cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21922575
title: Supplementary Material for: Optimizing survival benefit by surgical resection by the seven-eleven criteria in Barcelona clinic liver cancer stage A/B hepatocellular carcinoma beyond the Milan criteria

description: Introduction: Optimal treatment of hepatocellular carcinoma (HCC) beyond the Milan criteria is in debate. We aimed to identify candidates for surgical resection (SR) in Barcelona Clinic Liver Cancer (BCLC) –A/B HCC beyond the Milan criteria with survival benefit. Methods: Patients with BCLC-A/B HCC beyond the Milan criteria at the National Taiwan University Hospital during 2005 and 2019 were screened and those who received transarterial chemoembolization (TACE) or SR were consecutively included. The tumor burden was classified by the seven-eleven criteria into low (≤7), intermediate (7-11) or high (&gt;11). Multivariable cox proportional hazard regression analysis was used for outcome prediction. Results: Overall, 474 patients who received SR (n=247), and TACE (n=227) were enrolled. Patients underwent SR were significantly younger with better liver reserve. There were 76 (31%), and 129 (57%) deaths in the SR and TACE groups after a median follow-up of 3.9 and 2.1 years, respectively. The seven-eleven criteria could distinguish median overall survival (OS) among low (n=149), intermediate (n=203), and high (n=122) tumor burden groups (7.7 vs. 6.9 vs. 2.8 years, respectively, P &lt; 0.001). Patients receiving SR had a significantly higher median OS compared with TACE in those with intermediate (8.2 vs. 2.6 years, P &lt; 0.001) and high (5.6 vs. 1.5 years, P = 0.001) tumor burden. After adjustment for age, sex, and liver reserve, SR was predictive for better OS in intermediate (adjusted hazard ratio [aHR]: 0.45, 95% CI: 0.27-0.75) and high tumor burden groups (aHR: 0.54, 95% CI: 0.32-0.92). The survival benefit of SR especially confines to patients within 3 tumors. Conclusions: In patients with BCLC-A/B HCC beyond the Milan criteria with tumor burden beyond the up-to-7 criteria but within 3 tumors, SR has better OS than TACE and should be considered in resectable patients.
DOI: 10.6084/m9.figshare.21922575.v1
title: Supplementary Material for: Optimizing survival benefit by surgical resection by the seven-eleven criteria in Barcelona clinic liver cancer stage A/B hepatocellular carcinoma beyond the Milan criteria

description: Introduction: Optimal treatment of hepatocellular carcinoma (HCC) beyond the Milan criteria is in debate. We aimed to identify candidates for surgical resection (SR) in Barcelona Clinic Liver Cancer (BCLC) –A/B HCC beyond the Milan criteria with survival benefit. Methods: Patients with BCLC-A/B HCC beyond the Milan criteria at the National Taiwan University Hospital during 2005 and 2019 were screened and those who received transarterial chemoembolization (TACE) or SR were consecutively included. The tumor burden was classified by the seven-eleven criteria into low (≤7), intermediate (7-11) or high (&gt;11). Multivariable cox proportional hazard regression analysis was used for outcome prediction. Results: Overall, 474 patients who received SR (n=247), and TACE (n=227) were enrolled. Patients underwent SR were significantly younger with better liver reserve. There were 76 (31%), and 129 (57%) deaths in the SR and TACE groups after a median follow-up of 3.9 and 2.1 years, respectively. The seven-eleven criteria could distinguish median overall survival (OS) among low (n=149), intermediate (n=203), and high (n=122) tumor burden groups (7.7 vs. 6.9 vs. 2.8 years, respectively, P &lt; 0.001). Patients receiving SR had a significantly higher median OS compared with TACE in those with intermediate (8.2 vs. 2.6 years, P &lt; 0.001) and high (5.6 vs. 1.5 years, P = 0.001) tumor burden. After adjustment for age, sex, and liver reserve, SR was predictive for better OS in intermediate (adjusted hazard ratio [aHR]: 0.45, 95% CI: 0.27-0.75) and high tumor burden groups (aHR: 0.54, 95% CI: 0.32-0.92). The survival benefit of SR especially confines to patients within 3 tumors. Conclusions: In patients with BCLC-A/B HCC beyond the Milan criteria with tumor burden beyond the up-to-7 criteria but within 3 tumors, SR has better OS than TACE and should be considered in resectable patients.
DOI: 10.5281/zenodo.7742544
title: AMPSphere pre-computed resources and auxiliary files for the manuscript codes

