cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26050/wdcc/lm_pft_na_v1.1
title: LANDMATE PFT land cover dataset for North America 2015 (Version 1.1)

description: Project: Modelling human LAND surface modifications and its feedbacks on local and regional cliMATE - The project “Modelling human LAND surface modifications and its feedbacks on local and regional climate” (LANDMATE, https://www.hicss-hamburg.de/projects/landmate/index.php.en) is carried out within the framework of the Helmholtz Institute for Climate Service Science (HICSS), a cooperation between Climate Service Center Germany (GERICS) of the Helmholtz-Zentrum Hereon and Universität Hamburg. Within LANDMATE, scientists from GERICS and the Institute of Geography (CEN, Universität Hamburg) investigate the direct biophysical effects of land use and land cover change on the local and regional climate. The overall objectives of this project are to: I) Better represent dynamic land use characteristics in a regional climate model, II) Include land management practices into a regional climate model, III) Quantify biophysical impacts of land use dynamics on regional climate variability and change in Europe in the frame of WCRP CORDEX Flagship Pilot Study “Land Use and Climate Across Scales” (LUCAS, https://ms.hereon.de/cordex_fps_lucas/). 
Summary: The LANDMATE PFT dataset provides a land cover map for North America for the year 2015 in 0.1° (~10 km). The dataset is based on land cover data of the ESA Climate Change Initiative (ESA-CCI, native resolution: 300 m) which is translated into 16 plant functional types (PFTs) and non-vegetated classes employing the cross-walking procedure introduced by Reinhart et al. (2022), which was modified for North America. The translation is done under consideration of the Holdridge Life Zones (HLZs), a system that classifies land areas based on bioclimatic properties. Through the HLZs, regional distinction of the individual PFT distribution can be achieved. The land cover information is given as fractions per grid cell where each fraction represents the area covered by the respective land cover within each grid cell (0-1).
The LANDMATE PFT dataset (0.1° resolution) serves as base map for the historical and future land use and land cover dataset LUCAS LUC developed by Hoffmann et al. (2023).

Plant functional types and non-vegetative classes:
1 - Tropical broadleaf evergreen trees
2 - Tropical deciduous trees
3 - Temperate broadleaf evergreen trees
4 - Temperate deciduous trees
5 - Evergreen coniferous trees
6 - Deciduous coniferous trees
7 - Coniferous shrubs
8 - Deciduous shrubs
9 - C3 grass
10 - C4 grass
11 - Tundra
12 - Swamp
13 - Non-irrigated crops
14 - Irrigated crops
15 - Urban
16 - Bare

Version 1.0 of this dataset does not exist. Here we use Version 1.1 in the name for consistency reasons.
DOI: 10.6084/m9.figshare.19619510
title: Additional file 1 of OLA1 promotes colorectal cancer tumorigenesis by activation of HIF1α/CA9 axis

description: Additional file 1.
DOI: 10.6084/m9.figshare.19092319
title: Additional file 4 of Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development

description: Additional file 4 The protein sequences of Cellulose synthase genes in Glycine max.
DOI: 10.6084/m9.figshare.19092325.v1
title: Additional file 5 of Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development

description: Additional file 5 The protein sequences of Cellulose synthase genes in Arabidopsis thaliana.
DOI: 10.6084/m9.figshare.21192298
title: Additional file 2 of PACS-2 deficiency in tubular cells aggravates lipid-related kidney injury in diabetic kidney disease

description: Additional file 2: Table S1. The sequences of primer pairs.
DOI: 10.6084/m9.figshare.19092307.v1
title: Additional file 1 of Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development

description: Additional file 1. Supplementary data associated with this article can be found in the appendix. The information of 20 conserved motifs of Cellulose synthase genes in Phaseolus vulgaris detected by the online tool MEME.
DOI: 10.6084/m9.figshare.19092310.v1
title: Additional file 2 of Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development

description: Additional file 2 The information of cis-elements in promoter sequences of Cellulose synthase genes in Phaseolus vulgaris.
DOI: 10.6084/m9.figshare.19619510.v1
title: Additional file 1 of OLA1 promotes colorectal cancer tumorigenesis by activation of HIF1α/CA9 axis

