bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype
Authors: Rody Hugo V. S. , Bombardelli Renato G. H. , Creste Silvana , Camargo Luís E. A. , Van Sluys Marie-Anne , Monteiro-Vitorello Claudia B. 
Published: November 2019

AbstractBackgroundResistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genomic content of Resistance Gene Analogs (RGAs) of modern sugarcane cultivars to its degrees of resistance to diseases such as smut. However, due to the highly polyploid and heterozygous nature of sugarcane genome, large scale RGA predictions is challenging.ResultsWe predicted, searched for orthologs, and investigated the genomic features of RGAs within a recently released sugarcane elite cultivar genome, alongside the genomes of sorghum, one sugarcane ancestor (Saccharum spontaneum), and a collection of de novo transcripts generated for six modern cultivars. In addition, transcriptomes from two sugarcane genotypes were obtained to investigate the roles of RGAs differentially expressed (RGADE) in their distinct degrees of resistance to smut. Sugarcane references lack RGAs from the TNL class (Toll-Interleukin receptor (TIR) domain associated to nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains) and harbor elevated content of membrane-associated RGAs. Up to 39% of RGAs were organized in clusters, and 40% of those clusters shared synteny. Basically, 79% of predicted NBS-encoding genes are located in a few chromosomes.S. spontaneumchromosome 5 harbors most RGADE orthologs responsive to smut in modern sugarcane. Resistant sugarcane had an increased number of RGAs differentially expressed from both classes of RLK (receptor-like kinase) and RLP (receptor-like protein) as compared to the smut-susceptible. Tandem duplications have largely contributed to the expansion of both RGA clusters and the predicted clades of RGADEs.ConclusionsMost of smut-responsive RGAs in modern sugarcane were potentially originated in chromosome 5 of the ancestralS. spontaneumgenotype. Smut resistant and susceptible genotypes of sugarcane have a distinct pattern of RGADE. TM-LRR (transmembrane domains followed by LRR) family was the most responsive to the early moment of pathogen infection in the resistant genotype, suggesting the relevance of an innate immune system. This work can help to outline strategies for further understanding of allele and paralog expression of RGAs in sugarcane, and the results should help to develop a more applied procedure for the selection of resistant plants in sugarcane.
Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya
Authors: Kyany’a Cecilia , Nyasinga Justin , Matano Daniel , Oundo Valerie , Wacira Simon , Sang Willie , Musila Lillian 
Published: November 2019

AbstractBackgroundThe increase and spread of virulent-outbreak associated, methicillin and vancomycin resistant (MRSA/VRSA)Staphylococcus aureusrequire a better understanding of the resistance and virulence patterns of circulating and emerging strains globally. This study sought to establish the resistance phenotype, and strains of 32 non-duplicate clinical MRSA and MSSAS. aureusisolates from four Kenyan hospitals,identify their resistance and virulence genes and determine the genetic relationships of MRSA with global strains.MethodsAntimicrobial susceptibility profiles were determined on a Vitek 2, genomic DNA sequenced on an Illumina Miseq and isolates typed in-silico. Resistance and virulence genes were identified using ARIBA and phylogenies generated using RAxML.ResultsThe MRSA isolates were 100% susceptible to vancomycin, teicoplanin, linezolid, and tigecycline. Nine distinct CC, 12 ST and 15 spa types including the novel t17826 and STs (4705, 4707) were identified with CC8 and CC152 predominating. MRSA isolates distributed across 3 CCs; CC5-ST39 (1), CC8 – ST241 (4), a novel CC8-ST4705 (1), ST8 (1) and CC152 (1). There was > 90% phenotype-genotype concordance with key resistance genes identified only among MRSA isolates:gyrA,rpoB, andparCmutations,mecA,ant (4′)-lb, aph (3′)-IIIa, ermA, sat-4, fusA, mphCandmsrA. Kenyan MRSA isolates were genetically diverse and most closely related to Tanzanian and UK isolates. There was a significant correlation betweenmap,hlgA,selk,selqandcap8dvirulence genes and severe infections.ConclusionThe findings showed a heterogeneousS. aureuspopulation with novel strain types. Though limited by the low number of isolates, this study begins to fill gaps and expand our knowledge ofS. aureusepidemiology while uncovering interesting patterns of distribution of strain types which should be further explored. Although last-line treatments are still effective,the potential for outbreaks of both virulent and resistant strains remain, requiring sustained surveillance ofS. aureuspopulations.
Oligo-painting and GISH reveal meiotic chromosome biases and increased meiotic stability in synthetic allotetraploid Cucumis ×hytivus with dysploid parental karyotypes
Authors: Zhao Qinzheng , Wang Yunzhu , Bi Yunfei , Zhai Yufei , Yu Xiaqing , Cheng Chunyan , Wang Panqiao , Li Ji , Lou Qunfeng , Chen Jinfeng 
Published: November 2019

