cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6530027
title: Additional file 5: of Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen

description: The expression pattern of different genes in the root tissues of watermelon exposed to different levels of nitrogen (0.2Â mM, 9Â mM). (XLSX 453Â kb)
DOI: 10.6084/m9.figshare.6530021
title: Additional file 3: of Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen

description: Transcription factors (TFs) found to be affected in the leaf and root tissues of watermelon exposed to different levels of nitrogen (0.2Â mM, 9Â mM) (XLSX 76Â kb)
DOI: 10.6084/m9.figshare.14908120.v1
title: Additional file 2 of Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat

description: Additional file 2: Table S1. Corresponding ID of CCoAOMT genes in Arabidopsis and rice.Table S2. Characteristics of cis-acting regulatory elements in the promoter region of CCoAOMT genes in wheat.Table S3. GO enrichment analysis of the identified TaCCoAOMTs.Table S4. Differential expression analysis of TaCCoAOMT genes under abiotic stress.Table S5. Differential expression analysis of TaCCoAOMT genes under Fgtreatment.Table S6. Identification of miRNA bind sites in TaCCoAOMT genes.Table S7. Haplotype of CCoAOMT genes in five Triticum species.Table S8. The list of primers used for qRT-PCR in this study.
DOI: 10.6084/m9.figshare.6530036.v1
title: Additional file 1: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S7. Gene-specific primers used for qRT-PCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.24894921
title: Gospel across the millennium:Confucian cultureand innovation in China

description: Confucian culture has had a significant impact on contemporary Chinese society for thousands of years. However, whether it is a "gospel" or a "curse" for science and technology innovation in contemporary China is still controversial. To measure the extent of Confucian culture, we use the density of Confucian cultural sites and test its causal relationship with innovation. The data suggests that regions with a strong influence of Confucian culture have higher levels of innovation. This finding remains consistent even after conducting instrumental variable regression and multiple robustness tests. Mechanistic analyses demonstrate that Confucian culture can promote innovation by reinforcing good governance, improving education, and enhancing intellectual property protection. The study reveals that Confucianism has a stronger impact in regions with lower business credit. Additionally, it suggests that Confucianism and formal institutions can be interchangeable. Moreover, foreign cultures may diminish the influence of Confucianism in fostering innovation.
DOI: 10.6084/m9.figshare.6530027.v1
title: Additional file 5: of Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen

description: The expression pattern of different genes in the root tissues of watermelon exposed to different levels of nitrogen (0.2Â mM, 9Â mM). (XLSX 453Â kb)
DOI: 10.6084/m9.figshare.6530063
title: Additional file 3: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S2a. Expression information of DEGs in leaves at 1 day after BTH treatment. Table S2b. Expression information of DEGs in leaves at 3 day after BTH treatment. Table S2c. Expression information of DEGs in roots at 1 day after BTH treatment. Table S2d. Expression information of DEGs in roots at 3 day after BTH treatment. (XLSX 2340 kb)
DOI: 10.6084/m9.figshare.6530063.v1
title: Additional file 3: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S2a. Expression information of DEGs in leaves at 1 day after BTH treatment. Table S2b. Expression information of DEGs in leaves at 3 day after BTH treatment. Table S2c. Expression information of DEGs in roots at 1 day after BTH treatment. Table S2d. Expression information of DEGs in roots at 3 day after BTH treatment. (XLSX 2340 kb)
DOI: 10.6084/m9.figshare.6530048.v1
title: Additional file 2: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S1. The information of 3996 identified banana novel protein-coding transcripts in the study. (XLSX 4797 kb)
DOI: 10.6084/m9.figshare.1301971
title: Damage-induced BRCA1 phosphorylation by Chk2 contributes to the timing of end resection

