulgaristo high altitudes, or relaxed selection. We compared depth of coverage and editing rates between female and hermaphrodite plastid transcriptomes and found no significant differences between the two sexes. We identified 51 unique C to U editing sites in the plastid genomes ofS. vulgaris, 38 of them in protein coding regions, 2 in introns, and 11 in intergenic regions. The editing site in thepsbZgene was edited only in one of two plastid genomes under study.ConclusionsWe revealed no significant differences between the sexes in plastid transcriptomes of two haplotypes ofS. vulgaris. It suggests that gene expression of plastid genes is not affected by CMS in flower buds ofS. vulgaris, although both sexes may still differ in plastid gene expression in specific tissues. We revealed the difference between the plastid transcriptomes of twoS. vulgarishaplotypes in editing rate and in the coverage of several antisense transcripts. Our results document the variation in plastid genomes and transcriptomes inS. vulgaris.
The sugar transporter SWEET10 acts downstream of FLOWERING LOCUS T during floral transition of Arabidopsis thaliana
Authors: Andrés Fernando , Kinoshita Atsuko , Kalluri Naveen , Fernández Virginia , Falavigna Vítor S. , Cruz Tiago M. D. , Jang Seonghoe , Chiba Yasutaka , Seo Mitsunori , Mettler-Altmann Tabea , Huettel Bruno , Coupland George 
Published: February 2020

AbstractBackgroundFloral transition initiates reproductive development of plants and occurs in response to environmental and endogenous signals. InArabidopsis thaliana, this process is accelerated by several environmental cues, including exposure to long days. The photoperiod-dependent promotion of flowering involves the transcriptional induction ofFLOWERING LOCUS T(FT) in the phloem of the leaf.FTencodes a mobile protein that is transported from the leaves to the shoot apical meristem, where it forms part of a regulatory complex that induces flowering. Whether FT also has biological functions in leaves of wild-type plants remains unclear.ResultsIn order to address this issue, we first studied the leaf transcriptomic changes associated with FT overexpression in the companion cells of the phloem. We found that FT induces the transcription ofSWEET10, which encodes a bidirectional sucrose transporter, specifically in the leaf veins. Moreover,SWEET10is transcriptionally activated by long photoperiods, and this activation depends on FT and one of its earliest target genesSUPPRESSOR OF CONSTANS OVEREXPRESSION 1(SOC1). The ectopic expression ofSWEET10causes early flowering and leads to higher levels of transcription of flowering-time related genes in the shoot apex.ConclusionsCollectively, our results suggest that the FT-signaling pathway activates the transcription of a sucrose uptake/efflux carrier during floral transition, indicating that it alters the metabolism of flowering plants as well as reprogramming the transcription of floral regulators in the shoot meristem.
Relationship between fluoroquinolones and the risk of aortic diseases: a meta-analysis of observational studies
Authors: Dai Xiao-ce , Yang Xin-xin , Ma Lan , Tang Guan-min , Pan Yan-yun , Hu Hui-lin 
Published: February 2020

AbstractBackgroundOur aim was to determine the relationship between the use of fluoroquinolones and the risk of aortic diseases.MethodsPubMed, EMBASE and the Web of Science were searched from inception to July 6, 2019, to identify observational studies that evaluated the risk of aortic diseases associated in users of fluoroquinolones compared with nonusers or users of other antibiotics. The primary outcome was the first occurrence of aortic diseases. We used the GRADE approach to rate the strength of evidence. We used the inverse variance method random-effect model to estimate the odds ratios (ORs) with 95% CIs, and statistical heterogeneity was assessed by theI2statistic.ResultsThis meta-analysis enrolled 2,829,385 patients reported the relationship between fluoroquinolones and the risk of aortic diseases. Compared with nonusers or users of other antibiotics, users of fluoroquinolone had a significantly increased risk of aortic diseases (adjusted OR, 2.10; 95% CI, 1.65–2.68;P = .000,I2 = 16.4%). The quality of evidence was moderate, and the number needed to harm (NNH) for aortic diseases among patients was estimated to be 1301.ConclusionsThe fluoroquinolone use in patients significantly increases the risk of new-onset aortic diseases. Clinicians need to pay attention to these severe adverse events when considering fluoroquinolone use.
Sex differences in the evolution of left ventricle remodeling in rats with severe volume overload
Authors: Walsh-Wilkinson Elisabeth , Drolet Marie-Claude , Arsenault Marie , Couet Jacques 
Published: February 2020