Abstract

Background
Meiosis of newly formed allopolyploids frequently encounter perturbations induced by the merging of divergent and hybridizable genomes. However, to date, the meiotic properties of allopolyploids with dysploid parental karyotypes have not been studied in detail. The allotetraploid Cucumis ×hytivus (HHCC, 2n = 38) was obtained from interspecific hybridization between C. sativus (CC, 2n = 14) and C. hystrix (HH, 2n = 24) followed by chromosome doubling. The results of this study thus offer an excellent opportunity to explore the meiotic properties of allopolyploids with dysploid parental karyotypes.

Results
In this report, we describe the meiotic properties of five chromosomes (C5, C7, H1, H9 and H10) and two genomes in interspecific hybrids and C. ×hytivus (the 4th and 14th inbred family) through oligo-painting and genomic in situ hybridization (GISH). We show that 1) only two translocations carrying C5-oligo signals were detected on the chromosomes C2 and C4 of one 14th individual by the karyotyping of eight 4th and 36 14th plants based on C5- and C7-oligo painting, and possible cytological evidence was observed in meiosis of the 4th generation; 2) individual chromosome have biases for homoeologous pairing and univalent formation in F1 hybrids and allotetraploids; 3) extensive H-chromosome autosyndetic pairings (e.g., H-H, 25.5% PMCs) were observed in interspecific F1 hybrid, whereas no C-chromosome autosyndetic pairings were observed (e.g. C-C); 4) the meiotic properties of two subgenomes have significant biases in allotetraploids: H-subgenome exhibits higher univalent and chromosome lagging frequencies than C-subgenome; and 5) increased meiotic stability in the S14 generation compared with the S4 generation, including synchronous meiosis behavior, reduced incidents of univalent and chromosome lagging.

Conclusions
These results suggest that the meiotic behavior of two subgenomes has dramatic biases in response to interspecific hybridization and allopolyploidization, and the meiotic behavior harmony of subgenomes is a key subject of meiosis evolution in C. ×hytivus. This study helps to elucidate the meiotic properties and evolution of nascent allopolyploids with the dysploid parental karyotypes.
Postoperative cognitive dysfunction after robot-assisted radical cystectomy (RARC) with cerebral oxygen monitoring an observational prospective cohort pilot study
Authors: Li Yue , Huang Dan , Su Diansan , Chen Jie , Yang Liqun 
Published: November 2019

AbstractBackgroundThe incidence and risk factors of postoperative cognitive dysfunction (POCD) during robot-assisted radical cystectomy (RARC) in extreme Trendelenburg positioning and pneumoperitoneum are still controversial. The aim of this prospective observational study was to find the incidence rate as well as possible risk factors of POCD in RARC with cerebral oxygen monitoring.MethodsPatients who underwent RARC and open abdominal surgery in horizontal positioning were included. Preoperative and postoperative arterial blood gas (ABG), S-100β, C-reactive protein (CRP), and cognitive dysfunction scales were tested. Also, we used Z score to analyze and comprehensively evaluate POCD. Measurements of heart rate (HR), mean arterial pressure (MAP), central venous pressure (CVP), end-tidal CO2(etCO2), and cerebral oxygen were immediately obtained after different time points during the surgery.ResultsHere, 24 and 23 patients were included in the RARC group and in the control group, respectively. The incidence of POCD didn’t have significant difference in RARC group (45.8%), in contrast to the control group (26.1%). The laboratory tests of s100β and CRP between two groups didn’t contain significant difference as well. As duration of Trendelenburg and pneumoperitoneum prolonged, the cerebral oxygen saturation in the RARC group increased, which didn’t cause excessive perfusion nevertheless (rSO2<75%). We compared laboratory tests, age, education status, blood loss, and fluid input between POCD and non-POCD patients. A significant difference was found in the serum concentrations of CRP (72.59 ± 42.09 vs. 48.50 ± 26.53,P = 0.025) and age (69.20 ± 7.033 vs. 65.34 ± 5.228,P = 0.041).ConclusionRARC in extreme Trendelenburg positioning and pneumoperitoneum did not significantly increase the incidence of POCD and didn’t cause excessive perfusion. The inflammation marker CRP and age might be independent risk factors of POCD.Trial registrationClinicaltrials.govwith registration numberNCT03372135. Registered 1 November 2017 (retrospectively registered).
Neck circumference as an indicator of elevated blood pressure independent from body composition: implications from the China nation health survey (CNHS)
Authors: He Huijing , Pan Li , Liu Feng , Ma Jingang , Wang Li , Hu Zhiping , Li Yajun , Shan Guangliang 
Published: November 2019