description: Additional file 1.
DOI: 10.6084/m9.figshare.19092319.v1
title: Additional file 4 of Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development

description: Additional file 4 The protein sequences of Cellulose synthase genes in Glycine max.
DOI: 10.6084/m9.figshare.11761071
title: Deoxynivalenol globally affects the selection of 3’ splice sites in human cells by suppressing the splicing factors, U2AF1 and SF1

description: Deoxynivalenol (DON) is one of the most abundant mycotoxins and has adverse effects on several biological processes, posing risks of protein synthesis-disrupting effects and ribotoxic response. Therefore, chronic exposure to DON would fundamentally reshape the global expression pattern. Whether DON causes toxic effects on mRNA splicing, a fundamental biological process, remains unclear. In this study, we found that administration of the relative low dosage of DON dramatically changed the alternative splicing of pre-mRNA in HepG2 cells. The overall number of transcripts with aberrant selection of 3ʹ splice sites was significantly increased in DON-exposed HepG2 cells. This effect was further confirmed in two other human cell lines, HEK293 and Caco-2, suggesting that this DON-induced alteration in splicing patterns was universal in human cells. Among these DON-induced changes in alternative splicing, the expression levels of two related splicing factors, SF1 and U2AF1, which are essential for 3ʹ splice site recognitions, were strongly suppressed. Overexpression of either of the two splicing factors strongly alleviated the DON-induced aberrant selection of 3ʹ splice sites. Moreover, SF1 was required for human cell proliferation in DON exposure, and the restoration of SF1 expression partially reinstated the proliferation potential for DON-treated cells. In conclusion, our study suggests that DON, even at a low dosage, has great potential to change gene expression globally by affecting not only protein synthesis but also mRNA processing in human cells.
DOI: 10.6084/m9.figshare.11761071.v1
title: Deoxynivalenol globally affects the selection of 3’ splice sites in human cells by suppressing the splicing factors, U2AF1 and SF1

description: Deoxynivalenol (DON) is one of the most abundant mycotoxins and has adverse effects on several biological processes, posing risks of protein synthesis-disrupting effects and ribotoxic response. Therefore, chronic exposure to DON would fundamentally reshape the global expression pattern. Whether DON causes toxic effects on mRNA splicing, a fundamental biological process, remains unclear. In this study, we found that administration of the relative low dosage of DON dramatically changed the alternative splicing of pre-mRNA in HepG2 cells. The overall number of transcripts with aberrant selection of 3ʹ splice sites was significantly increased in DON-exposed HepG2 cells. This effect was further confirmed in two other human cell lines, HEK293 and Caco-2, suggesting that this DON-induced alteration in splicing patterns was universal in human cells. Among these DON-induced changes in alternative splicing, the expression levels of two related splicing factors, SF1 and U2AF1, which are essential for 3ʹ splice site recognitions, were strongly suppressed. Overexpression of either of the two splicing factors strongly alleviated the DON-induced aberrant selection of 3ʹ splice sites. Moreover, SF1 was required for human cell proliferation in DON exposure, and the restoration of SF1 expression partially reinstated the proliferation potential for DON-treated cells. In conclusion, our study suggests that DON, even at a low dosage, has great potential to change gene expression globally by affecting not only protein synthesis but also mRNA processing in human cells.
DOI: 10.6084/m9.figshare.19095298
title: The association between urinary phytoestrogens and depressive symptoms

