cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p9uwryr4
title: Datasets for the U.S. Geological Survey - Idaho National Laboratory groundwater and surface-water monitoring networks, v1.1

description: A collection of analysis-ready datasets for the U.S. Geological Survey - Idaho National Laboratory (USGS-INL) groundwater and surface-water monitoring networks, administered by the USGS-INL Project Office in cooperation with the U.S. Department of Energy. The data collected from wells and surface-water stations at the Idaho National Laboratory and surrounding areas have been used to describe the effects of waste disposal on water contained in the eastern Snake River Plain aquifer, located in the southeastern part of Idaho, and the availability of water for long-term consumptive and industrial use. The datasets include long-term monitoring records dating back to measurements from 1922. Geospatial data describing the areas from which samples were collected or observations were made are also included.
DOI: 10.6084/m9.figshare.22613360.v1
title: Additional file 8 of Identification and characterization of non-coding RNA networks in infected macrophages revealing the pathogenesis of F. nucleatum-associated diseases

description: Additional file 8: Supplementary Table 8. All identified lncRNAs in RNA-Seq.
DOI: 10.6084/m9.figshare.19396111
title: Additional file 9 of Phosphorylation regulation of cardiac proteins in Babesia microti infected mice in an effort to restore heart function

description: Additional file 9: Table S3. Proteins in each cluster.
DOI: 10.21223/n00mnu/v3u7hh
title: 05_Soil_Data-HERLB_PER_2022_LateBlight_Oxa.tab

description: :unav
DOI: 10.6084/m9.figshare.19396111.v1
title: Additional file 9 of Phosphorylation regulation of cardiac proteins in Babesia microti infected mice in an effort to restore heart function

description: Additional file 9: Table S3. Proteins in each cluster.
DOI: 10.6084/m9.figshare.22607378
title: Additional file 7 of FBXO22 promotes leukemogenesis by targeting BACH1 in MLL-rearranged acute myeloid leukemia

description: Additional file 7. Table S2. Mass spectrometry data
DOI: 10.6084/m9.figshare.7409471.v1
title: MOESM3 of The plasma peptidome

description: Additional file 3: Table S3. ANOVA and Tukey Kramer HSD test.
DOI: 10.6084/m9.figshare.11603637
title: Characterization of cold-tolerant trehalose-6-phosphate synthase from the deep-sea bacterium <i>Microbacterium sediminis</i> YLB-01

description: A gene encoding the enzyme trehalose-6-phosphate synthase (TPS), which is part of the TPS trehalose synthesis pathway, was cloned from the deep-sea psychrotolerant bacterium <i>Microbacterium sediminis</i> YLB-01 and expressed in <i>Escherichia coli</i> BL21. The exogenously expressed TPS exhibited highest similarity (80.93% identity) to <i>Microbacterium</i> sp. TPS. The purified recombinant TPS was cold-tolerant, with low thermostability. The optimum temperature for TPS activity was 40°C, and the enzyme retained 72.6% of its maximal activity at 4°C. The optimum pH was 7.5. TPS activity was cation-dependent, with Mg<sup>2+</sup>, Co<sup>2+</sup>, or Ba<sup>2+</sup> being essential for maximum activity. The kinetic constants of the recombinant TPS reaction rates confirmed that it was cold-tolerant. Molecular dynamics analysis showed that TPS was more flexible (0.8741Å) at 4°C than 1GZ5, its homolog in the mesophilic bacterium <i>E. coli</i>, and superposition of the 3D enzyme structures supported this. Enzymatic properties of recombinant trehalose-6-phosphate synthase (TPS).
DOI: 10.6084/m9.figshare.22613603
title: Additional file 2 of Characteristics of hospitalized patients with COVID-19 during the first to fifth waves of infection: a report from the Japan COVID-19 Task Force

description: Additional file 2. Supplementary Table 2. Comparison of imaging findings.
DOI: 10.6084/m9.figshare.21565115
title: The evolutionary landscape and expression pattern of plant lincRNAs

