bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum
Authors: Ashraf Javaria , Zuo Dongyun , Cheng Hailiang , Malik Waqas , Wang Qiaolian , Zhang Youping , Abid Muhammad Ali , Yang Qiuhong , Feng Xiaoxu , Yu John Z. , Song Guoli 
Published: July 2020

AbstractBackgroundGenome sequencing technologies have been improved at an exponential pace but precise chromosome-scale genome assembly still remains a great challenge. The draft genome of cultivatedG. arboreumwas sequenced and assembled with shotgun sequencing approach, however, it contains several misassemblies. To address this issue, we generated an improved reassembly ofG. arboreumchromosome 12 using genetic mapping and reference-assisted approaches and evaluated this reconstruction by comparing with homologous chromosomes ofG. raimondiiandG. hirsutum.ResultsIn this study, we generated a high quality assembly of the 94.64 Mb length ofG. arboreumchromosome 12 (A_A12) which comprised of 144 scaffolds and contained 3361 protein coding genes. Evaluation of results using syntenic and collinear analysis of reconstructedG. arboreumchromosome A_A12 with its homologous chromosomes ofG. raimondii(D_D08) andG. hirsutum(AD_A12 and AD_D12) confirmed the significant improved quality of current reassembly as compared to previous one. We found major misassemblies in previously assembled chromosome 12 (A_Ca9) ofG. arboreumparticularly in anchoring and orienting of scaffolds into a pseudo-chromosome. Further, homologous chromosomes 12 ofG. raimondii(D_D08) andG. arboreum(A_A12) contained almost equal number of transcription factor (TF) related genes, and showed good collinear relationship with each other. As well, a higher rate of gene loss was found in corresponding homologous chromosomes of tetraploid (AD_A12 and AD_D12) than diploid (A_A12 and D_D08) cotton, signifying that gene loss is likely a continuing process in chromosomal evolution of tetraploid cotton.ConclusionThis study offers a more accurate strategy to correct misassemblies in sequenced draft genomes of cotton which will provide further insights towards its genome organization.
Comparative analysis of single-cell transcriptomics in human and zebrafish oocytes
Authors: Can Handan , Chanumolu Sree K. , Gonzalez-Muñoz Elena , Prukudom Sukumal , Otu Hasan H. , Cibelli Jose B. 
Published: July 2020

AbstractBackgroundZebrafish is a popular model organism, which is widely used in developmental biology research. Despite its general use, the direct comparison of the zebrafish and human oocyte transcriptomes has not been well studied. It is significant to see if the similarity observed between the two organisms at the gene sequence level is also observed at the expression level in key cell types such as the oocyte.ResultsWe performed single-cell RNA-seq of the zebrafish oocyte and compared it with two studies that have performed single-cell RNA-seq of the human oocyte. We carried out a comparative analysis of genes expressed in the oocyte and genes highly expressed in the oocyte across the three studies. Overall, we found high consistency between the human studies and high concordance in expression for the orthologous genes in the two organisms. According to the Ensembl database, about 60% of the human protein coding genes are orthologous to the zebrafish genes. Our results showed that a higher percentage of the genes that are highly expressed in both organisms show orthology compared to the lower expressed genes. Systems biology analysis of the genes highly expressed in the three studies showed significant overlap of the enriched pathways and GO terms. Moreover, orthologous genes that are commonly overexpressed in both organisms were involved in biological mechanisms that are functionally essential to the oocyte.ConclusionsOrthologous genes are concurrently highly expressed in the oocytes of the two organisms and these genes belong to similar functional categories. Our results provide evidence that zebrafish could serve as a valid model organism to study the oocyte with direct implications in human.
Genome sequence and spore germination-associated transcriptome analysis of Corynespora cassiicola from cucumber
Authors: Gao Shigang , Zeng Rong , Xu Lihui , Song Zhiwei , Gao Ping , Dai Fuming 
Published: July 2020