description: The BRCA1 tumor suppressor plays an important role in homologous recombination (HR)-mediated DNA double-strand-break (DSB) repair. BRCA1 is phosphorylated by Chk2 kinase upon γ-irradiation, but the role of Chk2 phosphorylation is not understood. Here, we report that abrogation of Chk2 phosphorylation on BRCA1 delays end resection and the dispersion of BRCA1 from DSBs but does not affect the assembly of Mre11/Rad50/NBS1 (MRN) and CtIP at DSBs. Moreover, we show that BRCA1 is ubiquitinated by SCF<sup>Skp2</sup> and that abrogation of Chk2 phosphorylation impairs its ubiquitination. Our study suggests that BRCA1 is more than a scaffold protein to assemble HR repair proteins at DSBs, but that Chk2 phosphorylation of BRCA1 also serves as a built-in clock for HR repair of DSBs. BRCA1 is known to inhibit Mre11 nuclease activity. SCF<sup>Skp2</sup> activity appears at late G1 and peaks at S/G2, and is known to ubiquitinate phosphodegron motifs. The removal of BRCA1 from DSBs by SCF<sup>Skp2</sup>-mediated degradation terminates BRCA1-mediated inhibition of Mre11 nuclease activity, allowing for end resection and restricting the initiation of HR to the S/G2 phases of the cell cycle.
DOI: 10.6084/m9.figshare.6530030
title: Additional file 6: of Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen

description: The summary of five major transcription factor families in leaf and root tissues of watermelon exposed to different levels of N (0.2Â mM, 9Â mM) (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.6530078
title: Additional file 11: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: Panther enrichment for the entire network. (XLSX 117 kb)
DOI: 10.6084/m9.figshare.20161526
title: The injuries of spleen and intestinal immune system induced by 2-Gy <sup>60</sup>Co <b>γ</b>-ray whole-body irradiation

description: The aim of the present study was to investigate the injuries of spleen and intestinal immune system induced by 2 Gy <sup>60</sup>Co γ ray in mice. A total of 120 Balb/c mice were randomly divided into two groups: blank control (Ctrl) and model (IR). The IR mice were exposed to a single dose of total body irradiation (2 Gy, dose rate: 1 Gy/min) and sacrificed on 1st, 3rd, 7th, 14th and 21st day after irradiation. The indicators including general observations and body weight, the changes in peripheral hemogram, spleen index, histopathology examination and lymphocyte subsets of spleen. As well as the count and subsets of lymphocyte in gut-associated lymphoid tissue. Compared with the Ctrl group, the body weight, spleen index, peripheral blood cell and splenocyte amounts, intraepithelial lymphocytes number decreased significantly after exposure, accompanied by a notable decreased count of lymphocytes in Peyer’s patch and mesenteric lymph nodes. Moreover, ionizing radiation also broke the balance of CD4+/CD8+ and increased the Treg proportion in spleen, which then triggered immune imbalance and immunosuppression. In general, the spleen injuries occurred on 1st day after exposure, worse on 3rd day, and were relieved on 7th day. The intestinal immune injuries were observed on 1st day, and attenuated on 3rd day. On 21st day after exposure, the spleen volume and index have returned to normal, except for the distribution of lymphocyte subpopulations. Furthermore, all indicators of gut-associated lymphoid tissue, except for mesenteric lymph nodes lymphocyte count, had returned to normal levels on 21st day. In conclusion, our data showed the injuries of spleen and intestinal immune system induced by 2 Gy <sup>60</sup>Co γ ray whole-body irradiation. These findings may provide the bases for further radiation protection in the immunity.
DOI: 10.6084/m9.figshare.13360635
title: Morphology, ultrastructure and molecular phylogeny of <i>Johsia chumphonensis</i> gen. et sp. nov. and <i>Parvodinium parvulum</i> comb. nov. (Peridiniopsidaceae, Dinophyceae)

