bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do Species Mount Different Genetic Responses to Acute Drought Stress Across an Ecological Gradient?&nbsp;
Authors: Devitt Jessica Kay , Chung Albert , Schenk John J. 
Published: December 2020

Abstract
Background: How do xerophytic species thrive in environments that experience extreme annual drought? Although critical to the survival of many species, the genetic responses to drought stress in non-model organisms are unknown. We investigated this question in Mentzelia section Bartonia (Loasaceae), which occurs throughout western North America, including arid lands. To better understand the genetic responses to drought stress among species that occur in different habitats, the gene expression levels of three species from the genus Mentzelia that occur across a precipitation gradient were compared. Two de novo reference transcriptomes were generated and annotated. Leaf and root tissues were collected from control and drought shocked plants and compared to one another for differential expression. A target-gene approach was also implemented to better understand how drought-related genes from model and crop species function in non-model systems.Results: When comparing the drought-shock treatment plants to their respective control plants, we identified 165 differentially expressed clusters across all three species. Differentially expressed genes including those associated with water movement, photosynthesis, and genes that delayed senescence. The transcriptome profiling approach was coupled with a target genes approach that measured expression of 90 genes associated with drought tolerance in model organisms. Comparing differentially expressed genes with a log-fold values of 2 or greater between species and tissue types showed significant differences in drought response. In pariwise comparisons, species that occurred in drier environments differentially expressed greater genes in leaves when drought shocked than those from wetter environments, but expression in the roots mostly produced opposite results. Conclusions: Arid-adapted species mounted greater genetic responses compared to the temperate species, with differences in leaf and root tissue responses. Target genes revealed differences and similarities between functional processes within Mentzelia and other plant groups. Differences in drought response depending on tissue type suggests that genetic and physiological responses occur within one tissue type and not the other, and tissue responses could be evolving at different rates. We determined that drought tolerance is enhanced through pathways of delayed senescence and that genetic responses were tissue and habitat specific.
Genetic Dissection of Resistance to Common Rust (Puccinia Sorghi) in Tropical Maize (Zea mays L.) by Combined Genetic Mapping and Genomic Prediction
Authors: Zhang Xuecai , Ren Jiaojiao , Li Zhimin , Wu Penghao , Loladze Alexander , Zhang Ao , Liu Yubo , Hu Guanghui , Cao Shiliang , Qu Jingtao , Zheng Hongjian , Olsen Michael , Prasanna Boddupalli M. , Vicente Felix San 
Published: December 2020

Abstract
Background: Common rust is one of the major foliar diseases of maize, leading to significant grain yield losses and poor grain quality. The most sustainable strategy for controlling common rust is to develop resistant maize varieties, which requires a further understanding of genetic dissection of common rust resistance. Results: In this study, an association panel and two bi-parental doubled haploid (DH) populations were used to perform genome-wide association study (GWAS), linkage mapping, and genomic prediction analyses. All the populations were phenotyped in multi-environment trials for common rust resistance and genotyped with genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). GWAS revealed six SNPs significantly associated with common rust resistance at bins 1.05, 1.10, 3.04, 3.05, 4.08, and 10.04, respectively. The SNP effect of each SNP ranged from 0.13 to 0.17. Linkage mapping identified six quantitative trait loci (QTL) in the first DH population (DH1) and two QTL in the second DH population (DH2), distributed on chromosomes 1, 2, 3, 4, 6, 7, and 9, respectively. The phenotypic variation explained (PVE) of each QTL ranged from 3.55% to 12.45%. A new major QTL was detected in DH1 on chromosome 7 in the region between 144,585,945 and 149,528,489 bp, it had the highest LOD score of 7.82 and the largest PVE value of 12.45%. The genomic regions located at bins 1.05, 1.10, and 4.08 were detected by both GWAS and linkage mapping. GRMZM2G114893 (bin 1.05) and GRMZM2G138949 (bin 4.08) were identified as the putative candidate genes conferring common rust resistance. The genomic prediction accuracies observed in the association panel and two bi-parental DH populations were 0.61, 0.51, and 0.10, respectively. Conclusions: These results provided new insight into the genetic architecture of common rust resistance in maize and a better understanding of the application of genomic prediction for common rust resistance in maize breeding.
Metabolomic Insights into the Browning of the Peel of Bagging ‘Rui Xue’ Apple Fruit
Authors: zhao zhengyang , Wang Hui , Sun Lulong , Wang Shuang , Fan Miaomiao , Zhang Shuhui 
Published: December 2020