AbstractBackgroundCorynespora cassiicola, as a necrotrophic phytopathogenic ascomycetous fungus, can infect hundreds of species of plants and rarely causes human diseases. This pathogen infects cucumber species and causes cucumber target spot, which has recently caused large cucumber yield losses in China. Genome sequence and spore germination-associated transcriptome analysis will contribute to the understanding of the molecular mechanism of pathogenicity and spore germination ofC. cassiicola.ResultsFirst, we reported the draft genome sequences of the cucumber-sampledC. cassiicolaisolate HGCC with high virulence. Although conspecific, HGCC exhibited distinct genome sequence differences from a rubber tree-sampled isolate (CCP) and a human-sampled isolate (UM591). The proportion of secreted proteins was 7.2% in HGCC. A total of 28.9% (4232) of HGCC genes, 29.5% (4298) of CCP genes and 28.6% (4214) of UM591 genes were highly homologous to experimentally proven virulence-associated genes, respectively, which were not significantly different (P = 0.866) from the average (29.7%) of 10 other phytopathogenic fungi. Thousands of putative virulence-associated genes in various pathways or families were identified inC. cassiicola. Second, a global view of the transcriptome ofC. cassiicolaspores during germination was evaluated using RNA sequencing (RNA-Seq). A total of 3288 differentially expressed genes (DEGs) were identified. The majority of KEGG-annotated DEGs were involved in metabolism, genetic information processing, cellular processes, the organismal system, human diseases and environmental information processing.ConclusionsThese results facilitate the exploration of the molecular pathogenic mechanism ofC. cassiicolain cucumbers and the understanding of molecular and cellular processes during spore germination.
Screening diverse soybean genotypes for drought tolerance by membership function value based on multiple traits and drought-tolerant coefficient of yield
Authors: Yan Chunjuan , Song Shuhong , Wang Wenbin , Wang Changling , Li Haibo , Wang Feng , Li Shengyou , Sun Xugang 
Published: July 2020

Abstract
Background
Drought is a major limiting factor seriously influencing worldwide soybean production and its impact on yield, morphological and physiological traits depend on the timing it occurs and the intensity of water shortage. Only limited research has however been conducted on identifying the drought-tolerant genotypes at different growth stages (vegetative growth phase, reproductive growth phase and the whole growth phase) as well as evaluate the effectiveness and reliability of multiple phenotypic and yield-related characteristics in soybean.

Results
Two pot experiments and a 2-year field experiment were conducted to evaluate soybean drought tolerance at different growth stages. The membership function value of drought tolerance (MFVD) was used to identify drought-resistant cultivars during vegetative growth phase and reproductive growth stage; the relative drought index (RDI) of yield was used to assess drought-resistant cultivars during the whole growing period. In this study, regression models built based on MFVD indicated that the variation of drought tolerant coefficient (DC) of R/S, TRL, LAI and RSR could explain 73.70% of the total variation at vegetative growth phase. However, higher heritability only found in LAI and RSR, indicating the two traits could serve as reliable criteria for drought evaluation. Similarly, the DC of SPP, YPP, PH, PB, MSNN and STB could explain 94.30% of the total variation in MFVD according to stepwise multiple linear regression analyses at reproductive growth phase. Thus, these six traits were identified as indicators for screening drought resistance genotypes in soybean. In addition, correlation analysis revealed that the MFVD was significantly positively correlated with the DCRB, DCR/S, DCRSA, DCRSR and DCRBR at vegetative growth phase and DCYPP, DCSPP, DCRB, and DCPB at reproductive growth phase. This indicated that these traits were closely related to the drought resistance of plants.

Conclusions
LD24, JD36 and TF31 of vegetative growth phase, and TD37 and LD26 of reproductive growth phase were identified with drought tolerant and highly drought tolerant, respectively. Moreover, 30 accessions with drought tolerance were screened in the field trial and could be applied for the drought resistance of other genotypes by cross-breeding.
Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing
Authors: Sun Min , Huang Dejun , Zhang Ailing , Khan Imran , Yan Haidong , Wang Xiaoshan , Zhang Xinquan , Zhang Jian , Huang Linkai 
Published: July 2020

Abstract
Background
Heat and drought are serious threats for crop growth and development. As the sixth largest cereal crop in the world, pearl millet can not only be used for food and forage but also as a source of bioenergy. Pearl millet is highly tolerant to heat and drought. Given this, it is considered an ideal crop to study plant stress tolerance and can be used to identify heat-resistant genes.