description: AMPSphere is a comprehensive catalog of antimicrobial peptides predicted using Macrel (DOI: 10.7717/peerj.10555) from 63,410 public metagenomes, ProGenomes v2.2 database (82,400 high-quality microbial genomes), and c.a. 4k non-whitelisted microbial genomes from NCBI. Currently, AMPSphere is available as a web resource at https://ampsphere.big-data-biology.org/. AMPSphere v.2022-03 contains 863,498 sequences (avg length: 36 amino acids, range 8-98). DRAMP database was used to find confirmed sequences with strict homology to reference. This approach showed that 2,488 peptides were previously confirmed in our dataset. The present repository is a data dump for the precomputed resources and files needed for its generation and analysis as a complement to the GitHub repository. The complementary documentation is also available for each one of the files. To use the files just download them and apply the command `untar` to decompress the folders.
DOI: 10.5281/zenodo.7742543
title: AMPSphere pre-computed resources and auxiliary files for the manuscript codes

description: AMPSphere is a comprehensive catalog of antimicrobial peptides predicted using Macrel (DOI: 10.7717/peerj.10555) from 63,410 public metagenomes, ProGenomes v2.2 database (82,400 high-quality microbial genomes), and c.a. 4k non-whitelisted microbial genomes from NCBI. Currently, AMPSphere is available as a web resource at https://ampsphere.big-data-biology.org/. AMPSphere v.2022-03 contains 863,498 sequences (avg length: 36 amino acids, range 8-98). DRAMP database was used to find confirmed sequences with strict homology to reference. This approach showed that 2,488 peptides were previously confirmed in our dataset. The present repository is a data dump for the precomputed resources and files needed for its generation and analysis as a complement to the GitHub repository. The complementary documentation is also available for each one of the files. To use the files just download them and apply the command `untar` to decompress the folders.
DOI: 10.5258/soton/d2305
title: Dataset for Out-of-plane beam shaping with UV-written tilted Bragg gratings for beam delivery on quantum chips

description: Dataset for article published in Optics Express. This dataset contains: fig2a_ana_60_x.csv, fig2a_ana_60_y.csv, fig2a_ana_90_y.csv, fig2a_ana_120_y.csv, fig2a_num_60_x.csv, fig2a_num_90_x.csv, fig2a_num_120_x.csv, fig2a_ana_90_x.csv, fig3a_ana_60_y.csv, fig3a_ana_90_x.csv, fig3a_ana_90_y.csv, fig3a_ana_120_x.csv, fig3a_ana_120_y.csv, fig3a_ana_60_x.csv, fig3a_num_60_x.csv, fig3a_num_90_x.csv, fig3a_num_120_x.csv, fig3b_ana_60_y.csv, fig3b_ana_90_x.csv, fig3b_ana_90_y.csv, fig3b_ana_60_x.csv, fig3b_ana_120_x.csv, fig3b_ana_120_y.csv, fig3b_num_90_x.csv, fig3b_num_60_x.csv, fig3b_num_120_x.csv, fig2b_x.csv, fig2b_y.csv, fig4a_grat_x.csv, fig4a_grat_y.csv, fig4a_prop_x.csv, fig4a_prop_y.csv, fig4a_grat_z.csv, fig4b_des_x.csv, fig4b_des_y.csv, fig4b_gra_x.csv, fig4b_gra_y.csv, fig4b_sim_x.csv, fig4b_sim_y.csv, fig4a_prop_z.csv, fig5a_grat_x.csv, fig5a_grat_y.csv, fig5a_prop_x.csv, fig5a_prop_y.csv, fig5a_grat_z.csv, fig5b_des_x.csv, fig5b_des_y.csv, fig5b_gra_x.csv, fig5b_gra_y.csv, fig5b_sim_x.csv, fig5b_sim_y.csv, fig5a_prop_z.csv, fig6a_dng_x.csv, fig6a_dng_y.csv, fig6a_period_x.csv, fig6a_period_y.csv, fig6b_dng_x.csv, fig6b_dng_y.csv, fig6b_period_x.csv, fig6b_period_y.csv, fig7_gauss_x.csv, fig7_gauss_y.csv, fig7_super_x.csv, fig7_super_y.csv files are indices with _x and _y to indicated the data is on the x or y axis.
DOI: 10.48432/yetvpz
title: LiDAR survey on 500 hectares of Talisma, Rio Branco, Acre, Brasil, in 2013