Abstract
Background: Bagging is one of the most important techniques for the production of high-quality fruits. In the actual of cultivating, we found a new kind of browning in peel of apple fruit that occurs before harvest and worsen during storage period. There are many studies on metabonomic analysis of browning about storage fruits, but few studies on the mechanism of browning before harvest. This experiment was based on metabonomic studies to explore the effect of bagging on fruit peel browning.Results: In this study, five-year-old trees of ‘Rui Xue’ were used as materials. Bagging fruits without browning (BFW) and bagging fruits with browning (BFB) were set as the experimental groups, non-bagging fruits (NBF) were set as control (CT). Our results show that 131 metabolites of BFW were significantly up-regulation and 217 metabolites were significantly down-regulation compared with NBF; 198 metabolites of BFB were significantly up-regulationand and 178 metabolites were significantly down-regulation compared with BFW (Variable important in projection (VIP) > 1 and p-value < 0.05). The synthesis and accumulation of flavonoids and lipids were significantly changed after bagging; compared with NBF, 11 flavonoids and 6 lipids molecules were significantly decreased in the BFW (top 50 metabolites). Compared with BFW, 11 flavonoids and 7 lipids were further decreased in BFB, but, 12 triterpenes were significantly accumulated in BFB. As the peel browning, galactose metabolism, ABC membrane transporter protein, flavonoid biosynthesis and linoleic acid metabolism pathways were significantly changed in BFW and BFB compared with NBF. Physiological indicators show that, compared with NBF, the MDA in peel of BFW and BFB significantly increased by 0.46 times and 2.94 times, respectively; and the cell membrane permeability of BFW and BFB were significantly increased by 15.7% and 28.2%, respectively. We analyzed the expression of related genes in the metabolic pathways of flavonoids, compared with NBF, the flavonoid synthesis genes MdLAR were significantly up-regulated by 2.55 and 9.37 times in BFW and BFB, and the MdANR genes were also significantly up-regulated by 2.33 and 2.69 times, respectively. In addition to this, the downstream flavonoids-related polymeric genes MdLAC7 and MdLAC14 were the most significantly expressed. Compared with NBF, MdLAC7 was significantly up-regulated by 0.43 and 13.88 times in BFW and BFB, and MdLAC14 was also significantly up-regulated by 7.13 and 3.17 times, respectively. Conclusions: Our findings demonstrated that the microenvironment of fruit was changed by bagging, the destruction of cell structure, the increase of lipid peroxidation of cell membrane, the decrease of flavonoids and the increase of triterpenoids were the main reasons for the browning of peel about bagging ‘Rui Xue’.
Predictors of treatment failures of Plasmodium falciparum malaria in Vietnam: a 4-year single-center retrospective study
Authors: Duong Minh Cuong , Pham Oanh Kieu Nguyet , Nguyen Phong Thanh , Nguyen Chau Van Vinh , Nguyen Phu Hoan 
Published: December 2020

Abstract
BackgroundDrug-resistant falciparum malaria is an increasing public health burden. We examined the magnitude of Plasmodium falciparum infection and the patterns and predictors of treatment failure in Vietnam. MethodsMedical records of all 443 patients with malaria infection admitted to the Hospital for Tropical Diseases between January 2015 and December 2018 were used to extract information on demographics, risk factors, symptoms, laboratory tests, treatment, and outcomes. ResultsMore than half (59.8%, CI 55.1%-64.4%) of patient acquired P. falciparum infection of whom 21.9% (CI 17.1%-27.4%) had severe malaria, while 7.2% (CI 4.6%-10.9%) and 19.2% (CI 14.7%-24.5%) developed early treatment failure (ETF) and late treatment failure (LTF) respectively. ETF was 4.7% among patients referred from Binh Phuoc province and Central Highland, 12.9% from other areas in Vietnam, and 6.9% from Africa. LTF was 16.2% among patients from Binh Phuoc province and Central Highland, 22.6% from other areas in Vietnam, and 27.6% from Africa. Most patients (98.5%) recovered completely. Having severe malaria was a predictor of ETF (AOR 6.96, CI 2.55-19.02, P < 0.001). No predictor of LTF was identified.ConclusionP. falciparum remains the prevalent malaria parasite. Despite low mortality rate, severe malaria is not rare and is a significant predictor of ETF. To reduce the risk for ETF, studies are needed to examine the effectiveness of combination therapy including parenteral artesunate and a parenteral partner drug for severe malaria. The study alerts the possibility of drug-resistant malaria in Africa and other areas in Vietnam which are known as nonendemic areas of antimalarial drug resistance. A more comprehensive study using molecular technique in these regions is required to completely understand the magnitude of drug-resistant malaria and to design appropriate control strategies.
Association of Androgen Receptor Expression with Glucose Metabolic Features in Triple-Negative Breast Cancer
Authors: Lee Reeree , Lee Han-Byoel , Paeng Jin Chul , Choi Hongyoon , Whi Wonseok , Han Wonshik , Noh Dong-Young , Seok Ju Won , Kang Keon Wook , Cheon Gi Jeong 
Published: December 2020