description: Long intergenic non-coding RNAs (lincRNAs) are important regulators of cellular processes, including development and stress response. Many lincRNAs have been bioinformatically identified in plants, but their evolutionary dynamics and expression characteristics are still elusive. Here, we systematically identified thousands of lincRNAs in 26 plant species, including 6 non-flowering plants, investigated the conservation of the identified lincRNAs in different levels of plant lineages based on sequence and/or synteny homology and explored characteristics of the conserved lincRNAs during plant evolution and their co-expression relationship with protein-coding genes (PCGs). In addition to confirmation of the features well documented in literature for lincRNAs, such as species-specific, fewer exons, tissue-specific expression patterns and less abundantly expressed, we revealed that histone modification signals and/or binding sites of transcription factors were enriched in the conserved lincRNAs, implying their biological functionalities, as demonstrated by identifying conserved lincRNAs related to flower development in both the Brassicaceae and grass families and ancient lincRNAs potentially functioning in meristem development of non-flowering plants. Compared to PCGs, lincRNAs are more likely to be associated with transposable elements (TEs), but with different characteristics in different evolutionary lineages, for instance, the types of TEs and the variable level of association in lincRNAs with different conservativeness. Together, these results provide a comprehensive view on the evolutionary landscape of plant lincRNAs and shed new insights on the conservation and functionality of plant lincRNAs.
DOI: 10.6084/m9.figshare.22613705.v1
title: Additional file 1 of Bleeding in neonates with severe thrombocytopenia: a retrospective cohort study

description: Additional file 1.
DOI: 10.6084/m9.figshare.22613701.v1
title: Additional file 1 of Targeting tumor exosomal circular RNA cSERPINE2 suppresses breast cancer progression by modulating MALT1-NF-????B-IL-6 axis of tumor-associated macrophages

description: Additional file 1: Fig. S1. Analysis of the expression and character of cSERPINE2 in breast cancercells. Fig. S2. cSERPINE2 reshaped the immune microenvironment of breast cancer. Fig. S3 Tumor exosomal cSERPINE2 targeted macrophages to promote theproliferation and invasion of breast cancer cells. Fig. S4. Tumor exosomal cSERPINE2 upregulated the MALT1 expressionin macrophages by sponging miR‑513a-5p. Fig. S5. Tumor exosomal cSERPINE2 promoted the secretion of IL-6 in TAMs via activating the NF-κB pathway to promote the progression of breast cancer. Fig. S6. IL-6 secreted by TAMs promoted the expression of CCL2 in breastcancer cells via activating the JAK2-STAT3 pathway. Fig. S7. Characteristics of si-cSERPINE2-NPs and therapeutic efficacy of si-cSERPINE2-NPs in breast cancer invitro. Fig. S8. Toxicity evaluation of systemic injection of si-cSERPINE2-NPs in breast cancer. Supplementary Table S1. Correlation between cSERPINE2 expression and clinicopathological features in 136 patients withbreast cancer. Supplementary Table S2. Univariate and multivariate analyses of OS in breast cancer (n=136). Supplementary Table S3. Univariate and multivariate analyses of RFS in breast cancer (n=136). Supplementary Table S4. The primers (5’-3’) used for RT-qPCR in this study. Supplementary Table S5. The probe sequences (5’-3’) for FISH. Supplementary Table S6. Primers for EIF4A3 RIP. Supplementary Table S7. Primers for CHIP. Supplementary Table S8. The probe sequences (5’-3’) for RNA pull-down assay. Supplementary Table S9. Primers for in vitro transcription. Supplementary Table S10. Effective sequences (5’-3’) of lentivirus plasmids-overexpression. Supplementary Table S11. Effective sequences (5’-3’) of lentivirus plasmids-knockdown. Supplementary Table S12. miRNA mimics and inhibitor sequences (5’-3’).
DOI: 10.6084/m9.figshare.22613609
title: Additional file 4 of Characteristics of hospitalized patients with COVID-19 during the first to fifth waves of infection: a report from the Japan COVID-19 Task Force

description: Additional file 4. Supplementary Table 4. Comparison of patient characteristics among in-hospital deaths.
DOI: 10.6084/m9.figshare.22613807.v1
title: Additional file 1 of Apolipoprotein C3 is negatively associated with estrogen and mediates the protective effect of estrogen on hypertriglyceridemia in obese adults

description: Additional file 1. Supplementary Table 1. The correlation between ApoC2 and clinical parameters among all participants.
DOI: 10.6084/m9.figshare.22613600.v1
title: Additional file 1 of Characteristics of hospitalized patients with COVID-19 during the first to fifth waves of infection: a report from the Japan COVID-19 Task Force

description: Additional file 1. Supplementary Table 1. Comparison of laboratory parameters.
DOI: 10.6084/m9.figshare.22613615
title: Additional file 6 of Characteristics of hospitalized patients with COVID-19 during the first to fifth waves of infection: a report from the Japan COVID-19 Task Force

