bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fusarium head blight resistance in European winter wheat: insights from genome-wide transcriptome analysis
Authors: Buerstmayr Maria , Wagner Christian , Nosenko Tetyana , Omony Jimmy , Steiner Barbara , Nussbaumer Thomas , Mayer Klaus F. X. , Buerstmayr Hermann 
Published: June 2021

Abstract
Background
Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Resistance to FHB is quantitatively controlled by the combined effects of many small to medium effect QTL. Flowering traits, especially the extent of extruded anthers, are strongly associated with FHB resistance.

Results
To characterize the genetic basis of FHB resistance, we generated and analyzed phenotypic and gene expression data on the response to Fusarium graminearum (Fg) infection in 96 European winter wheat genotypes, including several lines containing introgressions from the highly resistant Asian cultivar Sumai3. The 96 lines represented a broad range in FHB resistance and were assigned to sub-groups based on their phenotypic FHB severity score. Comparative analyses were conducted to connect sub-group-specific expression profiles in response to Fg infection with FHB resistance level. Collectively, over 12,300 wheat genes were Fusarium responsive. The core set of genes induced in response to Fg was common across different resistance groups, indicating that the activation of basal defense response mechanisms was largely independent of the resistance level of the wheat line. Fg-induced genes tended to have higher expression levels in more susceptible genotypes. Compared to the more susceptible non-Sumai3 lines, the Sumai3-derivatives demonstrated higher constitutive expression of genes associated with cell wall and plant-type secondary cell wall biogenesis and higher constitutive and Fg-induced expression of genes involved in terpene metabolism. Gene expression analysis of the FHB QTL Qfhs.ifa-5A identified a constitutively expressed gene encoding a stress response NST1-like protein (TraesCS5A01G211300LC) as a candidate gene for FHB resistance. NST1 genes are key regulators of secondary cell wall biosynthesis in anther endothecium cells. Whether the stress response NST1-like gene affects anther extrusion, thereby affecting FHB resistance, needs further investigation.

Conclusion
Induced and preexisting cell wall components and terpene metabolites contribute to resistance and limit fungal colonization early on. In contrast, excessive gene expression directs plant defense response towards programmed cell death which favors necrotrophic growth of the Fg pathogen and could thus lead to increased fungal colonization.
Genome-wide identification of Brassicaceae B-BOX genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed
Authors: Zheng Li-wei , Ma Sheng-jie , Zhou Ting , Yue Cai-peng , Hua Ying-peng , Huang Jin-yong 
Published: June 2021

Abstract
Background
B-box (BBX) genes play important roles in plant growth regulation and responses to abiotic stresses. The plant growth and yield production of allotetraploid rapeseed is usually hindered by diverse nutrient stresses. However, no systematic analysis of Brassicaceae BBXs and the roles of BBXs in the regulation of nutrient stress responses have not been identified and characterized previously.

Results
In this study, a total of 536 BBXs were identified from nine brassicaceae species, including 32 AtBBXs, 66 BnaBBXs, 41 BoBBXs, 43 BrBBXs, 26 CrBBXs, 81 CsBBXs, 52 BnBBXs, 93 BjBBXs, and 102 BcBBXs. Syntenic analysis showed that great differences in the gene number of Brassicaceae BBXs might be caused by genome duplication. The BBXs were respectively divided into five subclasses according to their phylogenetic relationships and conserved domains, indicating their diversified functions. Promoter cis-element analysis showed that BBXs probably participated in diverse stress responses. Protein-protein interactions between BnaBBXs indicated their functions in flower induction. The expression profiles of BnaBBXs were investigated in rapeseed plants under boron deficiency, boron toxicity, nitrate limitation, phosphate shortage, potassium starvation, ammonium excess, cadmium toxicity, and salt stress conditions using RNA-seq data. The results showed that different BnaBBXs showed differential transcriptional responses to nutrient stresses, and some of them were simultaneously responsive to diverse nutrient stresses.