Abstract
Androgen receptor (AR) is a potential therapeutic target in triple-negative breast cancer (TNBC). We aimed to elucidate the association of AR expression with glucose metabolic features in TNBC. Two independent datasets were analyzed; FDG PET data of our institution and a public dataset of GSE135565. In PET analysis, patients with TNBC who underwent baseline PET between Jan 2013 and Dec 2017 were retrospectively enrolled. Clinicopathologic features and maximum standardized uptake value (SUVmax) of tumors were compared with AR expression. In GSE135565 dataset, glycolysis score was calculated by the pattern of glycolysis-related genes, and its association with SUVmax and AR gene expression were analyzed. A total of 608 female patients were included in the PET data of our institution. SUVmax was lower in AR-positive tumors and correlated with lower AR expression. In multivariate analyses, AR was a deterministic factor for low SUVmax, along with other key clinicopathologic features. In the GSE135565 dataset, AR expression also exhibited a negative correlation with SUVmax and the glycolysis score. Low glucose metabolism is a signature of AR expression in TNBC. It is suggested that evaluation of AR expression status needs to be considered in clinical practice particularly in TNBC with low glucose metabolism.
Short-term Fasting Enhances the Protection Against Listeria Monocytogenes Infection Through Changes of Intestinal&nbsp;CD103+ Dendritic Cells
Authors: Ju Young-Jun , Lee Kyung-Min , Kim Girak , Kye Yoon-Chul , Kim Han Wool , Chu Hyuk , Park Byung-Chul , Cho Jae-Ho , Han Seung Hyun , Yun Cheol-Heui 
Published: December 2020

Abstract
Gastrointestinal tract is the first organ to be directly affected upon fasting. However, little is known about how the fasting influences intestinal immune system. In the present study, we focused on the changes of intestinal dendritic cells (DCs) in mice upon short-term fasting and how the changes influence protective immunity against Listeria monocytogenes (LM) infection. We found that the fasting induces an increased number of CD103+CD11b- DCs in both small intestinal lamina propria (SI LP) and mesenteric lymph nodes (mLN) and the SI LP CD103+CD11b- DCs undergo an active proliferation and migration by increased levels of GM-CSF and CCR7, respectively. At 24 hours post-infection (hpi) of LM, there was a significant reduction of bacterial burden from the spleen, liver, and mLN of the short-term fasting mice compared to those of ad libitum mice. Accordingly, short-term fasting mice showed enhanced survival against LM infection when compared with ad libitum mice. Furthermore, significantly high amount of TGF-β2 and Aldh1a2 expression from CD103+CD11b- DCs in mouse infected with LM sequentially caused the following events: the increase of Foxp3+ Tregs, preferential change in the composition of CD103+ to CD103- DCs, and the induction of IFN-γ producing cells. Collectively, increase of intestinal CD103+ DCs by short-term fasting is a key player for protection against LM infection through the changes of functional features from tolerogenic to Th1 immunogenic.
Decoration of Graphene Oxide with Cobalt(II) Coordinated Silica and its Catalytic Activity for the Synthesis of Functionalized Indenopyrazolones
Authors: Mirheidari Mahnaz , Safaei‐Ghom Javad 
Published: December 2020

Abstract
We synthesized functionalized f-SiO2@GO@Co catalyst through decorating graphene oxide surface using SiO2 sphere with the help of ethylenediamine ligand and chelation with CoCl2.6H2O for increasing the catalyst activity to produce heterogenous catalyst. The heterogenous catalyst was characterized by FT-IR, XRD, SEM, Raman spectra, and TGA. We assessed activity of the catalyst in the synthesis of indenopyrazolones and results demonstrated high activity for the catalyst. The ability of the catalyst to increase the yield and reduction in reaction time as well as high catalytic activity, and recycling are prominent advantages of the catalyst.
Quantification of Malignant Lymph Nodes and Benign Lymph Nodes in Patients of Esophageal Squamous Cell Carcinoma With Dynamic 18F-FDG PET/CT
Authors: Wang Xiaohui , Cao Qingdong , Wang Xiaojing , Wang Ying , Li Dan , Bi Lei , Yang Shuai , Shan Hong , Jin Hongjun 
Published: December 2020