description: Present evidence outlining the association between different types of phytoestrogens and depressive symptoms in the general population is limited and contradictory. Data from the 2007–2010 National Health and Nutrition Examination Survey (NHANES) were used to examine their association. Phytoestrogens were measured in urine samples and depressive symptoms were assessed using the Patient Health Questionnaire-9 (PHQ-9). Logistic regression and restricted cubic spline models were used to evaluate associations. In one model, lignans and enterolactone were inversely associated with the prevalence of depressive symptoms. Compared with the lowest quartile (Q1), the odds ratios (ORs; 95% confidence intervals [CIs]) for participants in the highest quartile of lignans and enterolactone were 0.44 (0.27–0.72) and 0.42 (0.26–0.67) for depressive symptoms, respectively. Additionally, the dose-response relationships between urinary lignans or enterolactone and depressive symptoms showed a linear trend. Our results suggest that urinary lignans and enterolactone are inversely associated with the prevalence of depressive symptoms.
DOI: 10.6084/m9.figshare.19619776
title: Isolation and genomic characterization of <i>Klebsiella</i> Lw3 with polychlorinated biphenyl degradability

description: Bioremediation of sediment organic pollution has been intensely investigated, but the degradation of complex organic compounds, pesticide residues, and polychlorinated biphenyls (PCBs) remains poorly studied. In this study, sediments were collected from Zhanjiang Mangrove Reserve and inoculated in an inorganic salt medium using only biphenyl (BP) and PCBs as the carbon sources to obtain a PCB-degrading strain. A gram-negative bacterium that metabolized PCBs was isolated and identified as <i>Klebsiella</i> Lw3 by 16S rDNA phylogenetic analysis. Genomic sequencing showed that this bacterium possessed genes related to BP/PCB degradation, and its GC content was 58.2%; we identified 3326 cellular pathways. Gas chromatography–mass spectrometry was employed to test the PCB degrading ability; the results showed that the strain had a good degradation effect on PCB3 at concentrations of 5, 10, 20, 40, and 60 mg/L and that the final degradation rate was higher than 97% after 96 h. Interestingly, this strain showed good biodegradability of PCBs despite having no classical PCB degradation pathway, providing a new direction for <i>Klebsiella</i> research with practical significance for <i>in situ</i> bioremediation of PCB contamination. Overall, this study provides valuable insights into the genetic structure of PCB-degrading strains as well as eco-friendly and low-cost PCB degradation and lays a foundation for the discovery of new degradation pathways.
DOI: 10.6084/m9.figshare.19620197.v1
title: The biological behavior of tRNA-derived fragment tRF-Leu-AAG in pancreatic cancer cells

description: Pancreatic cancer (PC) is a life-threatening cancer with increasing incidence in developed countries. Reports indicate that tRNA-derived fragments (tRFs) are possible therapeutic targets and biomarkers for cancer treatment. Nonetheless, the effect of tRF-Leu-AAG on PC is unclear. This study aims to explore the role of tRF-Leu-AAG and upstream frameshift mutant 1 (UPF1) in the development of PC and its potential underlying mechanisms. High-throughput second-generation sequencing techniques were used to detect the expression of tRFs in cancerous and adjacent normal tissues from PC patients. The role of tRF-Leu-AAG proliferation in PC cells was investigated via the Cell Counting Kit-8 (CCK8) assay. The effect of tRF-Leu-AAG on the invasion and migration ability of PC cells was also determined by the transwell assay. Thereafter, the downstream target genes of tRF-Leu-AAG were comprehensively predicted using bioinformatics analysis databases. We also used the Dual-Luciferase Reporter assay to assess the nexus between tRF-Leu-AAG and UPF1. Eventually, Western Blot was used to validate the expression of UPF1 in PC cells. A total of 33 tRF expressions significantly varied from PC patients. RT-qPCR confirmed that the expression of tRF-Leu-AAG was observably up-regulated in PC cells as compared to the control cells. Importantly, knockdown of tRF-Leu-AAG observably inhibited cell proliferation, migration, and invasion. Furthermore, according to the predicted frameshift database results, the UPF1 acted as downstream target genes for tRF-Leu-AAG and significantly down-regulated UPF1 expression.
DOI: 10.6084/m9.figshare.21301415.v1
title: Additional file 3 of Transcriptome analysis of MYB transcription factors family and PgMYB genes involved in salt stress resistance in Panax ginseng

description: Additional file 3: Table S3. The classification, annotation and GO functional categorization of the PgMYB gene transcripts.
DOI: 10.6084/m9.figshare.19092307
title: Additional file 1 of Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development

