cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21533531.v1
title: Circadian clock disruption aggravates alcohol liver disease in an acute mouse model

description: Circadian rhythms are important for organisms to adapt to the environment and maintain homeostasis. Disruptions of circadian rhythms contribute to the occurrence, progression, and exacerbation of diseases, such as cancer, psychiatric disorders, and metabolic disorders. Alcohol-induced liver disease (ALD) is one of the most prevalent liver diseases. Disruptions of the circadian clock enhance the ALD symptoms using chronic mice models or genetic manipulated mice. However, chronic models are time consuming and clock gene deletions interfere with metabolisms. Here, we report that constant light (LL) condition significantly disrupted the circadian clock in an acute ALD model, resulting in aggravated ALD phenotypes in wild type mice. Comparative transcriptome analysis revealed that the alcohol feeding affected the circadian pathway, as well as metabolic pathways. The acute alcohol feeding plus the LL condition further interfered with metabolic pathways and dysregulated canonical circadian gene expressions. These findings support the idea that disrupting the circadian clock could provide an improved ALD mouse model for further applications, such as facilitating identification of potential therapeutic targets for the prevention and treatment of ALD. <b>Abbreviations:</b> ALD, alcohol-induced liver disease; LD, 12 h light _ 12 h dark; LL, constant light; HF, high-fat liquid control diet; ETH, ethanol-containing diet; NIAAA, National Institute on Alcohol Abuse and Alcoholism; TTFLs, transcription-translation feedback loops; FDA, US Foods and Drug Administration; NAFLD, non-alcoholic fatty liver disease; RER, respiratory exchange rate; DEGs, differentially expressed genes; H&E, haematoxylin and eosin; ALT, alanine transaminase; AST, aspartate transaminase; TG, triglycerides.
DOI: 10.5281/zenodo.10624626
title: asparagus_racemosus_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.20484799.v1
title: Additional file 4 of Identification of immune-related key genes in the peripheral blood of ischaemic stroke patients using a weighted gene coexpression network analysis and machine learning

description: Additional file 4. Table S3. The clinical features of the 128 samples in the training set (GSE22255 combined with GSE58294).
DOI: 10.5281/zenodo.10624625
title: asparagus_racemosus_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.21532674.v1
title: Additional file 2 of Motor neuron survival is associated with reduced neuroinflammation and increased autophagy after brachial plexus avulsion injury in aldose reductase-deficient mice

description: Additional file 2. Raw data of western blot.
DOI: 10.6084/m9.figshare.19959975.v1
title: Additional file 2 of Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets

description: Additional file 2: Figure S2. Light microscopy images of P. pentosaceus strains with strong antimicrobial activity under a 63x oil immersion objective. Supplementary Data 2. The alignment of 1240 16S rRNA gene sequences against the Silva version 132 16S rRNA gene database, NCBI nucleotide collection (nr/nt) database and DAIRYdb database using BLASTN.
DOI: 10.6084/m9.figshare.20484799
title: Additional file 4 of Identification of immune-related key genes in the peripheral blood of ischaemic stroke patients using a weighted gene coexpression network analysis and machine learning

description: Additional file 4. Table S3. The clinical features of the 128 samples in the training set (GSE22255 combined with GSE58294).
DOI: 10.6084/m9.figshare.19959978
title: Additional file 3 of Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets

description: Additional file 3: Figure S3. The antimicrobial activity of SMM914. (a) The pH of SMM914 products were determined via test papers. (b) Inhibitory effects of SMM914 against S. aureus and enterotoxigenic E. coli. The circular wells were filled with different products of SMM914, including MRS medium as the negative control (1&2) and the cell-free supernatant without any treatment (3&4), with 15 min heat inactivation (5&6), with pH adjustment using NaOH (7&8) or with 1 mg/mL protease K treatment (9&10). The substances (1, 3, 5, 7 and 9) were obtained from the fermentation broth after cultivation under anaerobic condition, while others (2, 4, 6, 8 and 10) were obtained from culture under aerobic condition. Figure S4. Growth curves and pH value curve of SMM914 after anaerobic or aerobic fermentation. (a) The optical density at 600 nm (OD600) was measured from a starting OD600 about 0.085. (b) The pH value was recorded with a pH meter. Data are the mean ± s.e.m, n = 3. (c) The antimicrobial activities in vitro of SMM914 against S. aureus and enterotoxigenic E. coli at different times of aerobic or anaerobic fermentation.
DOI: 10.6084/m9.figshare.19959979
title: Additional file 6 of Evolution and functional diversification of catalase genes in the green lineage