description: The LiDAR data Talismã (TAL_A01_2013_LiDAR) refers to the survey carried out in Rio Branco municipality, Acre state, Brazil. The data were collected under the project Sustainable Landscapes, a project supported by the United States Agency for International Development (USAID) and US Department of State. The United States Forest Service working in collaboration with the Brazilian Agricultural Research Corporation (Embrapa) have made possible the provision of high accuracy LiDAR data aiming at developing new methods and generating knowledge in the field. This dataset contains: a. Classified LAS formatted point cloud data – compressed LAS files: LAZ format (vendor delivered); b. Digital Terrain Model (vendor delivered); c. Map of LiDAR coverage area and block boundaries; “Data were acquired by the Sustainable Landscapes Brazil project supported by the Brazilian Agricultural Research Corporation (Embrapa), the US Forest Service, USAID and the US Department of State."
DOI: 10.34740/kaggle/dsv/5183494
title: 2021 World Population (updated daily)
DOI: 10.5281/zenodo.7745124
title: 3D genome organization around nuclear speckles drives mRNA splicing efficiency (dataset)

description: Figure 1 files: U1, U2, U4, U6 weighted bedgraphs, contact scores, and seqFISH processed data Figure 2 files: Splicing efficiency calculations from chromatin RNA seq and SPRITE Figure 3 files: MS2-MCP replicate data Figure 4 files: mouse (mESC and myocyte) and human (H1 hESC, H1-endoderm, HFF-c6, GM12878 SPRITE bedgraphs)
DOI: 10.5281/zenodo.7745123
title: 3D genome organization around nuclear speckles drives mRNA splicing efficiency (dataset)

description: Figure 1 files: U1, U2, U4, U6 weighted bedgraphs, contact scores, and seqFISH processed data Figure 2 files: Splicing efficiency calculations from chromatin RNA seq and SPRITE Figure 3 files: MS2-MCP replicate data Figure 4 files: mouse (mESC and myocyte) and human (H1 hESC, H1-endoderm, HFF-c6, GM12878 SPRITE bedgraphs)
DOI: 10.5281/zenodo.7703134
title: Material used in: Overview-of-the-initial-phase-of-scientific-production-on-COVID-19-during-the-pandemic: v1.0.1

description: This repo contains the raw database and all material produced used in the article "Overview of the initial phase of scientific production on COVID-19 during the pandemic".
DOI: 10.5258/soton/d2560
title: Datasest in support of the publication 'A wearable insole system to measure plantar pressure and shear for people with diabetes'

