bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying antibiotic prescribing patterns through multi-level latent profile analyses: a cross-sectional survey of primary care physicians in Hubei of China
Authors: Wang Dan , Liu Chaojie , Zhang Xinping , Liu Chenxi 
Published: March 2020

Abstract
Background Overuse of antibiotics significantly fuels the development of AMR, which threating the global population health. Great variations existed in antibiotic prescribing practices among physicians, indicating improvement potential for rational use of antibiotics. This study aims to identify antibiotic prescribing patterns of primary care physicians and potential determinants. Methods A cross-sectional survey was conducted on 551 physicians from 67 primary care facilities in Hubei selected through random cluster sampling, tapping into their knowledge, attitudes and prescribing practices toward antibiotics. Prescriptions (n=501,072) made by the participants from 1 January to 31 March 2018 were extracted from the medical records system. Seven indicators were calculated for each prescriber: average number of medicines per prescription, average number of antibiotics per prescription, percentage of prescriptions containing antibiotics, percentage of antibiotic prescriptions containing broad-spectrum antibiotics, percentage of antibiotic prescriptions containing parenteral administered antibiotics, percentage of antibiotic prescriptions containing restricted antibiotics, and percentage of antibiotic prescriptions containing antibiotics included in the WHO “Watch and Reserve” list. Two-level latent profile analyses were performed to identify the antibiotic prescribing patterns of physicians based on those indicators. Multi-nominal logistic regression models were established to identify determinants with the antibiotic prescribing patterns. Results On average, each primary care physician issued 909 (ranging from 100 to 11941 with a median of 474) prescriptions over the study period. The mean percentage of prescriptions containing antibiotics issued by the physicians reached 52.19% (SD=17.20%). Of those antibiotic prescriptions, an average of 82.29% (SD=15.83%) contained broad-spectrum antibiotics; 71.92% (SD=21.42%) contained parenteral administered antibiotics; 23.52% (SD=19.12%) contained antibiotics restricted by the regional government; and 67.74% (SD=20.98%) contained antibiotics listed in the WHO “Watch and Reserve” list. About 28.49% of the prescribers were identified as low antibiotic users, compared with 51.18% medium users and 20.33% high users. Higher use of antibiotics was associated with insufficient knowledge, indifference to changes, complacency with satisfied patients, low household income and rural location of the prescribers. Conclusion Great variation in antibiotic prescribing patterns exists among primary care physicians in Hubei of China. High use of antibiotics is not only associated with knowledge shortfalls but also low socioeconomic status of prescribers.
Identification of PGC-related ncRNAs and their relationship with the clinicopathologic features of gastric cancer
Authors: Ding Han-xi , Wu Ye-feng , Xu Qian , Yuan Yuan 
Published: March 2020

Abstract
Background Pepsinogen C (PGC) is considered to be the final product of mature differentiated gastric mucosa and the expression level of PGC in gastric mucosa decreased obviously in the courses of gastric cancer (GC) development. The mechanism of the down-regulation of PGC is still unclear and needs to be excavated. This study aims to identify the PGC-related ncRNAs, which may have potential to act as PGC post-transcriptional regulator, and further explore the relationship between these ncRNAs and clinicopathological parameters of GC. Methods Bioinformatics software was used to predict the target binding miRNAs for PGC and target binding circRNAs for candidate miRNAs. Dual-luciferase reporter assay was performed to validate the targeted complete complementary relationship. QRT-PCR was applied to detect the expression levels of PGC and PGC-related ncRNAs in GC tissues. Kaplan-Meier and Cox regression were used for the analysis of the relationship between these ncRNAs and prognostic significance of GC Results Hsa-let-7c was predicted to binding to PGC gene, hsa_circ_0001483 and hsa_circ_0001324 were targeted binding to hsa-let-7c, which was verified by dual-luciferase reporter assay. The hsa_circ_0001483 / hsa_circ_0001324 -hsa-let-7c-PGC axis was confirmed in GC tissues by qRT-PCR. The expression of hsa_circ_0001483 was correlated with peritumoral inflammatory cell infiltration level and lymphatic metastasis. Conclusions Hsa_circ_0001483, hsa_circ_0001324 and let-7c were newly identified and validated as PGC-related ncRNAs and were associated with the clinicopathological features of GC in some ways. The hsa_circ_0001483 / hsa_circ_0001324-hsa-let-7c-PGC axis was existed in GC, which may explain the downregulation of PGC in GC tissues.
A glycolysis-based 4-mRNA signature correlates with the prognosis and cell cycle process in patients with bladder cancer
Authors: Zhang Chen , Gou Xin , He Weiyang , Yang Huaan , Yin Hubin 
Published: March 2020