Abstract

Background
The independent association of neck circumference (NC) on elevated blood pressure is still uncertain in adults of China. The aim of this study is to explore such association and investigate the predictive value of NC on hypertension.

Methods
A total of 4279 adults aged 20–80 years participated in the cross-sectional study in 2014. Anthropometric information, NC, body composition indexes such as waist circumference, hip circumference and body fat percentage, and blood pressure were measured. General linear regression model was used to explore the association between NC and blood pressure; Logistic regression models were fitted to calculate the multi-variable adjusted prevalence, and the association of NC with hypertension.

Results
The overall prevalence of hypertension and pre-hypertension were 11.05 and 23.63%, respectively. NC was positively associated with both SBP and DBP (p < 0.001). The adjusted prevalence of hypertension increased with elevated NC quartiles in both sexes (p for trend < 0.001), from 17.81 to 42.93% in male and 9.72 to 21.31% in female. For male, NC was only associated with hypertension (OR: 1.15, 95% CI: 1.05–1.25) but not with pre-hypertension (OR: 0.97, 95% CI: 0.88–1.06). However, in female, NC was associated with both pre-hypertension and hypertension, the BMI adjusted ORs were 1.15 (1.03–1.28) and 1.24 (1.14–1.34). The sex-specific AUCs for NC predicting hypertension were 0.633 in male and 0.663 in female, similar with AUCs of other body fat indexes.

Conclusions
NC was associated with both pre-HTN and HTN independent from other body composition indexes. NC is a simple and useful anthropometric index to identify elevated blood pressure in Chinese adults.
Effect of community-based distribution of misoprostol on facility delivery: a scoping review
Authors: Tiruneh Gizachew Tadele , Yakob Bereket , Ayele Wubegzier Mekonnen , Yigzaw Muluneh , Roro Meselech Assegid , Medhanyi Araya Abrha , Hailu Etenesh Gebreyohannes , Bayou Yibeltal Tebekaw 
Published: November 2019

Abstract

Introduction
Community distribution of misoprostol to pregnant women in advance of labor is one of the compelling strategies for preventing postpartum hemorrhage. Concerns have been reported that misoprostol distribution could reduce facility delivery or lead to misuse of the medication. This scoping review was conducted to synthesize the evidence on the effect of community-based misoprostol distribution on rates of facility delivery, and to assess the frequency of mothers taking distributed misoprostol before delivery, and any harmful outcomes of such misuse.

Methods
We included peer-reviewed articles on misoprostol implementation from PubMed, Cochrane Review Library, Popline, and Google Scholars. Narrative synthesis was used to analyze and interpret the findings, in which quantitative and qualitative syntheses are integrated.

Results
Three qualitative studies, seven observational studies, and four experimental or quasi-experimental studies were included in this study. All before-after household surveys reported increased delivery coverage after the intervention: ranging from 4 to 46 percentage points at the end of the intervention when compared to the baseline. The pooled analysis of experimental and quasi-experimental studies involving 7564 women from four studies revealed that there was no significant difference in rates of facility delivery among the misoprostol and control groups [OR 1.011; 95% CI: 0.906–1.129]. A qualitative study among health professionals also indicated that community distribution of misoprostol for the prevention of postpartum hemorrhage is acceptable to community members and stakeholders and it is a feasible interim solution until access to facility birth increases.
In the community-based distribution of misoprostol programs, self-administration of misoprostol by pregnant women before delivery was reported in less than 2% of women, among seven studies involving 11,108 mothers. Evidence also shows that most women who used misoprostol pills, used them as instructed. No adverse outcomes from misuse in either of the studies reviewed.