description: Additional file 1. Supplementary data associated with this article can be found in the appendix. The information of 20 conserved motifs of Cellulose synthase genes in Phaseolus vulgaris detected by the online tool MEME.
DOI: 10.6084/m9.figshare.23295485
title: <strong>Genomic data and ecological niche modeling reveal the unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae</strong>

description: The  511-LCN gene, 38-mt gene, 79-pt gene and 42-HCSCN gene datasets in "<strong>Genomic data and ecological niche modeling reveal the unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae</strong>".
DOI: 10.6084/m9.figshare.12965633
title: Additional file 6 of Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

description: Additional file 6: Table S5. Details of over-represented gene categories during the osmotic phase.
DOI: 10.6084/m9.figshare.21717539.v1
title: A Tweedie Compound Poisson Model in Reproducing Kernel Hilbert Space

description: Tweedie models can be used to analyze nonnegative continuous data with a probability mass at zero. There have been wide applications in natural science, healthcare research, actuarial science, and other fields. The performance of existing Tweedie models can be limited on today’s complex data problems with challenging characteristics such as nonlinear effects, high-order interactions, high-dimensionality and sparsity. In this article, we propose a kernel Tweedie model, Ktweedie, and its sparse variant, SKtweedie, that can simultaneously address the above challenges. Specifically, nonlinear effects and high-order interactions can be flexibly represented through a wide range of kernel functions, which is fully learned from the data; In addition, while the Ktweedie can handle high-dimensional data, the SKtweedie with integrated variable selection can further improve the interpretability. We perform extensive simulation studies to justify the prediction and variable selection accuracy of our method, and demonstrate the applications in ratemaking and loss-reserving in general insurance. Overall, the Ktweedie and SKtweedie outperform existing Tweedie models when there exist nonlinear effects and high-order interactions, particularly when the dimensionality is high relative to the sample size. The model is implemented in an efficient and user-friendly R package ktweedie (https://cran.r-project.org/package=ktweedie).
DOI: 10.6084/m9.figshare.19092325
title: Additional file 5 of Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development

description: Additional file 5 The protein sequences of Cellulose synthase genes in Arabidopsis thaliana.
DOI: 10.6084/m9.figshare.19092328
title: Additional file 6 of Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development

description: Additional file 6 The raw data of characterization of the putative Cellulose Synthase genes in Phaseolus vulgaris.
DOI: 10.6084/m9.figshare.19619465
title: Additional file 1 of Tea plant roots respond to aluminum-induced mineral nutrient imbalances by transcriptional regulation of multiple cation and anion transporters

description: Additional file 1.
DOI: 10.6084/m9.figshare.19619465.v1
title: Additional file 1 of Tea plant roots respond to aluminum-induced mineral nutrient imbalances by transcriptional regulation of multiple cation and anion transporters

description: Additional file 1.
DOI: 10.6084/m9.figshare.16998951.v1
title: XRD raw data of (Al63Cu25Fe12)100-xCex (x = 1 at%) sample from Influence of cerium content on the microstructure and thermal expansion properties of suction cast Al-Cu-Fe alloys

description: 4CExrd
DOI: 10.6084/m9.figshare.19092310
title: Additional file 2 of Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development

description: Additional file 2 The information of cis-elements in promoter sequences of Cellulose synthase genes in Phaseolus vulgaris.
DOI: 10.6084/m9.figshare.16998960.v1
title: XRD raw data of (Al63Cu25Fe12)100-xCex (x = 0 at%) sample from Influence of cerium content on the microstructure and thermal expansion properties of suction cast Al-Cu-Fe alloys

description: 1CExrd
DOI: 10.6084/m9.figshare.21717539
title: A Tweedie Compound Poisson Model in Reproducing Kernel Hilbert Space