Abstract
Background: Bladder cancer is one of the most prevalent malignancies worldwide. However, traditional indicators have limited predictive effects on the clinical outcomes of bladder cancer. The aim of this study was to develop and validate a glycolysis-related gene signature for predicting the prognosis of patients with bladder cancer that have limited therapeutic options. Methods: mRNA expression profiling was obtained from patients with bladder cancer from The Cancer Genome Atlas (TCGA) database. Gene set enrichment analysis (GSEA) was conducted to identify glycolytic gene sets that were significantly different between bladder cancer tissues and paired normal tissues . A prognosis-related gene signature was constructed by univariate and multivariate Cox analysis. Kaplan-Meier curves and time-dependent receiver operating characteristic (ROC) curves were utilized to evaluate the signature. A nomogram combined with the gene signature and clinical parameters was constructed. Correlations between glycolysis-related gene signature and molecular characterization as well as cancer subtypes were analyzed. RT-qPCR was applied to analyze gene expression. Functional experiments were performed to determine the role of PKM2 in the proliferation of bladder cancer cells. Results: Using a Cox proportional regression model, we established that a 4-mRNA signature (NUP205, NUPL2, PFKFB1 and PKM) was significantly associated with prognosis in bladder cancer patients. Based on the signature, patients were split into high and low risk groups, with different prognostic outcomes. The gene signature was an independent prognostic indicator for overall survival. The ability of the 4-mRNA signature to make an accurate prognosis was tested in two other validation datasets. GSEA was performed to explore the 4-mRNA related canonical pathways and biological processes, such as the cell cycle, hypoxia, p53 pathway, and PI3K/AKT/mTOR pathway. A heatmap showing the correlation between risk score and cell cycle signature was generated. RT-qPCR revealed the genes that were differentially expressed between normal and cancer tissues. Experiments showed that PKM2 plays essential roles in cell proliferation and the cell cycle. Conclusion: The established 4‑mRNA signature may act as a promising model for generating accurate prognoses for patients with bladder cancer, but the specific biological mechanism needs further verification.
Transcriptome-based identification and validation of optimal reference genes for quantitative real-time PCR normalization in Psathyrostachys huashanica
Authors: Shen Chuan , Li Jingyuan , Wei Caiyan , Zhang Xudong , Wu Yunfeng 
Published: March 2020

Abstract
Background: P. huashanica ( Psathyrostachys huashanica ), known as an important resistance resource reservoir, is a rare and endangered plant growing suitably in Huashan mount region and would be urgently exploited in wheat genetic improvements sooner. During the utilization process, different IRGs (internal reference genes) need to be appropriately selected as standards based on biotic and abiotic stress conditions. It is crucial that Real-time RT-qPCR with combination of bioinformatics were adopted to explore the reliable IRGs from transcriptome of P . huashanica.Results: The present work reported new 3 species of IRGs, UBC2 , UBC17, 18S rRNA , which were screened from transcriptome of P. huashanica under biotic and abiotic stress conditions, using RT-qPCR and four algorithms, including geNorm, NormFinder, BestKeeper, and RefFinder, to analyse expression of sixteen candidate reference genes. These genes appear as following 18S rRNA (18S ribosomal RNA), EF1-α (eukaryotic elongation factor 1 alpha), UBC2 (ubiquitin-conjugating enzyme E2-2), UBC17 (ubiquitin-conjugating enzyme E2-17), α-TUB2A (alpha tubulin-2A), β-TUB3 (beta tubulin 3), ADF4 (Actin-depolymerising factor 4), ACTIN (actin), GAPDH (Glyceraldehyde-3-phosphate dehydrogenase), 60SARP (60S acidic ribosomal protein), UBQ (polyubiquitin), SamDC (S-Adenosylmethionine decarboxylase), EIF4A (eukaryotic initiation factor 4A), ARF (ADP-ribosylation factor), HIS1 (histone H1), and HIS2B (histone H2B). Analysis of gene expression demonstrated that the expression of UBC2 gene was most stable under ABA hormone stress, low temperature stress and high temperature stress, similarly, UBC17 gene under IAA hormone stress, salinity stress and drought stress, both UBC17 genes and 18S rRNA genes under abiotic and biotic stress, respectively. The most stable gene was UBC2 gene in the root, UBC17 gene in stem and leaf. In this study, α-TUB2A , UBC and ACTIN genes were verified as the suitable reference genes across all tested samples. To further validate the suitability of the selected reference genes, we evaluated the relative expression of PsaCPK3 (Calcium-dependent protein kinase) and PsaHSP70-1 (heat shock protein 70-1), which are stress-related genes that may be involved in response to adversity.Conclusions: This study has identified a set of the most stable IRGs suiting for RT-qPCR detection of a few target gene expressions from P . huashanica in different experimental conditions. In addition, this study should provide the accuracy information for gene expression analysis in P . huashanica .
Diet quality and its relationship with overweight and laboratory parameters in breast cancer patients undergoing treatment
Authors: Ng Krystal Lu Shin , Shariff Zalilah Mohd , Chan Yoke Mun 
Published: March 2020