Conclusions
The claim that community-based distribution of misoprostol would divert women who would have otherwise had institutional deliveries to have home deliveries and promote misuse of the medication are not supported with evidence. Therefore, community-based distribution of misoprostol can be an appropriate strategy for reducing maternal deaths which occur due to postpartum hemorrhages, especially in resource-limited settings.
IFN-γ down-regulates the PD-1 expression and assist nivolumab in PD-1-blockade effect on CD8+ T-lymphocytes in pancreatic cancer
Authors: Ding Guoping , Shen Tao , Yan Chen , Zhang Mingjie , Wu Zhengrong , Cao Liping 
Published: November 2019

Abstract

Background
Pancreatic cancer is characterized by a highly immunosuppressive tumor microenvironment and evasion of immune surveillance. Although programmed cell death 1 receptor (PD-1) blockade has achieved certain success in immunogenic cancers, the responses to the PD-1 antibody are not effective or sustained in patients with pancreatic cancer.

Methods
Firstly, PD-1 expressions on peripheral CD8+ T-lymphocytes of patients with pancreatic cancer and healthy donors were measured. In in vitro study, peripheral T-lymphocytes were isolated and treated with nivolumab and/or interferon-γ, and next, PD-1-blockade effects, proliferations, cytokine secretions and cytotoxic activities were tested after different treatments. In in vivo study, mice bearing subcutaneous pancreatic cancer cell lines were treated with induced T-lymphocytes and tumor sizes were measured.

Results
PD-1 protein expression is increased on peripheral CD8+ T cells in patients with pancreatic ductal adenocarcinoma compared with that in health donor. PD-1 expression on CD8+ T-lymphocytes was decreased by nivolumab in a concentration-dependent manner in vitro. IFN-γ could directly down-regulate expression of PD-1 in vitro. Furthermore, the combination therapy of nivolumab and IFN-γ resulted in greatest effect of PD-1-blockde (1.73 ± 0.78), compared with IFN-γ along (18.63 ± 0.82) and nivolumab along (13.65 ± 1.22). Moreover, the effects of nivolumab plus IFN-γ largest promoted the T-lymphocytes function of proliferations, cytokine secretions and cytotoxic activities. Most importantly, T-lymphocytes induced by nivolumab plus IFN-γ presented the best repression of tumor growth.

Conclusions
IFN-γ plus a PD-1-blockading agent could enhance the immunologic function and might play a crucial role in effective adoptive transfer treatments of pancreatic cancer.
Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition
Authors: Kalmár Alexandra , Nagy Zsófia Brigitta , Galamb Orsolya , Csabai István , Bodor András , Wichmann Barnabás , Valcz Gábor , Barták Barbara Kinga , Tulassay Zsolt , Igaz Peter , Molnár Béla 
Published: November 2019

Abstract

Background
Long non-coding RNAs (lncRNAs) play a fundamental role in colorectal cancer (CRC) development, however, lncRNA expression profiles in CRC and its precancerous stages remain to be explored. We aimed to study whole genomic lncRNA expression patterns in colorectal adenoma–carcinoma transition and to analyze the underlying functional interactions of aberrantly expressed lncRNAs.

Methods
LncRNA expression levels of colonic biopsy samples (20 CRCs, 20 adenomas (Ad), 20 healthy controls (N)) were analyzed with Human Transcriptome Array (HTA) 2.0. Expression of a subset of candidates was verified by qRT-PCR and in situ hybridization (ISH) analyses. Furthermore, in silico validation was performed on an independent HTA 2.0, on HGU133Plus 2.0 array data and on the TCGA COAD dataset. MiRNA targets of lncRNAs were predicted with miRCODE and lncBase v2 algorithms and miRNA expression was analyzed on miRNA3.0 Array data. MiRNA-mRNA target prediction was performed using miRWALK and c-Met protein levels were analyzed by immunohistochemistry. Comprehensive lncRNA-mRNA-miRNA co-expression pattern analysis was also performed.