Results
In this study, we used Pacbio sequencing data as a reference sequence to analyze the Illumina data of pearl millet that had been subjected to heat and drought stress for 48 h. By summarizing previous studies, we found 26,299 new genes and 63,090 new transcripts, and the number of gene annotations increased by 20.18%. We identified 2792 transcription factors and 1223 transcriptional regulators. There were 318 TFs and 149 TRs differentially expressed under heat stress, and 315 TFs and 128 TRs were differentially expressed under drought stress. We used RNA sequencing to identify 6920 genes and 6484 genes differentially expressed under heat stress and drought stress, respectively.

Conclusions
Through Pacbio sequencing, we have identified more new genes and new transcripts. On the other hand, comparing the differentially expressed genes under heat tolerance with the DEGs under drought stress, we found that even in the same pathway, pearl millet responds with a different protein.
Correlation between ischemia-modified albumin level and coronary collateral circulation
Authors: Chen Xin , Lin Yan , Tian Lihua , Wang Zhiquan 
Published: July 2020

Abstract
Objective
To investigate the correlation between ischemia-modified albumin (IMA) levels and coronary collateral circulation (CCC) in patients with chronic total occlusive (CTO).

Methods
Coronary angiography was performed in the Department of Cardiology, Zhongnan Hospital of Wuhan University from 2017 to 08 to 2019–02 to identify 128 patients with CTO lesions in at least one major coronary artery. According to the Rentrop evaluation criteria, the degree of CCC formation was divided into the poor CCC formation group (Rentrop0–1 grade,n = 69) and the good CCC formation group (Rentrop2–3 grade,n = 59). The IMA level of the patients was measured using an albumin-cobalt binding assay. The general data, routine blood panel, total bilirubin (TBIL), blood lipids, uric acid (UA), left ventricular ejection fraction (LVEF) and other indicators of the patients were recorded and analyzed while assessing the patients’ blood vessel occlusion.

Results
The proportion of platelet count and diabetes in the poor CCC group was higher than that in the good CCC group (P < 0.05). The ratio of ischemia-modified albumin and total bilirubin in the poor CCC group was lower than that in the good CCC group (P < 0.05). Multivariate logistic regression analysis showed that ischemia-modified albumin was positively correlated with CCC formation [OR = 1.190,95% CI (1.092–1.297),P < 0.001], while diabetes was negatively correlated with CCC formation [OR = 0.285,95% CI (0.094–0.864), P < 0.05]. Ischemic modified albumin predicted good formation of CCC according to the ROC curve, and the area under the ROC curve was 0.769(95% CI,0.686–0.851, P<0.001); the optimal cut-off value was 63.35 KU/L, and the sensitivity was 71.2%,specificity is 71%.

Conclusion
The IMA level is closely related to good formation of CCC. Higher IMA levels can be used as an effective predictor of good CCC formation in patients with CTO.
The effect of milrinone on mortality in adult patients who underwent CABG surgery: a systematic review of randomized clinical trials with a meta-analysis and trial sequential analysis
Authors: Ren Yu-shan , Li Lan-fang , Peng Tao , Tan Yu-jun , Sun Ying , Cheng Guo-liang , Zhang Gui-min , Li Jie 
Published: July 2020

Abstract
Background
As an inodilator, milrinone is commonly used for patients who undergo coronary artery bypass graft (CABG) surgery because of its effectiveness in decreasing the cardiac index and mitral regurgitation. The aim of this study was to perform a systematic review and meta-analysis of existing studies from the past 20 years to evaluate the impact of milrinone on mortality in patients who undergo CABG surgery.

Methods
We performed a systematic literature search on the application of milrinone in patients who underwent CABG surgery in studies published between 1997 and 2017 in BioMed Central, PubMed, EMBASE, and the Cochrane Central Register. The included studies evaluated milrinone groups compared to groups receiving either placebo or standard treatment and further compared the systemic administration.

Results
The network meta-analysis included 723 patients from 16 randomized clinical trials. Overall, there was no significant difference in mortality between the milrinone group and the placebo/standard care group when patients underwent CABG surgery. In addition, 9 trials (with 440 randomized patients), 4 trials (with 212 randomized patients), and 10 trials (with 470 randomized patients) reported that the occurrence of myocardial infarction (MI), myocardial ischemia, and arrhythmia was lower in the milrinone group than in the placebo/standard care group. Between the milrinone treatment and placebo/standard care groups, the occurrence of myocardial infarction, myocardial ischemia, and arrhythmia was significantly different. However, the occurrence of stroke and renal failure, the duration of inotropic support (h), the need for an intra-aortic balloon pump (IABP), and mechanical ventilation (h) between these two groups showed no differences.