description: Tweedie models can be used to analyze nonnegative continuous data with a probability mass at zero. There have been wide applications in natural science, healthcare research, actuarial science, and other fields. The performance of existing Tweedie models can be limited on today’s complex data problems with challenging characteristics such as nonlinear effects, high-order interactions, high-dimensionality and sparsity. In this article, we propose a kernel Tweedie model, Ktweedie, and its sparse variant, SKtweedie, that can simultaneously address the above challenges. Specifically, nonlinear effects and high-order interactions can be flexibly represented through a wide range of kernel functions, which is fully learned from the data; In addition, while the Ktweedie can handle high-dimensional data, the SKtweedie with integrated variable selection can further improve the interpretability. We perform extensive simulation studies to justify the prediction and variable selection accuracy of our method, and demonstrate the applications in ratemaking and loss-reserving in general insurance. Overall, the Ktweedie and SKtweedie outperform existing Tweedie models when there exist nonlinear effects and high-order interactions, particularly when the dimensionality is high relative to the sample size. The model is implemented in an efficient and user-friendly R package ktweedie (https://cran.r-project.org/package=ktweedie).
DOI: 10.6084/m9.figshare.16998963.v1
title: XRD raw data of (Al63Cu25Fe12)100-xCex (x = 0.5 at%) sample from Influence of cerium content on the microstructure and thermal expansion properties of suction cast Al-Cu-Fe alloys

description: 3CExrd
DOI: 10.6084/m9.figshare.12965642
title: Additional file 9 of Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

description: Additional file 9: Table S7. Details of over-represented gene categories during the ionic phase.
DOI: 10.6084/m9.figshare.19619776.v2
title: Isolation and genomic characterization of <i>Klebsiella</i> Lw3 with polychlorinated biphenyl degradability

description: Bioremediation of sediment organic pollution has been intensely investigated, but the degradation of complex organic compounds, pesticide residues, and polychlorinated biphenyls (PCBs) remains poorly studied. In this study, sediments were collected from Zhanjiang Mangrove Reserve and inoculated in an inorganic salt medium using only biphenyl (BP) and PCBs as the carbon sources to obtain a PCB-degrading strain. A gram-negative bacterium that metabolized PCBs was isolated and identified as <i>Klebsiella</i> Lw3 by 16S rDNA phylogenetic analysis. Genomic sequencing showed that this bacterium possessed genes related to BP/PCB degradation, and its GC content was 58.2%; we identified 3326 cellular pathways. Gas chromatography–mass spectrometry was employed to test the PCB degrading ability; the results showed that the strain had a good degradation effect on PCB3 at concentrations of 5, 10, 20, 40, and 60 mg/L and that the final degradation rate was higher than 97% after 96 h. Interestingly, this strain showed good biodegradability of PCBs despite having no classical PCB degradation pathway, providing a new direction for <i>Klebsiella</i> research with practical significance for <i>in situ</i> bioremediation of PCB contamination. Overall, this study provides valuable insights into the genetic structure of PCB-degrading strains as well as eco-friendly and low-cost PCB degradation and lays a foundation for the discovery of new degradation pathways.
DOI: 10.6084/m9.figshare.21301415
title: Additional file 3 of Transcriptome analysis of MYB transcription factors family and PgMYB genes involved in salt stress resistance in Panax ginseng

description: Additional file 3: Table S3. The classification, annotation and GO functional categorization of the PgMYB gene transcripts.
DOI: 10.6084/m9.figshare.12965642.v1
title: Additional file 9 of Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

description: Additional file 9: Table S7. Details of over-represented gene categories during the ionic phase.
DOI: 10.13145/bacdive3478.20191129.4.1
title: Archangium minus (Krzemieniewska and Krzemieniewski 1926) Lang et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive3479.20191129.4.1
title: Archangium minus (Krzemieniewska and Krzemieniewski 1926) Lang et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive3480.20191129.4.1
title: Archangium minus (Krzemieniewska and Krzemieniewski 1926) Lang et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive3481.20191129.4.1
title: Archangium minus (Krzemieniewska and Krzemieniewski 1926) Lang et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive3482.20191129.4.1
title: Archangium minus (Krzemieniewska and Krzemieniewski 1926) Lang et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive3483.20191129.4.1
title: Archangium minus (Krzemieniewska and Krzemieniewski 1926) Lang et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.