Conclusions
Taken together, the findings investigated in this study provided rich resources for studying Brassicaceae BBX gene family and enriched potential clues in the genetic improvement of crop stress resistance.
Comparative anatomical and transcriptomic insights into Vaccinium corymbosum flower bud and fruit throughout development
Authors: Yang Li , Liu Liangmiao , Wang Zhuoyi , Zong Yu , Yu Lei , Li Yongqaing , Liao Fanglei , Chen Manman , Cai Kailing , Guo Weidong 
Published: June 2021

Abstract
Background
Blueberry (Vaccinium spp.) is characterized by the production of berries that are smaller than most common fruits, and the underlying mechanisms of fruit size in blueberry remain elusive. V. corymbosum ‘O’Neal’ and ‘Bluerain’ are commercial southern highbush blueberry cultivars with large- and small-size fruits, respectively, which mature ‘O’Neal’ fruits are 1 ~ 2-fold heavier than those of ‘Bluerain’. In this study, the ontogenetical patterns of ‘O’Neal’ and ‘Bluerain’ hypanthia and fruits were compared, and comparative transcriptomic analysis was performed during early fruit development.

Results
V. corymbosum ‘O’Neal’ and ‘Bluerain’ hypanthia and fruits exhibited intricate temporal and spatial cell proliferation and expansion patterns. Cell division before anthesis and cell expansion after fertilization were the major restricting factors, and outer mesocarp was the key tissue affecting fruit size variation among blueberry genotypes. Comparative transcriptomic and annotation analysis of differentially expressed genes revealed that the plant hormone signal transduction pathway was enriched, and that jasmonate-related TIFYs genes might be the key components orchestrating other phytohormones and influencing fruit size during early blueberry fruit development.

Conclusions
These results provided detailed ontogenetic evidence for determining blueberry fruit size, and revealed the important roles of phytohormone signal transductions involving in early fruit development. The TIFY genes could be useful as markers for large-size fruit selection in the current breeding programs of blueberry.
Downstream of GA4, PbCYP78A6 participates in regulating cell cycle-related genes and parthenogenesis in pear (Pyrus bretshneideri Rehd.)
Authors: Zhang Haiqi , Han Wei , Wang Huibin , Cong Liu , Zhai Rui , Yang Chengquan , Wang Zhigang , Xu Lingfei 
Published: June 2021

Abstract
Background
Parthenocarpy results in traits attractive to both consumers and breeders, and it overcomes the obstacle of self-incompatibility in the fruit set of horticultural crops, including pear (Pyrus bretshneider). However, there is limited knowledge regarding the genetic and molecular mechanisms that regulate parthenogenesis.

Results
Here, in a transcriptional comparison between pollination-dependent fruit and GA4-induced parthenocarpy, PbCYP78A6 was identified and proposed as a candidate gene involved in parthenocarpy. PbCYP78A6 is similar to Arabidopsis thaliana CYP78A6 and highly expressed in pear hypanthia. The increased PbCYP78A6 expression, as assessed by RT-qPCR, was induced by pollination and GA4 exposure. The ectopic overexpression of PbCYP78A6 contributed to parthenocarpic fruit production in tomato. The PbCYP78A6 expression coincided with fertilized and parthenocarpic fruitlets development and the expression of fruit development-related genes as assessed by cytological observations and RT-qPCR, respectively. PbCYP78A6 RNA interference and overexpression in pear calli revealed that the gene is an upstream regulator of specific fruit development-related genes in pear.

Conclusions
Our findings indicate that PbCYP78A6 plays a critical role in fruit formation and provide insights into controlling parthenocarpy.
The INSPIRE Population Survey: development, dissemination and respondent characteristics
Authors: Siqeca Flaka , Obas Katrina , Yip Olivia , Stenz Samuel , Vounatsou Penelope , Briel Matthias , Schwenkglenks Matthias , Quinto Carlos , Blozik Eva , Zeller Andreas , Zullig Leah L. , De Geest Sabina , Deschodt Mieke 
Published: June 2021

Abstract
Background
Most older adults prefer to continue living at home despite increasing care needs and demand for services. To aid in maintaining independence, integrated care models for community-dwelling older people are promoted as the most cost-effective approach. The implementation of such care models is challenging and often the end-users are not involved or their needs are not considered. We conducted a population survey in order to understand the needs and preferences of home-dwelling older adults living in Canton Basel-Landschaft, Switzerland. The aims of this paper are to chronicle the development of the INSPIRE Population Survey, outline its variables and measurements, describe the marketing strategy utilized for survey dissemination and report on the response rate and respondent characteristics.

Methods
The INSPIRE Population Survey, conducted between March and August 2019, is a cross-sectional survey of older adults aged 75 and older living at home in Canton Basel-Landschaft. The questionnaire was developed by expert input and stakeholder involvement. Its readability and acceptability were pilot-tested with older people. To ensure the likelihood of a high and representative response rate, a meticulous step-by-step marketing strategy was developed prior to the dissemination of the questionnaire.