description: Additional file 6. Supplementary Table 6. Complications after hospitalization by COVID-19 waves with p value.
DOI: 10.6084/m9.figshare.22613609.v1
title: Additional file 4 of Characteristics of hospitalized patients with COVID-19 during the first to fifth waves of infection: a report from the Japan COVID-19 Task Force

description: Additional file 4. Supplementary Table 4. Comparison of patient characteristics among in-hospital deaths.
DOI: 10.6084/m9.figshare.22613705
title: Additional file 1 of Bleeding in neonates with severe thrombocytopenia: a retrospective cohort study

description: Additional file 1.
DOI: 10.21223/n00mnu/f1mf3a
title: 04_Weather_data-HERLB_PER_2022_LateBlight_Oxa.tab

description: :unav
DOI: 10.6084/m9.figshare.22613615.v1
title: Additional file 6 of Characteristics of hospitalized patients with COVID-19 during the first to fifth waves of infection: a report from the Japan COVID-19 Task Force

description: Additional file 6. Supplementary Table 6. Complications after hospitalization by COVID-19 waves with p value.
DOI: 10.6084/m9.figshare.22613678
title: Additional file 1 of Sourcing celadons with EDXRF and LA-ICP-MS from the Xunyang city burial complex, 202 B.C–907 A.D.

description: Additional file 1: Table S1. Major component data from EDXRF analysis of samples. Table S2. Major and REE component data from LA-ICP-MS analysis of samples’ clay body. Table S3. Major and REE component data from LA-ICP-MS analysis of samples' glaze. Table S4. The accuracy and precision of the secondary standards (LA-ICP-MS)
DOI: 10.6084/m9.figshare.22607425.v1
title: Additional file 1 of Chondroitin sulfate alleviates osteoporosis caused by calcium deficiency by regulating lipid metabolism

description: Additional file 1: Table S1. MRPP analysis showed significant differences in microbial community structure between group N and group C and between group C and group CS and between group CS and group Ca.
DOI: 10.6084/m9.figshare.22613678.v1
title: Additional file 1 of Sourcing celadons with EDXRF and LA-ICP-MS from the Xunyang city burial complex, 202 B.C–907 A.D.

description: Additional file 1: Table S1. Major component data from EDXRF analysis of samples. Table S2. Major and REE component data from LA-ICP-MS analysis of samples’ clay body. Table S3. Major and REE component data from LA-ICP-MS analysis of samples' glaze. Table S4. The accuracy and precision of the secondary standards (LA-ICP-MS)
DOI: 10.6084/m9.figshare.22613807
title: Additional file 1 of Apolipoprotein C3 is negatively associated with estrogen and mediates the protective effect of estrogen on hypertriglyceridemia in obese adults

description: Additional file 1. Supplementary Table 1. The correlation between ApoC2 and clinical parameters among all participants.
DOI: 10.6084/m9.figshare.8982233
title: "The gut microbiota influences skeletal muscle mass and function in mice" - NMR data of liver, serum and skeletal muscle of conventional mice, pathogen-free mice and germ-free mice

description: 600 MHz <sup>1</sup>H NMR spectrometry analysis of skeletal muscle (gastrocnemius), liver, and serum from pathogen-free mice, conventional mice and germ-free mice. <sup>1</sup>H NMR spectra were manually corrected for phase and baseline distortions and digitized using an in-house MATLAB (version R2014a, The Mathworks, Inc.; Natwick, MA, USA) script. Spectra were subsequently referenced to the internal chemical shift reference (trimethylsilyl-[2,2,3,3,-<sup>2</sup>H<sub>4</sub>]-propionate, TSP) at δ 0.0. Spectral regions corresponding to the internal standard (δ -0.5 to 0.5) and water (δ 4.5 to 5.5) were excluded.
DOI: 10.6084/m9.figshare.21565115.v1
title: The evolutionary landscape and expression pattern of plant lincRNAs