description: Dataset in support of the journal article to be published in the journal Sensors This dataset if available 'on request only' under a CC-BY-NC-ND licence. Please complete and return the attached form. Description: The excel files contain all experimental data used for generating Figure 4, Figure 5, Figure 8, Figure 9, Figure 10 and Table 1 Figure 4: (a) Applied static pressure from the Instron mechanical test machine, as a function of time. Measured pressure from the insole system and applied pressure from the test machine, obtained from the (b) static and (c) dynamic pressure test. Figure 5: (a) Applied static shear stress from the mechanical test machine, as a function of time. Measured shear stress from the insole system and applied shear stress from the test machine, obtained from the (b) static and (c) dynamic shear test. Figure 8: (a) Pressure, (b) medial-lateral (ML) shear and (c) anterior-posterior (AP) shear stress as a function of time from the heathy participant wearing a trainer. Figure 9: (a) Mean peak pressure and (b) medial-lateral (ML) and (c) anterior-posterior (AP) shear stress obtained over gait cycles, with three types of footwear. Figure 10: Mean peak plantar pressure distribution during walking obtained using XSENSOR system with and without the sensorised insole. The four sensing locations are highlighted to allow regional peak pressure value comparison. Table 1: Peak pressure safety evaluation for 5 participants with diabetes. MPP: Mean Peak Pressure values for each participant represent the average of 10 mid-gait steps. Effect calculated as absolute pressure with sensorised insole MPP minus Without Insole MPP (S-W)
DOI: 10.6084/m9.figshare.21731936
title: Supplementary Material for: Identification of key genes from the visceral adipose tissues of overweight/obese adults with hypertension through transcriptome sequencing

description: Overweight and obese (OW/OB) adults are at increased risk of hypertension due to visceral adipose tissue (VAT) inflammation. In this study, we explored gene level differences in the VAT of hypertensive and normotensive OW/OB patients. VAT samples obtained from six OW/OB adults (three hypertensive, three normotensive) were subjected to transcriptome sequencing analysis. Gene set enrichment analysis was conducted for all gene expression data to identify differentially expressed genes (DEGs) with |log2 (fold change)| ≥ 1 and q &lt; 0.05. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analyses were performed on the DEGs and hub genes were identified by constructing a protein-protein interaction (PPI) network. The proposed hub genes were validated using quantitative real-time PCR in ten other samples from five hypertensive and five normotensive patients. In addition, we performed ROC analysis and spearman correlation analysis. A total of 84 DEGs were identified between VAT samples from OW/OB patients with and without hypertension, among which 21 were significantly up-regulated and 63 were significantly down-regulated. Bioinformatics analysis revealed that spleen function was related to hypertension in OW/OB adults. Meanwhile, PPI network analysis identified the following top 10 hub genes: CD79A, CR2, SELL, CD22, IL7R, CCR7, TNFRSF13C, CXCR4, POU2AF1, and JAK3. Through qPCR verification, we found that CXCR4, CD22 and IL7R were statistically significant. QPCR verification suggested that RELA were statistically significant. However, qPCR verification indicated that NF-KB1 and KLF2 were not statistically significant. These hub genes were mainly regulated by the transcription factors RELA. The AUC of ROC analysis for CXCR4, IL7R and CD22 was 0.92. What’s more, VAT CXCR4 and CD22 were positively related to RELA relative expression levels. Take together, our research demonstrates that CXCR4, IL7R and CD22 related to VAT in hypertensive OW/OB adults could serve as future therapeutic targets.
DOI: 10.6084/m9.figshare.21731936.v1
title: Supplementary Material for: Identification of key genes from the visceral adipose tissues of overweight/obese adults with hypertension through transcriptome sequencing