Results
The overall response rate was 30.7% (n = 8,846), with variations between 20.6 and 34.5% across the different care regions in the canton. A generally higher response rate was found in the care regions with a higher density and which bordered the urban city of Basel. We received support from local stakeholders, policy makers and media through using a broad combination of marketing channels and targeting our community partners who have a strong relationship with our target audience.

Conclusions
Although recruiting older adults in research is challenging, our study shows that a high response rate can be achieved by developing the survey through expert input and by involving all important stakeholders, including older adults, throughout the entire process.
Cerebral large artery stenosis and occlusion in POEMS syndrome
Authors: Sugiyama Atsuhiko , Yokota Hajime , Misawa Sonoko , Mukai Hiroki , Sekiguchi Yukari , Koide Kyosuke , Suichi Tomoki , Matsushima Jun , Kishimoto Takashi , Tanei Zen-ichi , Saito Yuko , Ito Shoichi , Kuwabara Satoshi 
Published: June 2021

Abstract
Background
This study aimed to investigate the frequency and risk factors for cerebral artery stenosis and occlusion in patients with polyneuropathy, organomegaly, endocrinopathy, M-protein, and skin changes (POEMS) syndrome.

Methods
We reviewed results of magnetic resonance angiography (MRA) or computed tomography angiography (CTA) in 61 patients with POEMS syndrome seen between 2010 and 2017. Stenosis or occlusion was assessed in the initial MRA/CTA. Multivariate analysis was used to identify risk factors for artery stenosis/occlusion. In an autopsy case, pathologic examination was conducted of the occluded middle cerebral arteries.

Results
Stenosis (> 50 %) or occlusion of the major cerebral arteries was found in 29 (47.5 %) patients on the initial MRA/CTA. The internal carotid artery was involved most frequently (32.8 %), followed by the anterior (21.3 %) and middle (16.4 %) cerebral arteries. The basilar (1.3 %) and vertebral (3.6 %) arteries were rarely affected. Cerebral infarction developed in eight (13.1 %) patients. The serum vascular endothelial growth factor (VEGF) level was an independent predictor for stenosis/occlusion (odds ratio, 1.228; 95 % confidence interval, 1.042–1.447; P = 0.014). An autopsy study showed occluded middle cerebral arteries by fibrous and myxomatous thickening of intima with splitting of the internal elastic lamina. Follow-up MRA in 23 patients showed improved, worsened, and unchanged stenosis in 20.7 %, 8.7 %, and 69.6 %, respectively.

Conclusions
Cerebral large-vessel stenosis or occlusion is frequently seen in approximately half of patients with POEMS syndrome. Vasculopathy was related to serum VEGF levels and thereby disease activity. Assessment of cerebral vessels is recommended in these patients to improve management.
Impact of the COVID-19 pandemic and post-epidemic periods on the process of endovascular treatment for acute anterior circulation ischaemic stroke
Authors: Zhang Tangqin , Chen Chu , Xu Xiangjun , Xu Junfeng , Yang Ke , Xu Youqing , Yuan Lili , Yang Qian , Huang Xianjun , Zhou Zhiming 
Published: June 2021

Abstract
Background and purpose
The purpose of our study was to analyse endovascular treatment (EVT) in patients presenting acute anterior circulation ischemic stroke with large-vessel occlusion (AIS-LVO) during the pandemic and post-epidemic periods.

Methods
Patients with AIS-LVO of the anterior circulation who underwent EVT were enrolled. According to the times of Wuhan closure and reopening, patients were divided into a pre-pandemic group (from November 8, 2019, to January 22, 2020), pandemic group (from January 23, 2020, to April 8, 2020) and post-epidemic group (from April 9, 2020, to June 24, 2020). The primary endpoints were the time delay among symptom onset to arriving hospital door, to groining puncture and to vascular reperfusion. Secondary endpoints were the functional outcomes evaluated by 90-day modified Rankin scale (mRS) score.

Results
In total, the times from onset to reperfusion (OTR, median 356 min vs. 310 min, p = 0.041) and onset to door (OTD, median 238 min vs. 167 min, p = 0.017) were prolonged in the pandemic group compared to the pre-pandemic group, and the delay continue in the post-epidemic period. In the subgroup analysis, the time from door to imaging (DTI) was significantly prolonged during the pandemic period. Interestingly, the prolonged DTI was corrected in the directly admitted subgroup during post-epidemic period. In addition, the functional outcomes showed no significant differences across the three periods.