Abstract
Background Overweight is the common issue existed among breast cancer patients, leading to poor cancer prognosis and survival. However, previous studies have focused merely on single nutrient or food groups. This study aimed to determine whether diet quality was associated with overweight and laboratory parameters among breast cancer patients undergoing treatment. Methods A cross sectional study comprises of 163 patients was conducted from January to May 2017. Diet quality and level of physical activity of patients were ascertained using Healthy Eating Index (HEI)-2015 and International Physical Activity Questionnaire (IPAQ)-short form, respectively. Data were available on body mass index and biochemical data, including of serum albumin, serum hemoglobin and neutrophils count. Logistic regression was performed to identify the association between diet quality and overweight, serum albumin, serum hemoglobin and neutrophils count. Results The mean total HEI score (standard deviation) of the breast cancer patients was 63.86 (8.75). More than 80% of the subjects did not adhere to the dietary guidelines for whole grains, dairy, refined grains, and ratio of poly- and mono-unsaturated fatty acids to saturated fatty acids components. In the multivariate model, those who perceived higher score of total HEI-2015 were less likely to experience overweight (Q4 vs Q1: OR=0.36; 95% CI=0.13, 0.99) while reported higher concentration of serum hemoglobin (Q4 vs Q1: OR=0.36; 95% CI=0.13, 0.98; Q3 vs Q1: OR=0.35; 95% CI=0.13, 0.92). Non-significant associations of diet quality were shown for serum albumin and neutrophils count. Conclusions A majority of breast cancer patients require dietary modification, especially for fatty acids, grains and dairy products. Diet quality may associate with overweight. A balanced diet that address the problem of overweight may help to maintain a good nutritional status and to improve cancer care in breast cancer patients during treatment. Future prospective studies are required to confirm this association.
Sport policy and practice: Why a focus on retention is required for both health and performance
Authors: Eime Rochelle , Charity Melanie , Westerbeek Hans 
Published: March 2020