description: Additional file 6: Table S1. The detail information of CAT genes in each species.
DOI: 10.6084/m9.figshare.19959919.v1
title: Additional file 1 of Changes in a sensorimotor network, occipital network, and psychomotor speed within three months after focal surgical injury in pediatric patients with intracranial space-occupying lesions

description: Additional file 1:
DOI: 10.6084/m9.figshare.20484811.v1
title: Additional file 8 of Identification of immune-related key genes in the peripheral blood of ischaemic stroke patients using a weighted gene coexpression network analysis and machine learning

description: Additional file 8.Table S7. The immune cell infiltration pattern of 128 ischaemic stroke samples in the training set (GSE22255 combined with GSE58294).
DOI: 10.6084/m9.figshare.22581979.v2
title: Robust Low-Rank Tensor Decomposition with the L<sub>2</sub> Criterion

description: The growing prevalence of tensor data, or multiway arrays, in science and engineering applications motivates the need for tensor decompositions that are robust against outliers. In this article, we present a robust Tucker decomposition estimator based on the L<sub>2</sub> criterion, called the Tucker-L2E. Our numerical experiments demonstrate that Tucker-L2E has empirically stronger recovery performance in more challenging high-rank scenarios compared with existing alternatives. The appropriate Tucker-rank can be selected in a data-driven manner with cross-validation or hold-out validation. The practical effectiveness of Tucker-L2E is validated on real data applications in fMRI tensor denoising, PARAFAC analysis of fluorescence data, and feature extraction for classification of corrupted images.
DOI: 10.6084/m9.figshare.20484796.v1
title: Additional file 3 of Identification of immune-related key genes in the peripheral blood of ischaemic stroke patients using a weighted gene coexpression network analysis and machine learning

description: Additional file 3. Table S2. The expression profile of the 17468 genes in the testing set (GSE16561).
DOI: 10.6084/m9.figshare.20484846.v1
title: Additional file 1 of Development and preliminary validation of a public health emergency competency model for medical staffs of national health emergency teams in China

description: Additional file 1: Supplemental Table 1. Post hoc test for independent variable of regions. Supplemental Table 2. Post hoc test for the different ages. Supplemental Table 3. Post hoc test for independent variable of working experience. Supplemental Table 4. Post hoc test for independent variable of professional titles
DOI: 10.6084/m9.figshare.8426270
title: Additional file 4: of Early-life determinants of hypoxia-inducible factor 3A geneÂ (HIF3A) methylation: a birth cohort study

description: Summary tables of the univariate tests between rs3810298 genotype and (a) pre-eclampsia, (b) gestational diabetes, (c) birth weight, and (d) gestational age. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12096228.v1
title: Additional file 4 of Internal ammonium excess induces ROS-mediated reactions and causes carbon scarcity in rice

description: Additional file 4: Table S1. Summary of total DEGs identifided in rice roots and shoots following a 4 h rapid NH4+ accumulation treatment.
DOI: 10.6084/m9.figshare.12096234
title: Additional file 5 of Internal ammonium excess induces ROS-mediated reactions and causes carbon scarcity in rice

description: Additional file 5: Table S2. GO enrichment analysis of DEGsin rice roots and shoots following a 4 h rapid NH4+ accumulation treatment. (XLS 192 kb)
DOI: 10.34730/27ab0a28c11741558679c819d608f1e7
title: FastSurfer-HypVINN Segmentation Models for Sub-Segmentation of the Hypothalamus and Adjacent Sctructures