Conclusions
Total time and prehospital time were prolonged during the pandemic and post-epidemic periods. Urgent public education and improved in-hospital screening processes are necessary to decrease time delays.
Association between tirofiban monotherapy and efficacy and safety in acute ischemic stroke
Authors: Tao Chunrong , Zhu Yuyou , Zhang Chao , Song Jianlong , Liu Tianlong , Yuan Xiaodong , Luo Wenwu , Chen Changchun , Liu Dezhi , Zhu Yuanyuan , Liu Jie , Hu Wei 
Published: June 2021

Abstract
Background
Studies have suggested that glycoprotein IIb/IIIa antagonists such as tirofiban are beneficial for patients with acute coronary syndromes. However, it is still uncertain about the efficacy and safety of tirofiban in patients with acute ischemic stroke (AIS).

Methods
In this prospective non-randomized study, 255 AIS patients were recruited from 4 comprehensive stroke centers in China between January, 2017 and May, 2018. Among them,169 patients were treated with aspirin plus clopidogrel and 86 patients were treated with tirofiban. The primary functional outcome was the distribution of the 90 days’ modified Rankin Scale (mRS). The safety outcomes included the incidence of intracranial hemorrhage (ICH) at discharge and mortality at 3 months.

Results
In the propensity score matched cohort, tirofiban alone was noninferior to the dual antiplatelet with regard to the primary outcome (adjusted common odds ratio, 0.97; 95% confidence interval, 0.46 to 2.04; P = 0.93). Mortality at 90 days was 10% in the dual antiplatelet group and 8% in the tirofiban group (adjusted odds ratio 0.75; 95% CI 0.08 to 7.40, p = 0.81). There was no difference of the ICH rate between two groups (adjusted odds ratio 0.44; 95% CI 0.13 to 1.48, p = 0.18). In the inverse probability of treatment weighting-propensity score-adjusted cohort, similar differences were found for functional and safety outcomes.

Conclusions
Our study suggested that tirofiban use appears to be safe as monotherapy in AIS treatment compared with common dual antiplatelet therapy, however, no improvement in functional outcomes was found.

Trial registration
Chinese clinical trial registry, ChiCTR2000034443, 05/07/2020. Retrospectively registered.
Multiple sclerosis projection in Tehran, Iran using Bayesian structural time series
Authors: Amini Payam , Almasi-Hashiani Amir , Sahraian Mohammad Ali , Najafi Masood , Eskandarieh Sharareh 
Published: June 2021

Abstract
Background
The prevalence of Multiple Sclerosis (MS) has been increasing worldwide and the highest prevalence ratio among Asian countries was reported in Iran. This study aims to estimate the increase in MS occurrence during more than three decades in Tehran and forecast the future condition of the disease using time series approaches for the next ten years.

Methods
The cross-sectional study was conducted from 1999 to 2019 based on records of MS cases from Iranian MS Society (IMSS) registry system. The prevalence was estimated using population data presented by the Statistical Centre of Iran. Through Bayesian Structural Time Series (BSTS) model, we want to predict the prevalence of familial and sporadic MS in the next ten years. .

Results
Among 22,421 cases with MS, 16,831 (75.1 %) were female and 5589 (24.9 %) were male. Female to male ratio was 3.0:1 and the number of familial MS cases were 2982 (13.3 %) of subjects. Female gender was less responsible for higher rate of MS in familial definition (beta = 0.020) in comparison to sporadic cases (beta = 0.034). Forecasting by BSTS revealed an increase in MS prevalence for the next ten years so that the prevalence rate for total, familial and sporadic MS respectively begins with 189.50 (183.94-195.14), 25.69 (24.97–26.45) and 163.74(159.06-168.57) in 2020 and ends with 220.84 (171.48-266.92), 30.79 (24.16–37.15), and 189.33(146.97-230.19) in 2029.

Conclusions
According to the findings, MS prevalence increased during three decades and it will increase over the next ten years. Tehran province is one of the regions with highest MS prevalence in Asia. The results of present study indicated that females are at higher risk for MS than males in both sporadic and familial MS.
Genome instability-related long non-coding RNA in clear renal cell carcinoma determined using computational biology
Authors: Wang Yutao , Yan Kexin , Wang Linhui , Bi Jianbin 
Published: June 2021

Abstract
Background
There is evidence that long non-coding RNA (lncRNA) is related to genetic stability. However, the complex biological functions of these lncRNAs are unclear.