description: The family Peridiniopsidaceae encompasses mainly freshwater species of the genera <i>Peridiniopsis, Palatinus</i> and <i>Parvodinium</i>. Only one benthic, marine species ‘<i>Scrippsiella</i>’ <i>hexapraecingula</i> has been attributed to this family. Here we established five strains by isolating single <i>Parvodinium</i>-like cells from the marine Gulf of Thailand, Hainan Island waters (China), off Manado (Indonesia) and from a freshwater reservoir in Fuzhou (China). All strains were examined with light, scanning and transmission electron microscopy, and their SSU, ITS-5.8S and partial LSU rRNA regions were sequenced. Four marine strains share a plate formula of Po, cp, X, 4′, 2a, 6′′, 6C, 4S, 5′′′, 2′′′′ and are herein attributed to a new genus <i>Johsia</i> as <i>J. chumphonensis</i> gen. et sp. nov. Its theca is characterized by an epitheca 1.5 times as long as the hypotheca in dorsal view and a 2a plate about half the size of 1a. A type B eyespot was observed in <i>J. chumphonensis</i> comprising two rows of lipid globules within a chloroplast with a single row of crystals overlying the eyespot. Production of spherical cysts was observed in culture. The freshwater strain shows a plate pattern of Po, cp, X, 4′, 2a, 7′′, 6C, 5S, 5′′′, 2′′′′, characterized by two unequal antapical plates and a lack of antapical spines, fitting the description of <i>Peridinium parvulum</i>, which was transferred to <i>Parvodinium</i> as <i>P. parvulum</i> comb. nov. In this species, a type A eyespot was observed comprising four rows of lipid globules within a chloroplast. A molecular phylogeny was inferred based on concatenated data from SSU, ITS-5.8S and partial LSU rRNA gene sequences using maximum likelihood and Bayesian inference. Our results show that <i>Johsia</i> is nested within the Peridiniopsidaceae and is a sister clade to <i>Peridiniopsis borgei</i> and the strain UTEX1948 identified as ‘<i>Scrippsiella</i>’ <i>hexapraecingula</i> with three anterior intercalary plates.
DOI: 10.6084/m9.figshare.6530015.v1
title: Additional file 2: of Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen

description: The expression of chlorophyll, cytochrome 450, photosystem I, II, and phytochrome-related genes in watermelon leaves exposed to different levels of nitrogen supply (0.2Â mM, 9Â mM) (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.6530030.v1
title: Additional file 6: of Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen

description: The summary of five major transcription factor families in leaf and root tissues of watermelon exposed to different levels of N (0.2Â mM, 9Â mM) (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.6530048
title: Additional file 2: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S1. The information of 3996 identified banana novel protein-coding transcripts in the study. (XLSX 4797 kb)
DOI: 10.6084/m9.figshare.6530075
title: Additional file 4: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S3. GO terms of biological process enriched in banana leaves and roots. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.6530078.v1
title: Additional file 11: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: Panther enrichment for the entire network. (XLSX 117 kb)
DOI: 10.6084/m9.figshare.6530036
title: Additional file 1: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S7. Gene-specific primers used for qRT-PCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6530075.v1
title: Additional file 4: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S3. GO terms of biological process enriched in banana leaves and roots. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.6530090.v1
title: Additional file 5: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S4. The significantly enriched pathways of DEGs in banana leaves and roots. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6530090
title: Additional file 5: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S4. The significantly enriched pathways of DEGs in banana leaves and roots. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6530102
title: Additional file 12: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: List of GO BPs extracted from the g:Profiler enrichment of the entire network and relevant to PD. (XLSX 103 kb)
DOI: 10.6084/m9.figshare.20161526.v1
title: The injuries of spleen and intestinal immune system induced by 2-Gy <sup>60</sup>Co γ-ray whole-body irradiation