description: Long intergenic non-coding RNAs (lincRNAs) are important regulators of cellular processes, including development and stress response. Many lincRNAs have been bioinformatically identified in plants, but their evolutionary dynamics and expression characteristics are still elusive. Here, we systematically identified thousands of lincRNAs in 26 plant species, including 6 non-flowering plants, investigated the conservation of the identified lincRNAs in different levels of plant lineages based on sequence and/or synteny homology and explored characteristics of the conserved lincRNAs during plant evolution and their co-expression relationship with protein-coding genes (PCGs). In addition to confirmation of the features well documented in literature for lincRNAs, such as species-specific, fewer exons, tissue-specific expression patterns and less abundantly expressed, we revealed that histone modification signals and/or binding sites of transcription factors were enriched in the conserved lincRNAs, implying their biological functionalities, as demonstrated by identifying conserved lincRNAs related to flower development in both the Brassicaceae and grass families and ancient lincRNAs potentially functioning in meristem development of non-flowering plants. Compared to PCGs, lincRNAs are more likely to be associated with transposable elements (TEs), but with different characteristics in different evolutionary lineages, for instance, the types of TEs and the variable level of association in lincRNAs with different conservativeness. Together, these results provide a comprehensive view on the evolutionary landscape of plant lincRNAs and shed new insights on the conservation and functionality of plant lincRNAs.
DOI: 10.6084/m9.figshare.22613825.v1
title: Additional file 1 of RNA-seq analysis reveals the critical role of the novel lncRNA BIANCR in intramuscular adipogenesis through the ERK1/2 signaling pathway

description: Additional file 1. Reads information of RNA-seq.
DOI: 10.6084/m9.figshare.22613828
title: Additional file 2 of RNA-seq analysis reveals the critical role of the novel lncRNA BIANCR in intramuscular adipogenesis through the ERK1/2 signaling pathway

description: Additional file 2. Primers used in PCR and qRT-PCR.
DOI: 10.21223/n00mnu/qsk6na
title: 07_Data_dictionary-HERLB_PER_2022_LateBlight_Oxa.tab

description: :unav
DOI: 10.6084/m9.figshare.7409468
title: MOESM2 of The plasma peptidome

description: Additional file 2. Supplemental Table II.Â  The interleukins, growth factors, cytokines, chemokines and necrosis factors of human EDTA plasma.
DOI: 10.6084/m9.figshare.22607438
title: Additional file 1 of Brassinosteroids and gibberellic acid actively regulate the zinc detoxification mechanism of Medicago sativa L. seedlings

description: Additional file 1: Table S1. The primer sequences of the genes. Table S2. Spearman's Rho among different indexes such as zinc content, biomass and antioxidant enzymes. Table S3. Total variance explained of principal component analysis for all indicators. Table S4. Component Matrixa of principal component analysis for all indicators.
DOI: 10.6084/m9.figshare.22613701
title: Additional file 1 of Targeting tumor exosomal circular RNA cSERPINE2 suppresses breast cancer progression by modulating MALT1-NF-????B-IL-6 axis of tumor-associated macrophages

description: Additional file 1: Fig. S1. Analysis of the expression and character of cSERPINE2 in breast cancercells. Fig. S2. cSERPINE2 reshaped the immune microenvironment of breast cancer. Fig. S3 Tumor exosomal cSERPINE2 targeted macrophages to promote theproliferation and invasion of breast cancer cells. Fig. S4. Tumor exosomal cSERPINE2 upregulated the MALT1 expressionin macrophages by sponging miR‑513a-5p. Fig. S5. Tumor exosomal cSERPINE2 promoted the secretion of IL-6 in TAMs via activating the NF-κB pathway to promote the progression of breast cancer. Fig. S6. IL-6 secreted by TAMs promoted the expression of CCL2 in breastcancer cells via activating the JAK2-STAT3 pathway. Fig. S7. Characteristics of si-cSERPINE2-NPs and therapeutic efficacy of si-cSERPINE2-NPs in breast cancer invitro. Fig. S8. Toxicity evaluation of systemic injection of si-cSERPINE2-NPs in breast cancer. Supplementary Table S1. Correlation between cSERPINE2 expression and clinicopathological features in 136 patients withbreast cancer. Supplementary Table S2. Univariate and multivariate analyses of OS in breast cancer (n=136). Supplementary Table S3. Univariate and multivariate analyses of RFS in breast cancer (n=136). Supplementary Table S4. The primers (5’-3’) used for RT-qPCR in this study. Supplementary Table S5. The probe sequences (5’-3’) for FISH. Supplementary Table S6. Primers for EIF4A3 RIP. Supplementary Table S7. Primers for CHIP. Supplementary Table S8. The probe sequences (5’-3’) for RNA pull-down assay. Supplementary Table S9. Primers for in vitro transcription. Supplementary Table S10. Effective sequences (5’-3’) of lentivirus plasmids-overexpression. Supplementary Table S11. Effective sequences (5’-3’) of lentivirus plasmids-knockdown. Supplementary Table S12. miRNA mimics and inhibitor sequences (5’-3’).
DOI: 10.6084/m9.figshare.22613834.v1
title: Additional file 4 of RNA-seq analysis reveals the critical role of the novel lncRNA BIANCR in intramuscular adipogenesis through the ERK1/2 signaling pathway