description: Overweight and obese (OW/OB) adults are at increased risk of hypertension due to visceral adipose tissue (VAT) inflammation. In this study, we explored gene level differences in the VAT of hypertensive and normotensive OW/OB patients. VAT samples obtained from six OW/OB adults (three hypertensive, three normotensive) were subjected to transcriptome sequencing analysis. Gene set enrichment analysis was conducted for all gene expression data to identify differentially expressed genes (DEGs) with |log2 (fold change)| ≥ 1 and q &lt; 0.05. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analyses were performed on the DEGs and hub genes were identified by constructing a protein-protein interaction (PPI) network. The proposed hub genes were validated using quantitative real-time PCR in ten other samples from five hypertensive and five normotensive patients. In addition, we performed ROC analysis and spearman correlation analysis. A total of 84 DEGs were identified between VAT samples from OW/OB patients with and without hypertension, among which 21 were significantly up-regulated and 63 were significantly down-regulated. Bioinformatics analysis revealed that spleen function was related to hypertension in OW/OB adults. Meanwhile, PPI network analysis identified the following top 10 hub genes: CD79A, CR2, SELL, CD22, IL7R, CCR7, TNFRSF13C, CXCR4, POU2AF1, and JAK3. Through qPCR verification, we found that CXCR4, CD22 and IL7R were statistically significant. QPCR verification suggested that RELA were statistically significant. However, qPCR verification indicated that NF-KB1 and KLF2 were not statistically significant. These hub genes were mainly regulated by the transcription factors RELA. The AUC of ROC analysis for CXCR4, IL7R and CD22 was 0.92. What’s more, VAT CXCR4 and CD22 were positively related to RELA relative expression levels. Take together, our research demonstrates that CXCR4, IL7R and CD22 related to VAT in hypertensive OW/OB adults could serve as future therapeutic targets.
DOI: 10.25405/data.ncl.22220005
title: DataSourceFigure 5

description: Data from Figure 5 "The association of the native Rif1 or serine substituted Rif1 with different loci. " <br> This figure is from the following MCB article: <strong>"A CDK-dependent phosphorylation of a novel domain of Rif1 regulates its function during telomere damage and other types of stress"</strong>
DOI: 10.25405/data.ncl.22220005.v1
title: DataSourceFigure 5

description: Data from Figure 5 "The association of the native Rif1 or serine substituted Rif1 with different loci. " <br> This figure is from the following MCB article: <strong>"A CDK-dependent phosphorylation of a novel domain of Rif1 regulates its function during telomere damage and other types of stress"</strong>
DOI: 10.5281/zenodo.7743039
title: MUSES Leaf Area Index (LAI) Monthly Global 500m SIN Grid in 2014

description: The MUltiscale Satellite remotE Sensing (MUSES) product suite includes products with different spatial and temporal resolutions for parameters such as Normalized Difference Vegetation Index (NDVI), Near-Infrared Reflectance of Vegetation (NIRv), Leaf Area Index (LAI), Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), Fractional Vegetation Coverage (FVC), Gross Primary Production (GPP), Net Primary Production (NPP). For more information about the MUSES products, please refer to this website (https://muses.bnu.edu.cn/). This dataset is the MUSES global LAI product at 500m spatial resolution and monthly temporal resolution. The MUSES LAI product is provided on a Sinusoidal grid and spans from 2000 to 2019 (continuously updated). It was generated from time-series Moderate Resolution Imaging Spectroradiometer (MODIS) surface reflectance product using general regression neural networks (GRNNs) (Xiao <em>et al</em>., 2014; Xiao <em>et al.</em>, 2016). The MUSES LAI product is spatially complete and temporally continuous. This dataset is the MUSES LAI product in 2014. Please <em><strong>click here</strong> to download the MUSES LAI product <strong>in 2013</strong></em><strong>, </strong>and <em><strong>click here</strong> to download the MUSES LAI product <strong>in 2015</strong></em>. <strong>Dataset Characteristics:</strong> Spatial Coverage: Global Temporal Coverage: 2014 Spatial Resolution: 500m Temporal Resolution: 1 month Projection: Sinusoidal Data Format: HDF Scale: 0.01 Valid Range: 0 – 1000 <strong>Citation </strong>(Please cite this paper whenever these data are used)<strong>:</strong> Xiao Zhiqiang, <em>et al</em>. (2014). Use of General Regression Neural Networks for Generating the GLASS Leaf Area Index Product From Time-Series MODIS Surface Reflectance. <em>IEEE Transactions on Geoscience and Remote Sensing</em>, 52, 209-223. Xiao Zhiqiang, <em>et al</em>. (2016). Long-time-series global land surface satellite leaf area index product derived from MODIS and AVHRR surface reflectance. <em>IEEE Transactions on Geoscience and Remote Sensing</em>, 54, 5301-5318. Xiao Zhiqiang, Jinling Song, Hua Yang, Rui Sun and Juan Li. (2022). A 250 m resolution global leaf area index product derived from MODIS surface reflectance data. <em>International Journal of Remote Sensing</em>, 43(4), 1199-1225. Xiao Zhiqiang, <em>et al</em>. (2017). Evaluation of four long time-series global leaf area index products. <em>Agricultural and Forest Meteorology</em>, 246, 218-230. If you have any questions, please contact Prof. Zhiqiang Xiao (zhqxiao@bnu.edu.cn).
DOI: 10.5281/zenodo.7743038
title: MUSES Leaf Area Index (LAI) Monthly Global 500m SIN Grid in 2014