description: The hypothalamus plays a crucial role in the regulation of a broad range of physiological, behavioral, and cognitive functions. However, despite its importance, only a few small-scale neuroimaging studies have investigated its substructures, likely due to the lack of fully automated segmentation tools to address scalability and reproducibility issues of manual segmentation. While the only previous attempt to automatically sub-segment the hypothalamus with a neural network showed promise for 1.0 mm isotropic T1-weighted (T1w) magnetic resonance imaging (MRI), there is a need for an automated tool to sub-segment also high-resolutional (HiRes) MR scans, as they are becoming widely available, and include structural detail also from multi-modal MRI. We, therefore, introduce a novel, fast, and fully automated deep-learning method named HypVINN for sub-segmentation of the hypothalamus and adjacent structures on 0.8 mm isotropic T1w and T2w brain MR images that is robust to missing modalities. We extensively validate our model with respect to segmentation accuracy, generalizability, in-session test-retest reliability, and sensitivity to replicate hypothalamic volume effects (e.g., sex differences). The proposed method exhibits high segmentation performance both for standalone T1w images as well as for T1w/T2w image pairs. Even with the additional capability to accept flexible inputs, our model matches or exceeds the performance of state-of-the-art methods with fixed inputs. We, further, demonstrate the generalizability of our method in experiments with 1.0 mm MR scans from both the Rhineland Study and the UK Biobank—an independent dataset never encountered during training with different acquisition parameters and demographics. Finally, HypVINN can perform the segmentation in less than a minute (graphical processing unit [GPU]) and will be available in the open source FastSurfer neuroimaging software suite, offering a validated, efficient, and scalable solution for evaluating imaging-derived phenotypes of the hypothalamus.
description: Training checkpoints for HypVINN (https://github.com/Deep-MI/FastSurfer) - please cite the paper when using this resource (https://doi.org/10.1162/imag_a_00034).
DOI: 10.6084/m9.figshare.8426279
title: Additional file 9: of Comparative transcriptomic and metabolic analysis reveals the effect of melatonin on delaying anthracnose incidence upon postharvest banana fruit peel

description: Excel S1. Differentially expressed genes in banana peel after melatonin treatment. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.8426279.v1
title: Additional file 9: of Comparative transcriptomic and metabolic analysis reveals the effect of melatonin on delaying anthracnose incidence upon postharvest banana fruit peel

description: Excel S1. Differentially expressed genes in banana peel after melatonin treatment. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.12096240
title: Additional file 7 of Internal ammonium excess induces ROS-mediated reactions and causes carbon scarcity in rice

description: Additional file 7: Table S4. The sequences of primers used for real-time RT-PCR in this research (XLS 27 kb)
DOI: 10.6084/m9.figshare.12096276.v1
title: Additional file 4 of A qualitative transcriptional signature to reclassify histological grade of ER-positive breast cancer patients

description: Additional file 4: Table S2–4 Differential expressed gene identified in TCGA dataset. Table S2. Differential expressed gene identified in pHG1 and pHG3 samples. Table S3. Differential expressed gene identified in HG1 and HG3 samples reclassified from pHG1 and pHG3 samples. Table S4. Differential expressed gene identified in HG1 and HG3 samples reclassified from all samples.
DOI: 10.6084/m9.figshare.8426300
title: Additional file 1: of Rare diseases in China: analysis of 2014â 2015 hospitalization summary reports for 281 rare diseases from 96 tertiary hospitals

description: The four lists of TRDL 2017. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.8426300.v1
title: Additional file 1: of Rare diseases in China: analysis of 2014â 2015 hospitalization summary reports for 281 rare diseases from 96 tertiary hospitals

description: The four lists of TRDL 2017. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.14718013
title: Fat mass and obesity-associated protein (FTO) mediates signal transducer and activator of transcription 3 (STAT3)-drived resistance of breast cancer to doxorubicin

description: Excessive activation of signal transducer and activator of transcription 3 (STAT3) is implicated in breast cancer (BC) chemoresistance, but its underlying mechanism is not fully understood. There are STAT3 binding sites in fat mass and obesity-associated protein (FTO) promoter region, thus STAT3 may regulate the transcription of FTO. This study aimed to investigate the correlation between FTO and STAT3 in BC chemoresistance. Herein, FTO and STAT3 were highly expressed in doxorubicin-resistant BC (BC-DoxR) cells. CHIP assay verified the binding between STAT3 and FTO promoter in BC-DoxR cells. Dual luciferase reporter assay showed that FTO promoter activity was inhibited by S3I-201 (STAT3 inhibitor) but enhanced by epidermal growth factor (EGF, STAT3 activator) in BC-DoxR and BC cells. FTO mRNA and protein expression were suppressed by S3I-201 in BC-DoxR cells and EGF-stimulated BC cells. Notably, FTO regulated total N6-methyladenosine (m6A) levels in BC-DoxR and BC cells but could not affect STAT3 mRNA expression, indicating that FTO was not involved in the m6A modification of STAT3. However, FTO could activate STAT3 signaling in BC-DoxR and BC cells. Besides, FTO knockdown inhibited the doxorubicin resistance of BC-DoxR cells, while FTO overexpression enhanced the doxorubicin resistance and weakened the doxorubicin sensitivity of BC cells. Moreover, decreased doxorubicin resistance by STAT3 knockdown was abolished by FTO overexpression and decreased doxorubicin sensitivity by STAT3 overexpression was reversed by FTO knockdown, indicating that FTO was implicated in STAT3-mediated doxorubicin resistance and impairment of doxorubicin sensitivity of BC cells. Altogether, our findings provide a mechanism underlying BC doxorubicin resistance.
DOI: 10.6084/m9.figshare.19959988.v1
title: Additional file 9 of Evolution and functional diversification of catalase genes in the green lineage