Abstract
Background: Australia like many developed countries is largely an inactive nation. Participation in sport, a form of leisure-time physical activity, can contribute to a range of individual and community health benefits. National sport policy often has a dual focus on population-based participation, and elite performance. Whist there are various sport models depicting the pathway to elite, there has been no strategic population-level sport participation pathway model developed as a guide towards increasing sport participation across the lifespan. The aim of this study therefore is to explore sport participation across the lifespan and develop a neutral model that does not favour community or elite sport and that highlights the critical participation transition points including drop-out. Methods: We conducted a longitudinal analysis of sport participation records for 8 major sports from 2015-2017, whereby individual participation within sports was tracked from 2015 and subsequent years 2016 and 2017. Results: The total number of participants analysed was 579,696. In 2017, port participation rates were highest for those aged 10-14 years (61.3%), followed by those children within the 5-9 year age group (51.7%). However, 44.7% of all participants dropped out within two years of the base year. From these participation rates across the lifespan in conjunction with the published literature, on sport policy and participation, we developed the Sport Participation Pathway Model (SPPM). The SPPM depicts current sport participation and in doing so emphasises the significant drop-out of sport across the lifespan. Conclusion: At a population level, competitive club-based sport alone is not going to solve the physical inactivity epidemic. Our SPPM, and the new (retention related) data presented in this paper, demonstrates the population trends in participation in sport and the high drop-out of competitive club-based sport. We suggest that for people to (eventually) become active sport participants, the (recruitment) narrative could be changed towards (first) engaging people in leisure time physical activities. We feel that this can only be done by developing an integrated policy system across the PA-sport spectrum rather than looking at sport participation in a closed (club-based) system. The SPPM can be used to developing a more integrated PA-Sport participation model.
Demonstration of improved plant growth and biomass by At1g promoter-controlled root-preferential expression of AtGA20ox gene
Authors: Ly Linh Khanh , Bui Thao Phuong , Do Phat Tien , Le Anh Van Thi , Nguyen Phong Van , Pham Ngoc Bich , Zhang Zhanyuan J. , Chu Ha Hoang 
Published: March 2020

Abstract
Background: Overexpression of GA20 oxidase gene has been a recent trend for improving plant growth and biomass. Constitutive expression of GA20ox has successfully improved plant growth and biomass in several plant species. However, the constitutive expression of this gene causes side-effects, such as reduced leaf size and stem diameters, etc. To avoid these effects, different tissue-specific promoters had been identified and employed for GA20ox overexpression. In this study, we demonstrate the potential of At1g, a root-preferential promoter, for GA20ox expression to enhance plant biomass.Results: We examined the utility of At1g promoter to drive the expression of GUS (b-glucuronidase) reporter and GA20ox genes in tobacco and Melia azedarach. Histochemical GUS assays in tobacco showed that At1g was a root-preferential promoter whose expression was particularly strong in root tips. The ectopic expression of AtGA20ox gene under the control of At1g promoter showed the improved plant growth and biomass of both tobacco and M. azedarach transgenic plants compared to wild-type (WT) control plants. Stem length as well as stem and root fresh weights increased by up to 1.5-3 folds in transgenic tobacco and 2 folds in transgenic M. azedarach. Both tobacco and M. azedarach transgenic plants showed increases in the root xylem width, xylem over phloem ratio by 50%-100% as compared to WT plants. Importantly, no significant difference in the leaf shape and size was observed between At1g::AtGA20ox transgenic and WT plants. Moreover, transgenic M. azedarach showed a 135% increase in stem diameter even though no change was found in transgenic tobacco.Conclusions: These results demonstrate the great utility of At1g promoter, when driving AtGA20ox gene, for growth and biomass improvements in woody plants and potentially some other plant species.
A CBL-interacting Protein Kinase Gene, GhCIPK6, Increases Salt Tolerance in Transgenic Upland Cotton by Involving in Multiple Stress Signaling Pathways
Authors: Su Ying , Guo Anhui , Huang Yi , Wang Yumei , Hua Jinping 
Published: March 2020

Abstract
Background: Salt stress is one of the most damaging abiotic stresses in production of Upland cotton (Gossypium hirsutum). Upland cotton is defined as a medium salt-tolerant crop. Salinity hinders root development, shoots growth, and reduces the fiber quality.Results: Our previous study verified a GhCIPK6 gene response to salt stress in G. hirsutum. The homologs of GhCIPK6 were analyzed in A2 (G. arboreum), D5 (G. raimondii), and AD1 (G. hirsutum) genomes. GhCIPK6 localized to the vacuole and cell membrane. The GhCBL1-GhCIPK6 and GhCBL8-GhCIPK6 complexes localized to the nucleus and cytomembrane. Overexpression of GhCIPK6 enhanced expression levels of co-expressed genes induced by salt stress, which scavenged ROS and involved in multiple signaling pathways verified by RNA-seq analysis. Water absorption capacity and cell membrane stability of seeds from GhCIPK6 overexpressed lines was higher than that of wild-type seeds during imbibed germination stage. The germination rates and field emergence percentage of GhCIPK6 overexpressed lines were higher than that of control line under salt stress. Moreover, overexpressing of GhCIPK6 in cotton increased lint percentage, and fiber length uniformity under salt stress. Conclusions: We verified the function of GhCIPK6 by transformation and RNA-seq analysis. GhCIPK6 overexpressed lines exhibited higher tolerance to abiotic stresses, which functioned by involving in multiple stress responsive pathways. Therefore, GhCIPK6 has the potential for cotton breeding to improve stress-tolerance.
Identification of candidate genes for low temperature tolerance during germination of maize using a genome-wide association study and RNA-sequencing
Authors: Zhang Hong , Zhang Jiayue , Xu Qingyu , Wang Dandan , Di Hong , Huang Jun , Yang Xiuwei , Wang Zhoufei , Zhang Lin , Dong Ling , Wang Zhenhua , Zhou Yu 
Published: March 2020