Conclusions
Based on the current results, compared with placebo, milrinone might be unable to decrease mortality in adult CABG surgical patients but can significantly ameliorate the occurrence of MI, myocardial ischemia, and arrhythmia. These results provide evidence for the further clinical application of milrinone and of therapeutic strategies for CABG surgery. However, along with milrinone application in clinical use, sufficient data from randomized clinical trials need to be collected, and the potential benefits and adverse effects should be analyzed and reevaluated.
Antimicrobial stewardship in the primary care setting: from dream to reality?
Authors: Avent M. L. , Cosgrove S. E. , Price-Haywood E. G. , van Driel M. L. 
Published: July 2020

Abstract
Background
Clinicians who work in primary care are potentially the most influential healthcare professionals to address the problem of antibiotic resistance because this is where most antibiotics are prescribed. Despite a number of evidence based interventions targeting the management of community infections, the inappropriate antibiotic prescribing rates remain high.

Discussion
The question is how can appropriate prescribing of antibiotics through the use of Antimicrobial Stewardship (AMS) programs be successfully implemented in primary care. We discuss that a top-down approach utilising a combination of strategies to ensure the sustainable implementation and uptake of AMS interventions in the community is necessary to support clinicians and ensure a robust implementation of AMS in primary care. Specifically, we recommend a national accreditation standard linked to the framework of Core Elements of Outpatient Antibiotic Stewardship, supported by resources to fund the implementation of AMS interventions that are connected to quality improvement initiatives. This article debates how this can be achieved.

Summary
The paper highlights that in order to support the sustainable uptake of AMS programs in primary care, an approach similar to the hospital and post-acute care settings needs to be adopted, utilising a combination of behavioural and regulatory processes supported by sustainable funding. Without these strategies the problem of inappropriate antibiotic prescribing will not be adequately addressed in the community and the successful implementation and uptake of AMS programs will remain a dream.
Clinical presentation of asymptomatic and symptomatic heterosexual men who tested positive for urethral gonorrhoea at a sexual health clinic in Melbourne, Australia
Authors: Martín-Sánchez Mario , Ong Jason J. , Fairley Christopher K. , Chen Marcus Y. , Williamson Deborah A. , Maddaford Kate , Aung Ei T. , Carter Georgia , Bradshaw Catriona S. , Chow Eric P. F. 
Published: July 2020

Abstract
Background
Asymptomatic screening for gonorrhoea in heterosexual men is currently not recommended in many countries including Australia, given the prevalence is relatively low in the heterosexual population. We aimed to determine the proportion of urethral gonorrhoea cases among heterosexual men attending a sexual health clinic that was asymptomatic and symptomatic, the time since last sexual contact to the onset of symptoms and the time to clinic presentation following the onset of symptoms.

Methods
This was a cross-sectional study that included heterosexual men aged 16 years or above attending the Melbourne Sexual Health Centre (MSHC) in Australia between August 2017 and August 2018. Gonorrhoea cases were diagnosed by nucleic acid amplification testing (NAAT) and/or culture. Descriptive analyses were conducted for all gonorrhoea cases including demographic characteristics, recent sexual practices, reported urethral symptoms and duration, sexual contact with a person diagnosed with gonorrhoea, investigations performed and laboratory results.

Results
There were 116 confirmed cases of urethral gonorrhoea in heterosexual men over the study period of which 6.0% (95% CI: 2.7–12.1%) were asymptomatic. Typical urethral discharge was present in 80.2% (95% CI: 71.9–86.5%) of men. The mean time between last sexual contact and the onset of symptoms was 7.0 days, and between the onset of symptoms to presentation to the clinic was 5.6 days.

Conclusions
A small proportion of heterosexual men with urethral gonorrhoea do not have any symptoms. Heterosexual men with urethral symptoms usually seek for healthcare within a week, prompting rapid healthcare-seeking behaviour.
Physical health-related quality of life at higher achieved hemoglobin levels among chronic kidney disease patients: a systematic review and meta-analysis
Authors: Guedes Murilo , Guetter Camila R. , Erbano Lucas H. O. , Palone Andre G. , Zee Jarcy , Robinson Bruce M. , Pisoni Ronald , de Moraes Thyago Proença , Pecoits-Filho Roberto , Baena Cristina P. 
Published: July 2020

Abstract
Background
The impact of anemia treatment with erythropoietin stimulating agents (ESA) on health-related quality of life (HRQOL) in chronic kidney disease (CKD) patients is controversial, particularly regarding optimal hemoglobin (Hb) target ranges.

