ACcoding: A graph-based dataset for online judge programming.

A well-designed educational programming dataset is a valuable asset for students and educators. Such a dataset enables students to improve their programming performances continuously, provides researchers with significant data sources to identify students' learning behaviours and enhance the quality of programming education. Several existing datasets for programming education are either limited by a small number of participating students or a short span of learning records, bringing great challenges to investigate students' learning patterns in programming. We present a graph-based large-scale dataset specialized in programming learning on Online Judge (OJ) platform. The dataset, named ACcoding, was built by a university teaching group. As of the submission date of the initial manuscript of this paper (May 6, 2022), the dataset contains 4,046,652 task-solving records submitted by 27,444 students on 4,559 programming tasks over a span of 6 years. The large size of the dataset, combined with rich functional features, empowers educators to trace students' programming progress and choose appropriate programming tasks for specific training purposes. We also presents examples of applications used by the dataset.

Forkhead box P3 gene polymorphisms predispose to type 2 diabetes and diabetic nephropathy in the Han Chinese populations: a genetic-association and gender-based evaluation study.

BACKGROUND: Functional mutations or polymorphisms affecting forkhead box P3 (FOXP3) can lead to their abnormal FOXP3 gene expression and/or defective Treg cells generation, thus resulting in autoimmune disease and inflammatory disorders. FOXP3 also plays a key role in Type 2 diabetes mellitus (T2DM) and its complications, because the disease usually involves chronic low-grade inflammatory disorders and is associated with long-term immune system imbalance. This study aimed to investigate the association between FOXP3 polymorphisms and the susceptibility to T2DM and type 2 diabetes nephropathy (T2DN) within the Han Chinese populations. METHODS: Polymorphisms in rs3761548C/A and rs2294021C/T were examined in 400 patients (which include an equal number of T2DM and T2DN groups) and 200 healthy controls using PCR-HRM and sequence analysis. RESULTS: The genotype and allelic frequencies of the two single nucleotide polymorphisms (SNPs) were significantly different in T2DM and the progression of diabetes developing to T2DN. The further gender-based evaluation showed that in female subjects, rs3761548C/A was associated with an approximately 3-fold higher threat for T2DM and 4.5-fold for T2DN, while there was no noticeable association with rs2294021C/T; in males, the promoter polymorphism showed an increased predisposition of 5.4-fold and 3.4-fold predisposition to T2DM and T2DN, respectively, while rs2294021 polymorphism could impart a nearly 2-fold risk of developing T2DN. An additional analysis of combined genotypes (rs3761548 C/A-rs2294021C/T) revealed that CC-CC and CC-CT can be considered protective combinations in the predisposition of males with diabetes towards T2DN, while AA-CC and AA-TT have the opposite effect. CONCLUSIONS: This study demonstrated the possible involvement of individual and combined genetic associations of rs3761548C/A and rs2294021C/T polymorphisms with the susceptibility to diabetes and diabetic nephropathy in the Han Chinese population, as well as gender bias.

An Inflammation-Related Nine-Gene Signature to Improve Prognosis Prediction of Lung Adenocarcinoma.

BACKGROUND: A novel predictive model was rarely reported based on inflammation-related genes to explore clinical outcomes of lung adenocarcinoma (LUAD) patients. METHODS: Using TCGA database, we screened nine inflammation-related genes with a prognostic value, and LASSO regression was applied for model construction. The predictive value of the prognostic signature developed from inflammation-related genes was assessed by survival assays and multivariate assays. PCA and t-SNE analysis were performed to demonstrate clustering abilities of risk scores. RESULTS: Thirteen inflammation-related genes (BTG2, CCL20, CD69, DCBLD2, GPC3, IL7R, LAMP3, MMP14, NMUR1, PCDH7, PIK3R5, RNF144B, and TPBG) with prognostic values were finally identified. LASSO regression further screened nine candidates (BTG2, CCL20, CD69, IL7R, MMP14, NMUR1, PCDH7, RNF144B, and TPBG). Then, a prognostic prediction model using the above nine genes was constructed. A reliable clustering ability of risk score was demonstrated by PCA and t-SNE assays in 500 LUAD patients. The survival assays revealed that the overall survivals of the high-risk group were distinctly poorer than those of the low-risk group with 1-, 3-, and 5-year AUC values of 0.695, 0.666, and 0.694, respectively. Finally, multivariate assays demonstrated the scoring system as an independent prognostic factor for overall survival. CONCLUSIONS: Our study shows that the signature of nine inflammation-related genes can be used as a prognostic marker for LUAD.

Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment.

Blue light is an important signal that regulates the flowering of strawberry plants. To reveal the mechanism of early flowering under blue light treatment at the transcriptional regulation level, seedlings of cultivated strawberry (Fragaria × ananassa Duch.) "Benihoppe" were subjected to a white light treatment (WL) and blue light treatment (BL) until their flowering. To detect the expression patterns of genes in response to BL, a transcriptome analysis was performed based on RNA-Seq. The results identified a total of 6875 differentially expressed genes (DEGs) that responded to BL, consisting of 3138 (45.64%) downregulated ones and 3737 (54.36%) upregulated ones. These DEGs were significantly enriched into 98 GO terms and 71 KEGG pathways based on gene function annotation. Among the DEGs, the expression levels of genes that might participate in light signaling (PhyB, PIFs, and HY5) and circadian rhythm (FKF1, CCA1, LHY, and CO) in plants were altered under BL. The BBX transcription factors which responded to BL were also identified. The result showed that the FaBBX29, one of strawberry's BBX family genes, may play an important role in flowering regulation. Our results provide a timely, comprehensive view and a reliable reference data resource for further study of flowering regulation under different light qualities.

Sucrose synthase gene family in Brassica juncea: genomic organization, evolutionary comparisons, and expression regulation.

Sucrose synthase (SUS) plays an important role in sucrose metabolism and plant development. The SUS gene family has been identified in many plants, however, there is no definitive study of SUS gene in Brassica juncea. In this study, 14 SUS family genes were identified and comprehensively analyzed using bioinformatics tools. The analyzed parameters included their family member characteristics, chromosomal locations, gene structures and phylogenetic as well as transcript expression profiles. Phylogenetic analysis revealed that the 14 members could be allocated into three groups: SUS I, SUS II and SUS III. Comparisons of the exon/intron structure of the mustard SUS gene indicated that its structure is highly conserved. The conserved structure is attributed to purification selection during evolution. Expansion of the SUS gene family is associated with fragment and tandem duplications of the mustard SUS gene family. Collinearity analysis among species revealed that the SUS gene family could be lost or mutated to varying degrees after the genome was doubled, or when Brassica rapa and Brassica nigra hybridized to form Brassica juncea. The expression patterns of BjuSUSs vary among different stages of mustard stem swelling. Transcriptomics revealed that the BjuSUS01-04 expression levels were the most elevated. It has been hypothesized that they play an important role in sucrose metabolism during stem development. The expression levels of some BjuSUSs were significantly up-regulated when they were treated with plant hormones. However, when subjected to abiotic stress factors, their expression levels were suppressed. This study establishes SUS gene functions during mustard stem development and stress.

Broaden the sugar donor selectivity of blackberry glycosyltransferase UGT78H2 through residual substitutions.

Glycosylated secondary metabolites constitute a large proportion of nutrients or ingredients in consumed plants and related products. The glycosyl decoration largely depends on the activity of plant UDP-glycosyltransferases (UGTs). Mechanisms underlying the substrate selectivity and specificity of these reactions remain elusive. Here we report the cloning and functional characterization of a UGT, UGT78H2 in blackberry fruits. In vitro enzyme substrate specificity analysis and enzymatic kinetics evidenced that UGT78H2 glycosylate exclusively quercetin using uridine-5' diphosphate glucuronic acid (UDP-glucuronic acid) and uridine-5' diphosphate galactose (UDP-galactose). Site-directed mutagenesis was introduced into two residuals (N340P, K360N) previously unexplored. The mutation enhanced the protein catalyzing efficiency, especially toward UDP-galactose (23% higher), and expanded the sugar donor selectivity, which can use UDP-glucose as well. Molecular modeling and biochemical analysis results enable identification of the 23rd residue (360th in UGT78H2) of the PSPG (plant secondary product glycosyltransferase) motif as a key residue in defining this sugar selecting spectrum. Additionally, promoter of UGT78H2 was obtained. Transgenic analysis using the UGT78H2pro::GUS reporter system demonstrated that transcripts controlled by the promoter predominantly expressed in younger tissues. Subcellular localization study revealed that UGT78H2 was a soluble protein in the nucleus and cytoplasm. These results clarified the bio-function of UGT78H2 and provided a valid approach for substrate selectivity modification in horticultural plants, particularly for sugar donor selectivity.