Results
Based on our HTA results, a subset of literature-based CRC-associated lncRNAs showed remarkable expression changes already in precancerous colonic lesions. In both Ad vs. normal and CRC vs. normal comparisons 16 lncRNAs, including downregulated LINC02023, MEG8, AC092834.1, and upregulated CCAT1, CASC19 were identified showing differential expression during early carcinogenesis that persisted until CRC formation (FDR-adjusted p < 0.05). The intersection of CRC vs. N and CRC vs. Ad comparisons defines lncRNAs characteristic of malignancy in colonic tumors, where significant downregulation of LINC01752 and overexpression of UCA1 and PCAT1 were found. Two candidates with the greatest increase in expression in the adenoma-carcinoma transition were further confirmed by qRT-PCR (UCA1, CCAT1) and by ISH (UCA1). In line with aberrant expression of certain lncRNAs in tumors, the expression of miRNA and mRNA targets showed systematic alterations. For example, UCA1 upregulation in CRC samples occurred in parallel with hsa-miR-1 downregulation, accompanied by c-Met target mRNA overexpression (p < 0.05).

Conclusion
The defined lncRNA sets may have a regulatory role in the colorectal adenoma-carcinoma transition. A subset of CRC-associated lncRNAs showed significantly differential expression in precancerous samples, raising the possibility of developing adenoma-specific markers for early detection of colonic lesions.
Tumor-associated macrophages predict prognosis in diffuse large B-cell lymphoma and correlation with peripheral absolute monocyte count
Authors: Li Yan-Li , Shi Zhi-Hu , Wang Xian , Gu Kang-Sheng , Zhai Zhi-Min 
Published: November 2019

Abstract

Background
Diffuse large B-cell lymphoma (DLBCL) is characterized by its clinical and biological heterogeneity. The clinical prognostic implications of tumor-associated macrophages (TAMs) in DLBCL remain controversial and the correlation between TAMs and peripheral absolute monocyte count (AMC) has not yet been elucidated.

Methods
In 221 untreated, newly diagnosed patients with DLBCL, we evaluated the prognostic value of TAMs using immunohistochemical analysis, as well as the association of TAMs and AMC.

Results
We found that high CD68 or high CD163 expression was correlated with clinicopathological characteristics, high CD163 expression was an adverse predictor for both overall survival (OS) [hazard ratio (HR) = 2.265, P = 0.005] and progression- free survival (PFS) (HR = 1.925, P = 0.017) in patients with DLBCL. Patients with high CD68 or high CD163 expression had significantly poorer OS and PFS than those with low CD68 or low CD163 expression, respectively (CD68: OS: P<0.001, PFS: P<0.001; CD163: OS: P<0.001, PFS: P<0.001), even in the rituximab era. Moreover, high-risk patients could be further identified by the expression of CD68 or CD163, especially in those classified as low/intermediate risk by International Prognostic Index (IPI). Furthermore, the significant positive correlation was also detected between CD68 expression or CD163 expression and AMC (r = 0.256, P<0.001; r = 0.303, P<0.001).

Conclusions
Patients with high expression of TAMs tend to have poorer OS and PFS, even in the rituximab era, and have positive correlation with AMC. Therefore, the peripheral AMC is a useful prognostic marker reflecting the status of the tumor microenvironment (TME) in DLBCL.
Efficiency and safety of phenylephrine and tropicamide used in premature retinopathy: a prospective observational study
Authors: Alpay Atilla , Canturk Ugurbas Sılay , Aydemir Cumhur 
Published: November 2019

AbstractBackgroundTo determine effects and side effects of topical application of phenylephrine 2.5% and tropicamide 0.5% combination in preterm infants.MethodsIn this prospective observational study, 60 infants undergoing retinopathy of prematurity (ROP) screening were prospectively observed. Pupillary diameter, blood pressure, heart rate, and oxygen saturation were monitored before and after up to 24 h during ROP screening examinations.ResultsThe mean pupillary diameter 1 h after the instillation of drops was 5.58 ± 0.75 mm for both eyes. The mean systolic and diastolic pressure and oxygen saturation of infants did not change statistically until the end of the study. The average heart rate decreased by a mean of 4.96 beats/minute from the baseline following eye drops instillation. General condition deterioration, fall in oxygen saturation and bradycardia were observed in 4 infants that already had respiratory distress syndrome.ConclusionThe phenylephrine 2.5% plus tropicamide 0.5% drop is effective and safe as mydriatic combination for retinopathy of prematurity screening. In infants with an additional systemic disease such as respiratory distress syndrome, the side effects of mydriatic drops may be more common. Such babies should be kept under close observation.Trial registrationThe trial was retrospectively registered on 28 February 2018. TheClinicalTrials.govIdentifier is NCT03448640.