Method
TCGA - KIRC lncRNAs expression matrix and somatic mutation information data were obtained from TCGA database. “GSVA” package was applied to evaluate the genomic related pathway in each samples. GO and KEGG analysis were performed to show the biological function of lncRNAs-mRNAs. “Survival” package was applied to determine the prognostic significance of lncRNAs. Multivariate Cox proportional hazard regression analysis was applied to conduct lncRNA prognosis model.

Results
In the present study, we applied computational biology to identify genome-related long noncoding RNA and identified 26 novel genomic instability-associated lncRNAs in clear cell renal cell carcinoma. We identified a genome instability-derived six lncRNA-based gene signature that significantly divided clear renal cell samples into high- and low-risk groups. We validated it in test cohorts. To further elucidate the role of the six lncRNAs in the model’s genome stability, we performed a gene set variation analysis (GSVA) on the matrix. We performed Pearson correlation analysis between the GSVA scores of genomic stability-related pathways and lncRNA. It was determined that LINC00460 and LINC01234 could be used as critical factors in this study. They may influence the genome stability of clear cell carcinoma by participating in mediating critical targets in the base excision repair pathway, the DNA replication pathway, homologous recombination, mismatch repair pathway, and the P53 signaling pathway.

Conclusion subsections
These data suggest that LINC00460 and LINC01234 are crucial for the stability of the clear cell renal cell carcinoma genome.
Oral health problems facing refugees in Europe: a scoping review
Authors: Zinah Eiad , Al-Ibrahim Heba M. 
Published: June 2021

Abstract
Introduction
Europe has been experiencing a flow of refugees and asylum seekers driven by conflicts or poverty. Their oral health is often neglected despite its clear impact on quality of life.

Objective
To explore the status of oral health among refugees and asylum seekers groups by examining the available literature and to determine which evidence exists regarding the problems they face in terms of oral health.

Methods
The current paper followed PRISMA guidelines. A scoping review methodology was followed to retrieve 2911 records from five databases and grey literature. Twelve articles met the following inclusion criteria: experimental research concentrated on the oral and dental health of refugees and/or asylum seekers between 1995 and 2020 in English. Analysis was both descriptive and thematic, whilst a critical appraisal was applied using the Critical Appraisal Skills Program (CASP).

Results
Seven studies (58,3%) were quantitative, while five studies (41,6%) were qualitative. In general, the quality of most of the studies (83.3%) was good. Limited access to oral health care services was shown with a higher prevalence of oral diseases compared to the native populations of the host countries. Approaches to improve oral health have been implemented in some studies and have shown positive outcomes.

Conclusions
Oral health care strategies should consider the oral health problems facing refugees in Europe, and oral health promotion campaigns are essential to give adequate guidance on how to access oral health care in the host countries.
The causal effect and impact of reproductive factors on breast cancer using super learner and targeted maximum likelihood estimation: a case-control study in Fars Province, Iran
Authors: Almasi-Hashiani Amir , Nedjat Saharnaz , Ghiasvand Reza , Safiri Saeid , Nazemipour Maryam , Mansournia Nasrin , Mansournia Mohammad Ali 
Published: June 2021

Abstract
Objectives
The relationship between reproductive factors and breast cancer (BC) risk has been investigated in previous studies. Considering the discrepancies in the results, the aim of this study was to estimate the causal effect of reproductive factors on BC risk in a case-control study using the double robust approach of targeted maximum likelihood estimation.

Methods
This is a causal reanalysis of a case-control study done between 2005 and 2008 in Shiraz, Iran, in which 787 confirmed BC cases and 928 controls were enrolled. Targeted maximum likelihood estimation along with super Learner were used to analyze the data, and risk ratio (RR), risk difference (RD), andpopulation attributable fraction (PAF) were reported.

Results
Our findings did not support parity and age at the first pregnancy as risk factors for BC. The risk of BC was higher among postmenopausal women (RR = 3.3, 95% confidence interval (CI) = (2.3, 4.6)), women with the age at first marriage ≥20 years (RR = 1.6, 95% CI = (1.3, 2.1)), and the history of oral contraceptive (OC) use (RR = 1.6, 95% CI = (1.3, 2.1)) or breastfeeding duration ≤60 months (RR = 1.8, 95% CI = (1.3, 2.5)). The PAF for menopause status, breastfeeding duration, and OC use were 40.3% (95% CI = 39.5, 40.6), 27.3% (95% CI = 23.1, 30.8) and 24.4% (95% CI = 10.5, 35.5), respectively.

Conclusions
Postmenopausal women, and women with a higher age at first marriage, shorter duration of breastfeeding, and history of OC use are at the higher risk of BC.