description: Additional file 4. Sequencing data validated by qRT-PCR.
DOI: 10.6084/m9.figshare.22607428.v1
title: Additional file 2 of Chondroitin sulfate alleviates osteoporosis caused by calcium deficiency by regulating lipid metabolism

description: Additional file 2: Table S2. The differential metabolites of fecal metabolomics between the N group and the C group. The differential metabolites of fecal metabolomics between the C group and the Ca group. The differential metabolites of fecal metabolomics between the C group and the CS group. The differential metabolites of fecal metabolomics between the CS group and the Ca group.
DOI: 10.6084/m9.figshare.22613855
title: Additional file 11 of RNA-seq analysis reveals the critical role of the novel lncRNA BIANCR in intramuscular adipogenesis through the ERK1/2 signaling pathway

description: Additional file 11. GO terms and KEGG pathways for BIANCR.
DOI: 10.6084/m9.figshare.22613858
title: Additional file 12 of RNA-seq analysis reveals the critical role of the novel lncRNA BIANCR in intramuscular adipogenesis through the ERK1/2 signaling pathway

description: Additional file 12. The sequence of BIANCR.
DOI: 10.6084/m9.figshare.20016129.v1
title: Mammals in atlantic forest remnants of Barbacena, Minas Gerais

description: Abstract Habitat loss and fragmentation are the main causes of biodiversity decline, since changes in environmental and ecological conditions directly affect species richness, abundance, and distribution. This study aimed to identify medium- and large-sized mammals occurring in three Atlantic Forest remnants located in the Barbacena campus of the Federal Institute of Southeast Minas Gerais (IFSudesteMG). The species were recorded in track plots and through active search for direct and indirect signs. 16 species distributed in six orders and 14 families were identified, including some vulnerable and threatened species such as Lycalopex vetulus (meadow fox), Lontra longicaudis (otter), and Callicebus nigrifrons (black-fronted titi monkey). Canis familiaris (domestic dog) and Didelphis sp. (opossum) were the species most frequently observed in the track plots. The largest fragment had the greatest species richness, with 15 species, or 93.75% of the total. The number of species shared among the three sampled areas was 31.2%. The similarities identified between the fragments indicate the need for higher connectivity among them, through the creation of ecological corridors to allow the movement and, consequently, gene flux among the populations, favoring the maintenance of important ecosystem services in the region. Although small, the study area plays a major role in mammal conservation in the region, preserving species from the Cerrado and the Atlantic Forest domains. To reduce potential impacts on the local fauna, management and conservation efforts should be put forward.
DOI: 10.6084/m9.figshare.20016129
title: Mammals in atlantic forest remnants of Barbacena, Minas Gerais

description: Abstract Habitat loss and fragmentation are the main causes of biodiversity decline, since changes in environmental and ecological conditions directly affect species richness, abundance, and distribution. This study aimed to identify medium- and large-sized mammals occurring in three Atlantic Forest remnants located in the Barbacena campus of the Federal Institute of Southeast Minas Gerais (IFSudesteMG). The species were recorded in track plots and through active search for direct and indirect signs. 16 species distributed in six orders and 14 families were identified, including some vulnerable and threatened species such as Lycalopex vetulus (meadow fox), Lontra longicaudis (otter), and Callicebus nigrifrons (black-fronted titi monkey). Canis familiaris (domestic dog) and Didelphis sp. (opossum) were the species most frequently observed in the track plots. The largest fragment had the greatest species richness, with 15 species, or 93.75% of the total. The number of species shared among the three sampled areas was 31.2%. The similarities identified between the fragments indicate the need for higher connectivity among them, through the creation of ecological corridors to allow the movement and, consequently, gene flux among the populations, favoring the maintenance of important ecosystem services in the region. Although small, the study area plays a major role in mammal conservation in the region, preserving species from the Cerrado and the Atlantic Forest domains. To reduce potential impacts on the local fauna, management and conservation efforts should be put forward.