description: Additional file 9: Table S4. The 3D structure predication for three CATs in Arabidopsis.
DOI: 10.6084/m9.figshare.8426303.v1
title: MOESM1 of The volumetric-tumour histogram-based analysis of intravoxel incoherent motion and non-Gaussian diffusion MRI: association with prognostic factors in HER2-positive breast cancer

description: Additional file 1. All the parameters of histogram analysis for the whole tumour in different groups.
DOI: 10.6084/m9.figshare.13669395
title: Additional file 5 of Identification of DNA repair-related genes predicting pathogenesis and prognosis for liver cancer

description: Additional file 5. The raw data of GSE101728 from GEO database.
DOI: 10.6084/m9.figshare.13670722
title: Supplementary Data 2

description: Supporting data for paper "Mapping the maximum extents of urban green spaces in 1039 citiesusing dense satellite images" (https://iopscience.iop.org/article/10.1088/1748-9326/ac03dc/meta)<br>
DOI: 10.6084/m9.figshare.13670728
title: Supplementary Data 3

description: Supporting data for paper "Mapping the maximum extents of urban green spaces in 1039 citiesusing dense satellite images" (https://iopscience.iop.org/article/10.1088/1748-9326/ac03dc/meta)<br>
DOI: 10.6084/m9.figshare.13670734
title: Supplementary Data 4

description: Supporting data for paper "Mapping the maximum extents of urban green spaces in 1039 citiesusing dense satellite images" (https://iopscience.iop.org/article/10.1088/1748-9326/ac03dc/meta)<br>
DOI: 10.6084/m9.figshare.20486541
title: Drought has inconsistent effects on seed trait composition despite their strong association with ecosystem drought sensitivity

description:   
1. Seeds provide the basis of genetic diversity in perennial grassland communities and their traits may influence ecosystem resistance to extreme drought. However, we know little about how drought effects the community functional composition of seed traits and the corresponding implications for ecosystem resistance to drought.
2. We experimentally removed 66% of growing season precipitation for four years across five arid and semiarid grasslands in northern China and assessed how this multi-year drought impacted community-weighted means (CWM) of seed traits, seed trait functional diversity, and aboveground net primary productivity (ANPP).
3. Experimental drought had limited effects on CWM traits and the few effects that did occur varied by site and year. For three separate sites, and in different years, drought reduced seed length and phosphorus content but increased both seed and seed-coat thickness. Additionally, drought led to increased seed functional evenness, divergence, dispersion, and richness, but only in some sites, and mostly in later years following cumulative effects of water limitation. However, we observed a strong negative relationship between drought-induced reductions in ANPP and CWMs of seed-coat thickness, indicating that a high abundance of dominant species with thick seeds may increase ecosystem resistance to drought. Seed trait functional diversity was not significantly predictive of ANPP, providing little evidence for a diversity effect. 
4. Our results suggest that monitoring community composition with a focus on seed traits may provide a valuable indicator of ecosystem resistance to future droughts despite inconsistent responses of seed trait composition overall. This highlights the importance of developing a comprehensive seed and reproductive traits database for arid and semiarid grassland biomes.
DOI: 10.6084/m9.figshare.20484993
title: Additional file 1 of The predictive value of the Singh index for the risk of InterTAN intramedullary fixation failure in elderly patients with intertrochanteric fractures

description: Additional file 1.
DOI: 10.6084/m9.figshare.19959919
title: Additional file 1 of Changes in a sensorimotor network, occipital network, and psychomotor speed within three months after focal surgical injury in pediatric patients with intracranial space-occupying lesions

description: Additional file 1:
DOI: 10.6084/m9.figshare.13669392
title: Additional file 4 of Identification of DNA repair-related genes predicting pathogenesis and prognosis for liver cancer

description: Additional file 4. The raw data of GSE101685 from GEO database.
DOI: 10.6084/m9.figshare.13669395.v1
title: Additional file 5 of Identification of DNA repair-related genes predicting pathogenesis and prognosis for liver cancer

