cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12661523.v1
title: Supplementary Material for: Changes in Background Liver Function in Patients with Hepatocellular Carcinoma over 30 Years: Comparison of Child-Pugh Classification and Albumin Bilirubin Grade

description: <b><i>Background:</i></b> Background liver function in patients with hepatocellular carcinoma (HCC) has improved remarkably with advances in various treatments. Recently, the Child-Pugh classification (CPC) system has been recognized as limited in its ability to assess patients with good hepatic reserve. We compared the albumin-bilirubin (ALBI) grade, which is suitable for a more detailed evaluation of patients with good liver function, with CPC over a 30-year period. <b><i>Methods:</i></b> A total of 2,347 patients were analyzed. Patients were stratified by year of diagnosis into 6 groups: Group A (1990–1994, <i>n</i> = 376), Group B (1995–1999, <i>n</i> = 434), Group C (2000–2004, <i>n</i> = 438), Group D (2005–2009, <i>n</i> = 444), Group E (2010–2014, <i>n</i> = 392), and Group F (2015–2018, <i>n</i> = 263). We compared ALBI grade and CPC across the groups. <b><i>Results:</i></b> The prevalence of patients with CPC A at diagnosis increased throughout the study period, reaching nearly 80% in Groups E and F (<i>p</i> &lt; 0.001). By contrast, the percentage of patients with ALBI grade 1 disease remained approximately 50% in Groups E and F (<i>p</i> &lt; 0.001). Modified ALBI (mALBI) grade 2a corresponds to patients with CPC A who have poor hepatic function. There were significant survival differences between patients with mALBI grade 1 versus 2a, 1 versus 2b, and 2a versus 2b disease, respectively (<i>p</i> &lt; 0.0001), in patients with CPC A. <b><i>Conclusions:</i></b> CPC is not suitable for assessing patients with recently diagnosed HCC and good remnant hepatic function. In such patients with HCC, the prognosis can be stratified by ALBI grade rather than CPC.
DOI: 10.6084/m9.figshare.12661484
title: English speed-related adjectives in attributive usages and other constructions

description: This resource provides the dataset discussed in Schäfer (2020). Centered on the adjective 'quick', it consists of two core parts: <br>A. Adjective-noun collocations for 'quick' and related adjectives, annotated for the semantic category of the noun.<br>B. Collocations of three of these adjectives in the ADJ-to-INFINITIVAL constructions, and, for 'quick' and 'slow', collocations of their preverbal and postverbal adverb counterparts, 'quickly' and 'slowly'.<br>The methodology is described in detail in that paper. The corpus used was the Britisch National Corpus (BNC 2007).<br><br>The individual files are described in the README file.<br><br>References<br>BNC. 2007. <em>The British National Corpus</em>, version 3 (BNC XML edition). www.natcorp.ox.ac.uk<br>SCHÄFER, Martin (2020). From quick to quick-to-infinitival: On what is lexeme specific across paradigmatic and syntagmatic distributions. <i>English Language and Linguistics,</i> 1-31. doi:10.1017/S1360674320000167
DOI: 10.6084/m9.figshare.12661505.v2
title: Datasets for A 2015 inventory of embodied carbon emissions for Chinese power transmission

description: The detail input and embodied carbon emissions inventory covering 191 typical power transmission infrastructure projects in China in 2015, including 145 types of alternating current (AC) transmission line projects, 37 typical AC substation projects, 8 typical direct current (DC) transmission line projects and 1 typical DC converter station project.
DOI: 10.6084/m9.figshare.12661415
title: CyTOF_acquisition_1-3.FCS

description: 40-Ab panel CyTOF data of 2 blood and 2 tumor samples, and 9 reference samples selected to contain positive and negative populations for each marker included in the study's Ab-panel. Samples were multiplexed with a 20-well barcoding plate, and obtained from a single run (provided as 3 FCS files).
DOI: 10.15131/shef.data.12661355
title: The importance of the bacterial cell wall in uranium (VI) biosorption

description: The bacterial cell envelope, in particular the cell wall, is considered the main controlling factor in the biosorption of aqueous uranium (VI) by microorganisms. However, the specific roles of the cell wall, associated biomolecules, and other components of the cell envelope are not well defined. Here we report findings on the biosorption of uranium by isolated cell envelope components and associated biomolecules, with P. putida 33015 and B. subtilis 168 investigated as representative strains for the differences in Gram-negative and Gram-positive cell envelope architecture, respectively. The cell wall and cell surface membrane were isolated from intact cells using a French Pressure Cell and characterised by X-Ray Photoelectron Spectroscopy (XPS) and Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FT-IR) spectroscopy. Uranium biosorption was investigated as a function of cell envelope component and pH, comparing with intact cells and was quantified by ICP-OES.<br>Supplementary information includes characterisation of XPS spectra, uranium speciation, additional adsorption isotherms, langmuir fittings and detailed FT-IR characterisation of cell envelope components.<br><br>Data includes raw XPS and FT-IR spectra, peak identifications and uranium isotherm fittings from data collected by ICP-OES.<br>
DOI: 10.6084/m9.figshare.12661505.v1
title: Datasets for A 2015 inventory of embodied carbon emissions for Chinese power transmission