Abstract
BackgroundMost esophageal squamous cell carcinoma (ESCC) imaging diagnoses can be performed by routine CT and ultrasound, but it is difficult to detect metastatic lymph nodes or minor lesions. Functional imaging diagnosis based on 18F-FDG PET/CT has potential advantages for detection of metastatic lymph nodes, or differentiation of benign from malignant lymph nodes, and for typing and staging of ESCC. The purpose of this study is to provide 18F-FDG PET/CT imaging for ESCC patient to quantify the difference between malignant lymph nodes (MLN) and benign lymph nodes (BLN) for ESCC. MethodsDynamic 18F-FDG PET/CT was performed in 46 patients (26 patients without MLN (N0 stage) and 20 with MLN (non-N0 stage) who were pathologically confirmed for ESCC. Visual and quantitative differences were measured in primary tumor (PT), MLN and BLN regions of interest (ROIs). Finally, 52 MLN and 133 BLN (83 from N0 stage and 50 from non-N0 stage) were included for analysis. Pharmacokinetic analysis was performed by a Patlak model using Matlab program to obtain the influx constant (Ki). Maximum standardized uptake value (SUVmax) was also determined from the static and dynamic PET/CT scans. Based on the receiver operator characteristic (ROC) curve, the sensitivity and specificity for each parameter in differentiation diagnosis were evaluated. ResultsKi and SUVmax in PT non-N0 group was slightly higher than in N0 groups (0.04 ± 0.02 vs 0.03 ± 0.03, 8.01 ± 3.90 vs 7.08 ± 5.39, respectively), but with no significant difference (p > 0.05). And Ki and SUVmax in MLN were higher than BLN with statistically significant difference (KiMLN vs KiBLN ( 0.021 ± 0.014 vs 0.006 ± 0.004, p < 0.0001); (SUVmaxMLN vs SUVmaxBLN (4.35 ± 2.27 vs 1.89 ± 0.85, p < 0.0001); The sensitivity both Ki and SUVmax were 80.77 %, the specificity for Ki was 89.47%, and SUVmax 87.22% respectively. And the diagnostic accuracy Ki (90.61%) was slightly better than SUVmax (88.16%). Conclusions﻿Quantitative parameters (both Ki and SUVmax) of 18F-FDG in ESCC patients are sensitive diagnostic measurements capable to identify MLNs from BLNs.
The Effect of Metabolic Syndrome on Head and Neck Cancer Incidence Risk: A Population-based Prospective Cohort Study
Authors: Jiang Huaili , Zhou Lei , He Qiansheng , Jiang Kanglun , Huang Xinsheng , Yuan Jinqiu 
Published: December 2020

Abstract
BackgroundThere are limited evidences clarifying the impact of metabolic syndrome (MS) and its components on head and neck cancer (HNC) incidence risk. We explored the correlation between MS, MS components, and the combined effects of MS and C-reactive protein (CRP) and HNC risk. MethodsThis is a prospective analysis of 474,929 participants from the UK Biobank cohort. Cox proportional hazard regression was utilized to assess the hazard ratio (HR) and 95% confidence interval (CI), and to explore the non-linear correlation between an individual MS component and HNC risk. ResultsIndividuals with MS (HR, 1.05; 95%CI, 0.90-1.22) had no higher risk of HNC than those without MS and those with more MS components showed no higher HNC risk. Nevertheless, we observed that MS component hyperglycaemia (HR, 1.22; 95%CI, 1.02-1.45) was independently correlated with elevated HNC risk. In a non-linear manner, waist circumference and high-density lipoprotein (HDL) showed a U-shape association with HNC risk. Further linear analysis indicated that male waist circumference, female waist circumference (when ≥93.16 cm), male HDL (when ≥1.45mmo/L) and blood glucose were positively correlated with HNC risk. Increased CRP (≥1.00mg/dL) elevated HNC risk and individuals with MS and CRP≥ 1.00mg/dL had the highest HNC risk (HR, 1.29; 95%CI, 1.05-1.58). ConclusionsAlthough MS are not correlated with elevated HNC risk, high male waist circumference, high female waist circumference (≥93.16 cm), high male HDL (≥1.45mmo/L) and high blood glucose are independent risk factors of HNC. We also recommended a potential combined effect of MS and CRP in head and neck tumorigenesis.
Pan-cancer Analysis Combining with Experiments Indicates the Sensitivity of Renal Carcinogenesis to DLGAP5 Expression
Authors: Feng Yun , Li Fang , Guo Xianli , Wang Fenghui , Shi Haiyan , Du Juan , Zhang Huahua , Gao Yi , Li Dan , Yan Jing , Yao Yan , Hu Weihong , Han Jiaqi , Zhang Mengjie , Ding Ruxin , Wang Xiaofei , Huang Chen , Zhang Jing 
Published: December 2020