Abstract
Background
Aortic valve regurgitation (AR) results in left ventricle (LV) volume overload (VO) leading to its dilation and hypertrophy (H). We study a rat model of severe AR induced by puncturing one or two leaflets using a catheter. Most of our studies were conducted in male animals. Recently, we started investigating if sex dimorphism existed in the AR rat model. We observed that AR females developed as much LVH as males but morphological remodeling differences were present. A head-to-head comparison of LV morphological and functional changes had never been performed in AR males (M) and females (F) using the latest modalities in cardiac imaging by echocardiography.

Methods
We performed a longitudinal study to evaluate the development of LV hypertrophy caused by chronic AR in male and female rats over 6 months. Sham-operated (sham) animals were used as controls.

Results
LV diastolic volumes (EDV) increased more over 6 months in sham males than in females (38% vs. 23% for EDV, both p < 0.01). AR resulted in significant LV dilation for both sexes (54% vs. 51% increase in EDV) vs. baseline values. Since normal cardiac growth was less in females, dilation from AR was relatively more important for them (88% (M) vs. 157% (F) increase in EDV over sham). AR caused LV wall thickening in both males and females. It happened sooner for AR females and was more important than in males (25% (M) vs. 56% (F) increase in septum thickness at 2 months and 10% (M) vs. 30% (F) at 6 months). We then evaluated if AR was associated with changes in LV strain using speckle-tracking 2D echocardiography. Global longitudinal strain remained similar between AR and sham animals. Circumferential strain was negatively modulated by AR but only in females and early after VO induction (13% (M) vs. 26% (F)).

Conclusion
AR resulted in more LV dilation and quicker wall thickening in female AR rats compared to males. Global circumferential strain was negatively modulated in AR females but not in males. AR also seemed to lead to a more spherical LV shape in females whereas; it kept mostly an ellipsoid shape in males. This can influence validity of mass estimation of the dilated LV in females by echocardiography.
Epidemiology of acute rubella infection in Zambia during the pre-vaccination period (2005–2016) as a baseline for monitoring rubella epidemiology in the post-rubella vaccine introduction era
Authors: Mazaba Mazyanga L. , Siziya Seter , Monze Mwaka , Cohen Daniel 
Published: February 2020

Abstract
Background
Rubella is highly under reported in Zambia as in most sub-Saharan countries despite being a disease of major public health concern especially among women of childbearing age. In September 2016, Zambia introduced a combined measles-rubella vaccine in children 0–14 years. In this study, we estimated the proportion positive for acute rubella among suspected but negative measles cases between 2005 and 2016 and determined its correlates for monitoring rubella epidemiology post-rubella vaccine introduction.

Methods
In a retrospective study, 4497 measles IgM negative serum samples from 5686 clinically suspected measles cases were examined for rubella IgM antibodies using the Siemens, Enzygnost® ELISA kit at the national measles laboratory. Data on demographics, year and month of onset were extracted from the surveillance data. Multivariate logistic regression analysis using backward variable selection was conducted to determine independent predictors for acute rubella. The magnitude of association was estimated using adjusted odds ratio with a 95% confidence interval.

Results
Overall, a proportion of 29.2% (1313/4497) affecting mostly those between 5 and 24 years was determined. Only age, province, month and year were independently associated with acute rubella. The regional proportions varied from 21.8–37.3% peaking in the month of October. Persons in the age group 10–14 years (Adjusted Odds Ratio [AOR] = 2.43; 95% CI [2.01–2.95]) were more likely while those aged < 1 year less likely (AOR = 0.31; 95% CI [021–0.48]) to have acute rubella compared to those aged 25 years or older. Persons in 2010 were less likely (AOR = 0.12; CI [0.05, 0.28]) to have acute rubella compared to those in 2016. While acute rubella was more likely to occur between July and November compared to December, it was less likely to occur between February and May.