Functional differences of BaPDS1 and BaPDS2 genes in Chinese kale.

This study presents a systematic analysis of the functional differences between two genes that encode phytoene desaturase (PDS) in Chinese kale. The promoter sequences of both BaPDS1 and BaPDS2 were amplified and cloned, and their lengths were 2005 bp and 2000 bp, respectively. The mining of cis-acting elements in the promoters showed that the two BaPDS genes are mainly associated with light and phytohormone responsiveness. Light quality, light intensity and plant hormone treatments were conducted in seedlings of Chinese kale, and the results indicated that the response of the two genes to different factors differed. Among them, BaPDSs collectively respond to the treatment with salicylic acid and abscisic acid. With regard to response differences, BaPDS1 is sensitive to red and blue light, blue light, and strong light, while BaPDS2 responds to blue light, weak light, darkness, gibberellin and methyl jasmonate. In addition, both BaPDS1 and BaPDS2 are likely targeted to the chloroplast. Furthermore, single and double mutants of BaPDSs were generated via CRISPR/Cas9 technology. Phenotypic analysis showed that the double mutant with edited PDS1 and PDS2 was a pure albino, while the single mutants with edited PDS1 or PDS2 were partly whitened. In summary, BaPDS1 and BaPDS2 genes played different and indispensable roles in Chinese kale, and their functions were partially complementary.

Melatonin affects the growth and cadmium accumulation of Malachium aquaticum and Galinsoga parviflora.

Phytoremediation technology has become one of the main techniques for remediating soils polluted by heavy metals because it does not damage the environment, but heavy metal-tolerant plants have the disadvantages of low biomass and slow growth. A pot experiment was conducted to study the effects of melatonin (Mel) on growth and cadmium (Cd) accumulation in the Cd accumulator Malachium aquaticum and hyperaccumulator Galinsoga parviflora by spraying different concentrations of Mel on them. The results showed that shoot biomass, photosynthetic pigment content and antioxidant enzyme activity were increased in both species after Mel was sprayed on their leaves. Mel reduced the Cd content in shoots of M. aquaticum and increased it in those of G. parviflora. In general, Cd accumulation was greatest in M. aquaticum when Mel was 200 µmol L-1 (120.71 µg plant-1, increased by 15.97% than control) and in G. parviflora when Mel was 100 µmol L-1 (132.40 µg plant-1, increased by 68.30% than control). Our results suggest it is feasible to improve the remediation efficiency of lightly Cd-contaminated soil by spraying G. parviflora with100 µmol L-1 Mel.

Correlation analysis of gene polymorphisms and ß-lactam allergy.

A total of 64 patients with ß-lactam allergy and 30 control subjects were enrolled in a case-control study. This study is aimed to analyze the relationship between ß-lactam allergy and 10 single nucleotide polymorphisms (SNPs) in interleukin-10 (IL-10), IL-13, IL-4Rα, high-affinity immunoglobulin E-receptor ß chain (FcεRIß), interferon γ receptor 2 (IFNGR2), and CYP3A4, and within the Han Chinese population of Northwest China. Genotyping for the SNPs was conducted using the Sequenom MassARRAY(®) platform. SPSS 17.0 was employed to analyze the statistical data and SHEsis was used to perform the haplotype reconstruction and analyze linkage disequilibrium of SNPs of IL-10 and IL-13. The results showed that the genotype distribution of CYP3A4 rs2242480/CT differed significantly between case and control groups of males (P=0.022; odds ratio (OR)=0.167, 95% confidence interval (CI): 0.032-0.867). Further analysis showed that CCA, CCG, and TAA haplotypes of IL-10 had no significant correlation in patients with ß-lactam allergy. The correlation between CCT and CAC haplotypes of IL-13 and ß-lactam allergy needs to be further studied. The analysis did not reveal any differences in the distribution of others gene polymorphisms between cases and controls.