Abstract
Background: Discs large-associated protein 5 (DLGAP5), a kinetochore ﬁbers-binding protein, has been found to function as a oncoprotein in many cancers. However, its expression patterns in normal and cancer tissues across pan-cancer, as well as the cell lines, are far from clear. Methods: Data from genotype-tissue expression (GTEx) and The Cancer Genome Atlas (TCGA) was used to analyze the DLGAP5 expression in normal tissues and cancer cell lines, respectively. The analysis of DLGAP5 expression in cancer tissues and adjacent tissues was based on data from a combined TCGA and GTEx. The associations between the expression, prognosis and cancer immune infiltrates in pan-cancer were also investigated based on TCGA and Tumor Immune Estimation Resource (TIMER), respectively. Furthermore, the analysis results of ccRCC was verified using cell lines via RNAi, western blotting, and the cytological analysis.Results: The low expression levels of DLGAP5 were observed in 31 types of common human tissues, including kidney tissue. However, its expression displayed upregulation in all the 21 tested cancer cell lines, of which kidney cancer cell lines showed a minimal upregulation. As predicted, the significant overexpression of DLGAP5 occurred in at least 26 types of common cancer tissues compared with the adjacent normal tissues. Surprisingly, in three types of kidney cancer (KICH, KIRC/ccRCC, KIRP), DLGAP5 exhibited a statistically significant, but minor, overexpression among 26 types of tested cancers. Furthermore, the survival probability of some tested cancers, including kidney cancer, were significantly related to the upregulated expression of DLGAP5. In addition, among 33 types of tested cancers, KIRC/ccRCC, LGG and LIHC showed a significant positive correlation between DLGAP5 expression and immune infiltration levels. DLGAP5 expression level was also significantly positive correlated with clinical TNM stage of ccRCC patients. Regarding ccRCC tissues and the cell lines, upregulation expression of DLGAP5 was also detected. Its knockdown inhibited the cells viability and proliferation, and compromised the cells migration and invasion. Conclusions: DLGAP5 overexpression occurred in common human cancers, including the kidney cancers. Notably, ccRCC, seemed to be particularly sensitive to the expression. DLGAP5, therefore, may be as a robust independent prognostic biomarker in ccRCC diagnosis.
Non-Invasive Tool to Distinguish Between Acute Rejection and Stable Graft Function Using Urinary mRNA Signature Reflecting Allograft Status in Kidney Transplantation
Authors: Seo Jung-Woo , Lee Yu-Ho , Tae Dong Hyun , Park Seon Hwa , Moon Ju-Young , Jeong Kyung Hwan , Kim Chan-Duck , Chung Byung Ha , Park Jae Berm , Kim Yeong Hoon , Seok Junhee , Joo Sun Hyung , Lee Seung Whan , Lee Sang-Ho 
Published: December 2020

Abstract
Background: Urine has been regarded as the best resource based on the assumption that urine can directly reflect the state of the allograft or ongoing injury in kidney transplantation. Previous studies, suggesting the usefulness of urinary mRNA as a biomarker of acute rejection, imply that urinary mRNA mirrors the transcriptional activity of the kidneys. Methods: We absolutely measured 14 data-driven candidate genes using quantitative PCR without pre-amplification in the cross-sectional specimens collected from Korean kidney transplant patients. We developed a clinical application model adopting urinary mRNAs for allograft rejection using a binary logistic regression and finally verified its usefulness in a large-scale validation group.Results: We measured the candidate genes in 103 training samples. Expression of 8/14 genes were significantly different between acute rejection and stable graft function with normal pathology and long-term graft survival. Also, CXCL9 was distinctly expressed in allografts with acute rejection in in situ hybridization analysis. This result, consistent with the qPCR result, implies that urinary mRNA could reflect the magnitude of allograft injury. We developed AR prediction model by differently combined mRNAs and the area under the curve (AUC) of the model was 0.89 in training set. The model was validated in 391 independent samples, and the AUC of the model was 0.84 with a fixed manner. In addition, the decision curve analysis indicated a range of reasonable threshold probabilities for biopsy. Conclusions. Therefore, we suggest urinary mRNA signature may serve as a non-invasive monitoring tool of acute rejection and intragraft immune injury.