description: The MUltiscale Satellite remotE Sensing (MUSES) product suite includes products with different spatial and temporal resolutions for parameters such as Normalized Difference Vegetation Index (NDVI), Near-Infrared Reflectance of Vegetation (NIRv), Leaf Area Index (LAI), Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), Fractional Vegetation Coverage (FVC), Gross Primary Production (GPP), Net Primary Production (NPP). For more information about the MUSES products, please refer to this website (https://muses.bnu.edu.cn/). This dataset is the MUSES global LAI product at 500m spatial resolution and monthly temporal resolution. The MUSES LAI product is provided on a Sinusoidal grid and spans from 2000 to 2019 (continuously updated). It was generated from time-series Moderate Resolution Imaging Spectroradiometer (MODIS) surface reflectance product using general regression neural networks (GRNNs) (Xiao <em>et al</em>., 2014; Xiao <em>et al.</em>, 2016). The MUSES LAI product is spatially complete and temporally continuous. This dataset is the MUSES LAI product in 2014. Please <em><strong>click here</strong> to download the MUSES LAI product <strong>in 2013</strong></em><strong>, </strong>and <em><strong>click here</strong> to download the MUSES LAI product <strong>in 2015</strong></em>. <strong>Dataset Characteristics:</strong> Spatial Coverage: Global Temporal Coverage: 2014 Spatial Resolution: 500m Temporal Resolution: 1 month Projection: Sinusoidal Data Format: HDF Scale: 0.01 Valid Range: 0 – 1000 <strong>Citation </strong>(Please cite this paper whenever these data are used)<strong>:</strong> Xiao Zhiqiang, <em>et al</em>. (2014). Use of General Regression Neural Networks for Generating the GLASS Leaf Area Index Product From Time-Series MODIS Surface Reflectance. <em>IEEE Transactions on Geoscience and Remote Sensing</em>, 52, 209-223. Xiao Zhiqiang, <em>et al</em>. (2016). Long-time-series global land surface satellite leaf area index product derived from MODIS and AVHRR surface reflectance. <em>IEEE Transactions on Geoscience and Remote Sensing</em>, 54, 5301-5318. Xiao Zhiqiang, Jinling Song, Hua Yang, Rui Sun and Juan Li. (2022). A 250 m resolution global leaf area index product derived from MODIS surface reflectance data. <em>International Journal of Remote Sensing</em>, 43(4), 1199-1225. Xiao Zhiqiang, <em>et al</em>. (2017). Evaluation of four long time-series global leaf area index products. <em>Agricultural and Forest Meteorology</em>, 246, 218-230. If you have any questions, please contact Prof. Zhiqiang Xiao (zhqxiao@bnu.edu.cn).
DOI: 10.5281/zenodo.7745084
title: Spatial predictions of suitable environments for palsas and peat plateaus in the Northern Hemisphere for recent and future periods

description: Here we provide raster files of suitable environments for palsas and peat plateaus in the Northern Hemisphere. These files are results of a scientific study by Könönen et al. (2022, preprint). Files are provided in TIFF-format, and they describe the occurrence probability of the suitable environments for palsas and peat plateaus. Könönen, O. H., Karjalainen, O., Aalto, J., Luoto, M., and Hjort, J.: Environmental spaces for palsas and peat plateaus are disappearing at a circumpolar scale, The Cryosphere Discuss. [preprint], https://doi.org/10.5194/tc-2022-135, in review, 2022.