description: <b><i>Purpose</i></b><i>:</i> The aim of the present study was to investigate the injuries of spleen and intestinal immune system induced by 2 Gy <sup>60</sup>Co γ ray in mice. <b><i>Materials and methods:</i></b> A total of 120 Balb/c mice were randomly divided into two groups: blank control (Ctrl) and model (IR). The IR mice were exposed to a single dose of total body irradiation (2 Gy, dose rate: 1 Gy/min) and sacrificed on 1<sup>st</sup>, 3<sup>rd</sup>, 7<sup>th</sup>, 14<sup>th</sup> and 21<sup>st</sup> day after irradiation. The indicators including general observations and body weight, the changes in peripheral hemogram, spleen index, histopathology examination and lymphocyte subsets of spleen. As well as the count and subsets of lymphocyte in gut associated lymphoid tissue. <b><i>Results:</i></b> Compared with the Ctrl group, the body weight, spleen index, peripheral blood cell and splenocyte amounts, intraepithelial lymphocytes number decreased significantly after exposure, accompanied by a notable decreased count of lymphocytes in peyer’s patch and mesenteric lymph nodes. Moreover, ionizing radiation also broke the balance of CD4+/CD8+ and increased the Treg proportion in spleen, which then triggered immune imbalance and immunosuppression. In general, the spleen injuries occurred on 1<sup>st</sup> day after exposure, worse on 3<sup>rd</sup> day, and were relieved on 7<sup>th</sup> day. The intestinal immune injuries were observed on 1<sup>st</sup> day, and attenuated on 3<sup>rd</sup> day. On 21<sup>st</sup> day after exposure, the spleen volume and index have returned to normal, except for the distribution of lymphocyte subpopulations. Furthermore, all indicators of gut associated lymphoid tissue, except for mesenteric lymph nodes lymphocyte count, had returned to normal levels on 21<sup>st</sup> day. <b><i>Conclusion:</i></b> In conclusion, our data showed the injuries of spleen and intestinal immune system induced by 2 Gy <sup>60</sup>Co γ ray whole-body irradiation. These findings may provide the bases for further radiation protection in the immunity.
DOI: 10.6084/m9.figshare.20161526.v2
title: The injuries of spleen and intestinal immune system induced by 2-Gy <sup>60</sup>Co <b>γ</b>-ray whole-body irradiation

description: The aim of the present study was to investigate the injuries of spleen and intestinal immune system induced by 2 Gy <sup>60</sup>Co γ ray in mice. A total of 120 Balb/c mice were randomly divided into two groups: blank control (Ctrl) and model (IR). The IR mice were exposed to a single dose of total body irradiation (2 Gy, dose rate: 1 Gy/min) and sacrificed on 1st, 3rd, 7th, 14th and 21st day after irradiation. The indicators including general observations and body weight, the changes in peripheral hemogram, spleen index, histopathology examination and lymphocyte subsets of spleen. As well as the count and subsets of lymphocyte in gut-associated lymphoid tissue. Compared with the Ctrl group, the body weight, spleen index, peripheral blood cell and splenocyte amounts, intraepithelial lymphocytes number decreased significantly after exposure, accompanied by a notable decreased count of lymphocytes in Peyer’s patch and mesenteric lymph nodes. Moreover, ionizing radiation also broke the balance of CD4+/CD8+ and increased the Treg proportion in spleen, which then triggered immune imbalance and immunosuppression. In general, the spleen injuries occurred on 1st day after exposure, worse on 3rd day, and were relieved on 7th day. The intestinal immune injuries were observed on 1st day, and attenuated on 3rd day. On 21st day after exposure, the spleen volume and index have returned to normal, except for the distribution of lymphocyte subpopulations. Furthermore, all indicators of gut-associated lymphoid tissue, except for mesenteric lymph nodes lymphocyte count, had returned to normal levels on 21st day. In conclusion, our data showed the injuries of spleen and intestinal immune system induced by 2 Gy <sup>60</sup>Co γ ray whole-body irradiation. These findings may provide the bases for further radiation protection in the immunity.
DOI: 10.6084/m9.figshare.6530102.v1
title: Additional file 12: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: List of GO BPs extracted from the g:Profiler enrichment of the entire network and relevant to PD. (XLSX 103 kb)
DOI: 10.6084/m9.figshare.6530150.v1
title: Additional file 14: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: List of ORFs in LD with PD-GWAS top SNPs. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6530114.v1
title: Additional file 6: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S5. Differentially expressed genes involved in protein kinases and transcription factors. (XLSX 225 kb)
DOI: 10.6084/m9.figshare.6530135
title: Additional file 7: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S6. Expression information of DEGs in Figs.Â 5 and 6. (XLSX 123 kb)
DOI: 10.6084/m9.figshare.19113034.v1
title: Additional file 3 of Identification and validation of serum autoantibodies in children with B-cell acute lymphoblastic leukemia by serological proteome analysis