description: Additional file 5. The raw data of GSE101728 from GEO database.
DOI: 10.6084/m9.figshare.10000901
title: MOESM7 of Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

description: Additional file 7: Table S1. Motif identification based on PFAM database. Table S2. Characteristics of cis-acting regulatory elements in the promoter region of these identified barley MAPK cascade genes. Table S3. Duplicated MAPK cascade gene pairs identified in barley. Table S4. The Ka/Ks ratios for orthologous MAPK cascade proteins between barley and brachypodium. Table S5. The Ka/Ks ratios for orthologous HvMAPK cascade proteins between barley and rice sorghum. Table S6. The Ka/Ks ratios for orthologous MAPK cascade proteins between barley and maize. Table S7. The Ka/Ks ratios for orthologous MAPK cascade proteins between barley and sorghum. Table S8. The Ka/Ks ratios for orthologous MAPK cascade proteins between barley and soybean. Table S9. The Ka/Ks ratios for orthologous MAPK cascade proteins between barley and grape. Table S10. GO annotation of the identified barley MAPK cascade genes. Table S11. List of the putative miRNAs targeted on HvMAPK cascade genes identified by psRNATarget online tool. Table S12. Accession number and sample information of RNA-seq data using in this study.
DOI: 10.6084/m9.figshare.10000901.v1
title: MOESM7 of Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

description: Additional file 7: Table S1. Motif identification based on PFAM database. Table S2. Characteristics of cis-acting regulatory elements in the promoter region of these identified barley MAPK cascade genes. Table S3. Duplicated MAPK cascade gene pairs identified in barley. Table S4. The Ka/Ks ratios for orthologous MAPK cascade proteins between barley and brachypodium. Table S5. The Ka/Ks ratios for orthologous HvMAPK cascade proteins between barley and rice sorghum. Table S6. The Ka/Ks ratios for orthologous MAPK cascade proteins between barley and maize. Table S7. The Ka/Ks ratios for orthologous MAPK cascade proteins between barley and sorghum. Table S8. The Ka/Ks ratios for orthologous MAPK cascade proteins between barley and soybean. Table S9. The Ka/Ks ratios for orthologous MAPK cascade proteins between barley and grape. Table S10. GO annotation of the identified barley MAPK cascade genes. Table S11. List of the putative miRNAs targeted on HvMAPK cascade genes identified by psRNATarget online tool. Table S12. Accession number and sample information of RNA-seq data using in this study.
DOI: 10.6084/m9.figshare.12096582.v1
title: Additional file 2 of The circRNA circSEPT9 mediated by E2F1 and EIF4A3 facilitates the carcinogenesis and development of triple-negative breast cancer

description: Additional file 2: Figure S1. Relative expression levels of E2F1 and EIF4A3 were determined by qRT-PCR. (a) Relative expression of E2F1 expression were evaluated in TNBC cells transfected with E2F1 overexpression plasmids or siRNA. (b) The relative expression of EIF4A3 was detected in TNBC cells transfected with EIF4A3 overexpression or knockdown plasmids. The data are presented as the mean ± SD, **P &lt; 0.01, ***P &lt; 0.001. Figure S2. Overexpression of circSEPT9 increased proliferation, migration and invasion of TNBC cells by colony formation, EdU, CCK-8, wound healing and transwell assays. (a) Cell proliferation ability was evaluated by colony formation. (b) EdU assay of TNBC cells was performed to evaluate cell proliferation (magnification, × 100, Scale bar, 100 μm). (c) The growth curves of cells were measured by using CCK-8 assay. (d) Transwell invasion assay were used to assess the invasion abilities of TNBC cells (magnification, × 100, Scale bar, 100 μm). (e and f) The migration abilities of TNBC cells were measured by transwell migration (magnification, × 100, Scale bar, 100 μm) and wound healing (magnification, × 50, Scale bar, 100 μm) assays. The data are presented as the mean ± SD, *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001. Figure S3. The expressions of LIF and LIF-STAT3 signal pathway related molecules were detected in tumor tissues of mice by IHC (magnification, × 200, Scale bar, 100 μm).
DOI: 10.6084/m9.figshare.13669398
title: Additional file 6 of Identification of DNA repair-related genes predicting pathogenesis and prognosis for liver cancer

description: Additional file 6. The raw data from TCGA database and the raw data of qRT-PCR.