Conclusions
Rubella virus was circulating in Zambia between 2005 and 2016 affecting mostly persons in the age group 5–24 years peaking in the hot dry season month of October. Although vaccination against rubella has been launched, these baseline data are important to provide a reference point when determining the impact of the vaccination program implemented.
CNN-based survival model for pancreatic ductal adenocarcinoma in medical imaging
Authors: Zhang Yucheng , Lobo-Mueller Edrise M. , Karanicolas Paul , Gallinger Steven , Haider Masoom A. , Khalvati Farzad 
Published: February 2020

AbstractBackgroundCox proportional hazard model (CPH) is commonly used in clinical research for survival analysis. In quantitative medical imaging (radiomics) studies, CPH plays an important role in feature reduction and modeling. However, the underlying linear assumption of CPH model limits the prognostic performance. In this work, using transfer learning, a convolutional neural network (CNN) based survival model was built and tested on preoperative CT images of resectable Pancreatic Ductal Adenocarcinoma (PDAC) patients.ResultsThe proposed CNN-based survival model outperformed the traditional CPH-based radiomics approach in terms of concordance index and index of prediction accuracy, providing a better fit for patients’ survival patterns.ConclusionsThe proposed CNN-based survival model outperforms CPH-based radiomics pipeline in PDAC prognosis. This approach offers a better fit for survival patterns based on CT images and overcomes the limitations of conventional survival models.
Vancomycin-associated acute kidney injury in Hong Kong in 2012–2016
Authors: Qin Xuzhen , Tsoi Man-Fung , Zhao Xinyu , Zhang Lin , Qi Zhihong , Cheung Bernard M. Y. 
Published: February 2020

Abstract
Background
To study the incidence of vancomycin-associated acute kidney injury (VA-AKI) in Hong Kong and identify risk factors for VA-AKI.

Method
Patients with vancomycin prescription and blood level measurement in 2012–2016 were identified using the Hong Kong Hospital Authority Clinical Data Analysis and Reporting System. Acute kidney injury was defined using KDIGO criteria. Patients without creatinine measurements, steady-state trough vancomycin level or who had vancomycin treatment < 3 days were excluded. Results were analyzed using SPSS version 22.0. Logistic regression was used to identify the predictors for VA-AKI. Odds ratio and 95% confidence interval were estimated.

Results
One thousand four hundred fifty patients were identified as VA-AKI from 12,758 records in Hong Kong in 2012–2016. The incidence was respectively 10.6, 10.9, 11.3, 12.2, 11.2% from 2012 to 2016. The incidence of VA-AKI was 16.3, 12.2, 11.3 and 6.2% in patients aged 1–12, 12–60, elderly aged > 60 and newborn and infants, respectively. Baseline creatinine, serum trough vancomycin level, systematic disease history including respiratory failure, hypertension, congestive heart failure, chronic renal failure, anemia and type II diabetes, and concomitant diuretics, piperacillin-tazobactam (PTZ) and meropenem prescription were significantly higher in VA-AKI patients older than 12 years. Logistic regression showed that older age group, higher baseline creatinine, serum trough vancomycin level, respiratory failure, chronic renal failure and congestive heart failure, concomitant diuretics, PTZ and meropenem prescription, and longer hospital stay were all associated with increased risk of VA-AKI.

Conclusion
The incidence of VA-AKI in Hong Kong is low but shows no decline. Patients with higher baseline creatinine, multi-organ diseases and multiple drugs administration should have their vancomycin level monitored to decrease the risk of VA-AKI.
Stillbirth rates and associated risk factors at the Buea and Limbe regional hospitals, Cameroon: a case-control study
Authors: Egbe Thomas Obinchemti , Ewane Edwin Nkwelle , Tendongfor Nicholas 
Published: February 2020

Abstract
Background
Stillbirths bring grief to both mother and family but have been underreported in Cameroon. We aimed at determining the stillbirth rates and associated risk factors in the Buea Regional Hospital (BRH) and the Limbe Regional Hospital (LRH), Cameroon.