Methods
We conducted a systematic review and meta-analysis of observational studies and randomized controlled trials (RCT) with ESA to estimate the effect of different achieved Hb values on physical HRQOL and functionality. We searched PubMed, EMBASE, CENTRAL, PEDro, PsycINFO and Web of Science databases, until May 2020. Two authors independently extracted data from studies. We included observational and RCTs that enrolled CKD patients undergoing anemia treatment with ESA with different achieved Hb levels among groups. We excluded studies with achieved Hb < 9 g/dL. For the meta-analysis, we included RCTs with control groups achieving Hb 10–11.5 g/dL and active groups with Hb > 11.5 g/dL. We analyzed the standardized mean difference (SMD) between groups for physical HRQOL.

Results
Among 8496 studies, fifteen RCTs and five observational studies were included for the systematic review. We performed the meta-analysis in a subset of eleven eligible RCTs. For physical role and physical function, SMDs were 0.0875 [95% CI: − 0.0025 – 0.178] and 0.08 [95% CI: − 0.03 – 0.19], respectively. For fatigue, SMD was 0.16 [95% CI: 0.09–0.24]. Subgroup analysis showed that trials with greater achieved Hb had greater pooled effects sizes — 0.21 [95% CI: 0.07–0.36] for Hb > 13 g/dL vs. 0.09 [95% CI: 0.02–0.16] for Hb 11.5–13 g/dL. Proportion of older and long-term diabetic patients across studies were associated with lower effect sizes.

Conclusion
Achieved hemoglobin higher than currently recommended targets may be associated with small but potentially clinically significant improvement in fatigue, but not in physical role or physical function. Younger and non-diabetic patients may experience more pronounced benefits of higher Hb levels after treatment with ESAs.
Early prediction of cerebral-cardiac syndrome after ischemic stroke: the PANSCAN scale
Authors: Lian Haijuan , Xu Xiaomeng , Shen Xuhui , Chen Jinhua , Mao Dandan , Zhao Yan , Yao Meiqi 
Published: July 2020

Abstract
Background
Cerebral-cardiac syndrome, newly developed cardiac damage manifestations subsequent to cerebral injuries, is a common complication of stroke and leads to increased morbidity and mortality. The current study is aimed to develop a risk prediction scale to stratify high-risk population of CCS among ischemic stroke patients.

Methods
The study included 410 cases from four tertiary medical centers from June 2018 to April 2019. The risk prediction model was established via logistic regression from the derivation cohort including 250 cases admitted between June 2018 and December 2018. Another 160 cases admitted from January 2019 to April 2019 were included as the validation cohort for external validation. The performance of the model was determined by the area under curve of the receiver operating characteristic curve. A rating scale was developed based on the magnitude of the logistic regression coefficient.

Results
The prevalence of CCS was 55.2% in our study. The predictive model derived from the derivation cohort showed good calibration by Hosmer-Lemeshow test (P = 0.492), and showed sensitivity of 0.935, specificity of 0.720, and Youden index of 0.655. The C-statistic for derivation and validation cohort were 0.888 and 0.813, respectively. Our PANSCAN score (0 to 10 points) was then established, which consists of the following independent risk factors: PT(12 s–14 s = 0; otherwise = 1), APTT(30s–45s = 0, otherwise = 1), Neutrophils(50–70% = 0; otherwise = 1), Sex(female = 1), Carotid artery stenosis(normal or mild = 0; moderate to severe = 2), Age(≥65 years = 1), NIHSS score(1 to 4 = 2; ≥5 = 3). Patients scored 3 or more points were stratified as high risk.

Conclusion
The risk prediction model showed satisfactory prediction effects. The PANSCAN scale provides convenient reference for preventative treatment and early management for high-risk patients.

Trial registration
The study was retrospectively registered in Chinese Trial Registry. The date of registration is April 17, 2019. Trial registration number: ChiCTR1900022587.