description: Additional file 3. Raw data of mass spectrometry.
DOI: 10.6084/m9.figshare.19112859
title: Additional file 4 of Albumin levels predict mortality in sepsis patients with acute kidney injury undergoing continuous renal replacement therapy: a secondary analysis based on a retrospective cohort study

description: Additional file 4: Table S4.
DOI: 10.6084/m9.figshare.6530150
title: Additional file 14: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: List of ORFs in LD with PD-GWAS top SNPs. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.21200786
title: Additional file 7 of Analysis of controlling genes for tiller growth of Psathyrostachys juncea based on transcriptome sequencing technology

description: Additional file 7.
DOI: 10.6084/m9.figshare.21200780
title: Additional file 5 of Analysis of controlling genes for tiller growth of Psathyrostachys juncea based on transcriptome sequencing technology

description: Additional file 5.
DOI: 10.6084/m9.figshare.6530258
title: Additional file 5: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: g:Pprofiler enrichment for the entire network. (XLSX 172 kb)
DOI: 10.6084/m9.figshare.19113054
title: Additional file 1 of Cyclic multiplex fluorescent immunohistochemistry and machine learning reveal distinct states of astrocytes and microglia in normal aging and Alzheimer’s disease

description: Additional File 1: Table S1. Demographic and neuropathological characteristics of study subjects. Description: Abbreviations: ADNC = AD neuropathological changes; APOE = Apolipoprotein E genotype; CAA = cerebral amyloid angiopathy; CVD = cerebrovascular disease; F = female; LBD = Lewy body disease; M = male; NA = Not available/applicable; NOS = not otherwise specified; NP Dx = neuropathological diagnosis. Table S2. Primary and secondary antibodies used in this study and sequence of immunohistochemistry cycles. Description: Note: GFAP and DAPI detection are needed in all the cycles to guarantee an adequate alignment of the images. Abbreviations: AF488 = AlexaFluor 488; Cy = cyanine; Dk = donkey; Gt = goat; Ms = mouse; Rb = rabbit. All secondary antibodies were purchased from Jackson ImmunoResearch Labs, West Grove, PA. Table S3. Results of mixed effects regression models. Description: Results of mixed effects regression models with diagnosis (CTRL vs. AD) or state (homeostatic vs. intermediate vs. reactive) as a fixed effect, respectively, and subject ID as random effect in both cases, are reported. Table S4. Model performance statistics for CTRL vs. AD binary classifiers. Description: Model performance statistics for the binary classification task of CTRL vs. AD for both the gradient boosting machine (GBM) and the convolutional neural network (CNN) machine learning models are reported. For all heuristics except for AUC and AUCPR (which are not threshold-dependent), the threshold was chosen by maximizing the accuracy. 95% confidence intervals were estimated by bootstrapping the hold-out test set across 500 iterations. Table S5. Results of Bayesian hyperparameter optimization. Description: The final hyperparameters determined by the Optuna hyperparameter tuning framework are reported. The Optuna optimizer maximized the out-of-sample area under the receiver operating characteristic (ROC) curve (AUC), which in turn was determined by 3-fold cross-validation for each trial.
DOI: 10.6084/m9.figshare.21200786.v1
title: Additional file 7 of Analysis of controlling genes for tiller growth of Psathyrostachys juncea based on transcriptome sequencing technology

description: Additional file 7.
DOI: 10.5523/bris.19aoqe6od86n72kigbdpzp89em
title: Associations between self-reported sleep quality, fatigue severity, factors associated with successful cessation, and cessation beliefs among regular smokers

description: This online cross-sectional observational study of regular smokers (n = 412, 60% male) explored associations between self-reported sleep quality, fatigue severity, factors associated with successful cessation, and cessation beliefs among regular smokers.
DOI: 10.6084/m9.figshare.6530279
title: Additional file 7: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: g:Pprofiler enrichment for the PS IIHs. (XLSX 29 kb)