Materials and methods
This was a hospital-based unmatched case-control study in which files of women with stillbirth (cases) were analysed. A woman with a live birth in the same maternity during the same period served as a control. Data were collected using a pre-tested questionnaire. The stillbirth rate was the number of stillbirths per thousand births. Logistic regression analysis was used to identify independent factors associated with stillbirth.

Results
Stillbirth rates at the BRH and LRH were 33.72 and 36.45 per 1000 live births. The factors that were independently associated with stillbirth were: referral status (AOR 3.95; 95% CI: 1.85–6.58, p = 0.000), late booking visit - after 12 weeks (AOR 13.64; 95% CI: 1.49–124.83, p = 0.021), preeclampsia (AOR 3.21; 95% CI: 1.23–8.35, p = 0.01), placental abruption (AOR 21.46; 95% CI: 2.36–194.77, p = 0.006), moderate anaemia (AOR 2.04; 95% CI: 1.09–3.83, p = 0.03), labour dystocia (AOR 5.37; 95% CI: 1.77–15.92, p = 0.003), low birth weight (AOR 5.27; 95% CI: 1.48–3.53, p = 0.000), and preterm delivery (AOR 2.81; 95% CI: 1.48–3.35, p = 0.002).

Conclusion
Stillbirth rates are high in both health facilities. Risk factors of stillbirths include referral from another health facility, anaemia, preeclampsia and late booking visit, placental abruption, labour dystocia, preterm birth, and low birth weight. Term, post-term and macrosomia were protective of stillbirth. We recommend electronic data storage in hospitals in Cameroon.
The influence of radiotherapy techniques on the plan quality and on the risk of secondary tumors in patients with pituitary adenoma
Authors: Treutwein Marius , Steger Felix , Loeschel Rainer , Koelbl Oliver , Dobler Barbara 
Published: February 2020

Abstract
Background
This planning study compares different radiotherapy techniques for patients with pituitary adenoma, including flatness filter free mode (FFF), concerning plan quality and secondary malignancies for potentially young patients. The flatness filter has been described as main source of photon scatter.

Material and methods
Eleven patients with pituitary adenoma were included. An Elekta Synergy™ linac was used in the treatment planning system Oncentra® and for the measurements. 3D plans, IMRT, and VMAT plans and non-coplanar varieties were considered. The plan quality was evaluated regarding homogeneity, conformity, delivery time and dose to the organs at risk. The secondary malignancy risk was calculated from dose volume data and from measured dose to the periphery using different models for carcinoma and sarcoma risk.

Results
The homogeneity and conformity were nearly unchanged with and without flattening filter, neither was the delivery time found substantively different. VMAT plans were more homogenous, conformal and faster in delivery than IMRT plans. The secondary cancer risk was reduced with FFF both in the treated region and in the periphery. VMAT plans resulted in a higher secondary brain cancer risk than IMRT plans, but the risk for secondary peripheral cancer was reduced. Secondary sarcoma risk plays a minor role. No advantage was found for non-coplanar techniques. The FFF delivery times were not shortened due to additional monitor units needed and technical limitations. The risk for secondary brain cancer seems to depend on the irradiated volume. Secondary sarcoma risk is much smaller than carcinoma risk in accordance to the results of the atomic bomb survivors. The reduction of the peripheral dose and resulting secondary malignancy risk for FFF is statistically significant. However, it is negligible in comparison to the risk in the treated region.

Conclusion
Treatments with FFF can reduce secondary malignancy risk while retaining similar quality as with flattening filter and should be preferred. VMAT plans show the best plan quality combined with lowest peripheral secondary malignancy risk, but highest level of second brain cancer risk. Taking this into account VMAT FFF seems the most advantageous technique for the treatment of pituitary adenomas with the given equipment.