Abstract
Background: Maize ( Zea mays L.) is the largest agricultural crop in the world based on acreage and yield, however, it is inherently sensitive to low temperatures. The growth and yield of maize can be affected by low temperature during its whole growth period, particularly during germination. Therefore, it is urgent to identify the new gene(s) related to the low temperature tolerance during maize germination. Results: In this study, 14 phenotypic traits related to seed germination were used to explore the genetic architecture of maize through genome-wide association analysis (GWAS). A total of 30 single nucleotide polymorphisms (SNPs) associated with low temperature tolerance were detected (–log10( P ) > 4); 14 candidate genes were detected as being directly associated with these SNPs and 81 candidate genes were identified when the screen was extended to a distance of 30 kb from these SNPs. The candidate genes were predicted by conjoint analysis with RNA-sequencing (RNA-seq) to evaluate whole-genome gene expression levels. A total of nine differentially expressed genes (DEGs) (|log2foldchange|≥0.585， P <0.05) were found within distance of 30 kb, including two DEGs ( GRMZM2G101383 and GRMZM2G402584 ), which were associated with SNPs directly. The differential expression of these candidate genes was verified using qRT-PCR. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms of DEGs GRMZM2G052129 and GRMZM2G038964 were, ‘fatty acid metabolic process’, ‘Mitogen-activated protein kinase (MAPK) signal transduction’, and so on, which are related to the fluidity of the cell membrane and low temperature signal transduction. Conclusion: Therefore, further functional analysis of GRMZM2G052129 and GRMZM2G038964 will provide valuable information for understanding the genetic mechanism of low temperature tolerance during germination in maize.
Modeling the Effects of Citrus sinensis Essential Oil and Nitrite on Growth Probability of Clostridium botulinum Type A in Broth Media
Authors: Rezaei Mohammad A. , Razavilar Vadood , Anvar Amirali , Mashak Zohreh 
Published: March 2020

Background:
Nitrite is a multifunctional food additive used for control of toxigenic
Clostridium botulinum in foodstuffs. However, there is a growing concern about the carcinogenic
and teratogenic effects of nitrite. The present research was done to assess the effects of Citrus
sinensis essential oil and nitrite on the growth probability of C. botulinum type A using predictive
mathematical modeling technique in broth media.

Methods:
Essential oil of C. sinensis was collected using Clevenger. Multifactorial design included
diverse C. sinensis, nitrite and NaCl concentrations and also different pH ranges and storage
temperatures were arranged in BHI broth medium. C. botulinum type A strains were then inoculated
and their growth model was analyzed.

Results:
The synergistic inhibitory effects of nitrite and C. sinensis were significant (P<0.05).
C. sinensis (0.045%) and nitrite (20 ppm) strongly decreased the growth of C. botulinum (log P%= -
2.2 versus log P%= 1.15). Decreasing temperature up to 25°C significantly affected growth probability
of C. botulinum (P<0.05). Increasing NaCl concentration up to 3% did not cause any significant
differences in the growth of C. botulinum (P= 0.062). Bacterial growth in broth media was
completely inhibited at pH 5.5 and also in media contained C. sinensis (0.045%) and nitrite (60 ppm)
at pH 6.5 (log P%= -3.76).

Conclusion:
Using certain concentrations of C. sinensis essential oil with other suboptimal factors
(pH and temperature) and nitrite can control the growth of C. botulinum in broth media.