Phylogenetic insight into subgenera Idaeobatus and Malachobatus (Rubus, Rosaceae) inferring from ISH analysis.

BACKGROUND: Rubus is a large and taxonomically complex genus exhibiting agamospermy, polyploidy and frequent hybridization. The objective of this work was to elucidate rDNA disrtibution pattern and investigate genomic composition of polyploids in 16 Rubus taxa (2n = 2x, 3x, 4x, 8x) of two subgenera Idaeobatus and Malachobatus by ISH method. RESULTS: The basic Rubus genome had one 45S rDNA locus, and all the polyploids (except R. setchuenensis) had the expected multiples of this number. Diploid and tetraploid Rubus taxa carried two 5S rDNA, whereas the triploid and octoploid species only had three. The duplicated 45S rDNA sites tended to be conserved, whereas those of 5S rDNA tended to be eliminated after polyploidization. The accession R03-20 was an autotriploid R. parvifolius, while R03-27 and R03-57 were naturally-occurred triploid hybrids between R. parvifolius and R. coreanus. GISH results suggested that R. parvifolius had close relationship with polyploids from Malachobatus. CONCLUSIONS: The polyploids from Malachobatus were probable allopolyploid. In addition, Rubus parvifolius might be involved in hybridization, polyploidization and speciation of some Idaeobatus and Malachobatus species.

Prevention and treatment of viral respiratory infections by traditional Chinese herbs.

OBJECTIVE: This review focuses on current knowledge of traditional Chinese herbs on prevention and treatment of viral respiratory infections, especially caused by Severe Acute Respiratory Syndromes (SARS) virus, respiratory syncytial virus (RSV) and influenza viruses. DATA SOURCES: The data used in this review were obtained from PubMed and CNKI up to May 2013. Terms of Chinese herbs and infections of respiratory tract were used in the search. STUDY SELECTION: Articles related that Chinese herbs preventing and treating infections in respiratory tract were retrieved and reviewed. The risk of bias of included studies was assessed by the method in the "Cochrane Handbook of Systematic Reveiws of Interventionsand studies" with high risk of bias were excluded. Four criteria for selections were set as following: randomized controlled trial, particular effective compound or derivative, reproducible result and animal test. RESULTS: Infectious respiratory tract diseases cause most mortality among infectious illnesses around the world. As traditional medicines, Chinese herbs have been widely used to deal with diseases for centuries and have been proved effective in practice. The administration of some Chinese herbs stimulates, suppresses or regulates the activity of immune system, thus protecting the respiratory tract or relieving infections of pathogens. Many herbs have remarkable antiviral effects, therefore they are used as substitutes of antimicrobial drugs. Based on the theory of traditional Chinese medicine, mix-using herbs provide a synergistic benefit on preventing and healing respiratory tract infections. Many commercial herbal medicines containing one or more compounds have been successfully applied to prevent and treat viral infections of respiratory tract clinically. CONCLUSIONS: Traditional Chinese herbs could directly inhibit pathogens infecting respiratory tract, or coordinate the activity of immune system to avoid or relieve infections. With the emergence of antidrug pathogens or new variants, Chinese herbs give strong evidence to protect human health.

[Research progress in glucose-6-phosphate dehydrogenase in higher plants].

Glucose-6-phosphate dehydrogenase (G6PDH) catalyzes the first and rate-limiting step of the oxidative pentose phosphate pathway, existing in both cytosolic and plastidic compartments of higher plants. Its main function is to provide reducing power (NADPH) and pentose phosphates for reductive biosynthesis and maintenance of the redox state of the cell. In addition, the expression of this enzyme is related to different biotic and abiotic stresses. In this review, we analyzed the isoenzyme, regulation and biological function of G6PDH. Meanwhile, we summarized the progress work of G6PDH involved in stress resistance, gene cloning, enzyme-deficiency and cluster analysis. Problems should be solved were also discussed.