description: The detail input and embodied carbon emissions inventory covering 191 typical power transmission infrastructure projects in China in 2015, including 145 types of alternating current (AC) transmission line projects, 37 typical AC substation projects, 8 typical direct current (DC) transmission line projects and 1 typical DC converter station project.
DOI: 10.6084/m9.figshare.12661340
title: debarcoding_scheme.csv

description: A binary barcoding scheme of 6-choose-3 = 20 barcodes with columns corresponding to barcode channel masses (101, 104, 105, 106, 108, 110) and rows corresponding to barcodes (7 empty, 9 references, 2 PBMC and 2 tumor samples) – Used for single-cell deconvolution of multiplexed of samples.
DOI: 10.15131/shef.data.12661355.v2
title: The importance of the bacterial cell wall in uranium (VI) biosorption

description: The bacterial cell envelope, in particular the cell wall, is considered the main controlling factor in the biosorption of aqueous uranium (VI) by microorganisms. However, the specific roles of the cell wall, associated biomolecules, and other components of the cell envelope are not well defined. Here we report findings on the biosorption of uranium by isolated cell envelope components and associated biomolecules, with P. putida 33015 and B. subtilis 168 investigated as representative strains for the differences in Gram-negative and Gram-positive cell envelope architecture, respectively. The cell wall and cell surface membrane were isolated from intact cells using a French Pressure Cell and characterised by X-Ray Photoelectron Spectroscopy (XPS) and Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FT-IR) spectroscopy. Uranium biosorption was investigated as a function of cell envelope component and pH, comparing with intact cells and was quantified by ICP-OES.<br>Supplementary information includes characterisation of XPS spectra, uranium speciation, additional adsorption isotherms, langmuir fittings and detailed FT-IR characterisation of cell envelope components.<br><br>Data includes raw XPS and FT-IR spectra, peak identifications and uranium isotherm fittings from data collected by ICP-OES.<br>
DOI: 10.6084/m9.figshare.12661334
title: ref_bead_counts.csv

description: A table of mean dual counts for the six different bead channels (columns) obtained from 12 previous acquisitions (rows). – Used as a reference to assess the measurement sensitivity for the current run.
DOI: 10.6084/m9.figshare.12661337
title: spillover_matrix.csv

description: A spillover matrix calculated with CATALYST from beads single-stained with each of the 40 antibodies included in the panel used in this study. The matrix contains, for each measurement channel (rows), the percentage of signal received by all other channels (columns). – Used for correction of spillover.<br>
DOI: 10.6084/m9.figshare.12661415.v1
title: CyTOF_acquisition_1-3.FCS

description: 40-Ab panel CyTOF data of 2 blood and 2 tumor samples, and 9 reference samples selected to contain positive and negative populations for each marker included in the study's Ab-panel. Samples were multiplexed with a 20-well barcoding plate, and obtained from a single run (provided as 3 FCS files).
DOI: 10.15131/shef.data.12661355.v1
title: The importance of the bacterial cell wall in uranium (VI) biosorption

description: The bacterial cell envelope, in particular the cell wall, is considered the main controlling factor in the biosorption of aqueous uranium (VI) by microorganisms. However, the specific roles of the cell wall, associated biomolecules, and other components of the cell envelope are not well defined. Here we report findings on the biosorption of uranium by isolated cell envelope components and associated biomolecules, with P. putida 33015 and B. subtilis 168 investigated as representative strains for the differences in Gram-negative and Gram-positive cell envelope architecture, respectively. The cell wall and cell surface membrane were isolated from intact cells using a French Pressure Cell and characterised by X-Ray Photoelectron Spectroscopy (XPS) and Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FT-IR) spectroscopy. Uranium biosorption was investigated as a function of cell envelope component and pH, comparing with intact cells and was quantified by ICP-OES.<br>Data includes raw XPS and FT-IR spectra, peak identifications and uranium isotherm fittings from data collected by ICP-OES.<br>
DOI: 10.6084/m9.figshare.12661331
title: ref_marker_levels.csv

description: A table of the 98th expression percentiles for each target (columns) across 7 previous acquisitions (rows). – Used to assess the staining efficiency of the current run.
DOI: 10.6084/m9.figshare.12661334.v1
title: ref_bead_counts.csv

description: A table of mean dual counts for the six different bead channels (columns) obtained from 12 previous acquisitions (rows). – Used as a reference to assess the measurement sensitivity for the current run.
DOI: 10.6084/m9.figshare.12661325
title: ref_cell_counts.csv

description: A table of the number of cells measured in 7 previous acquisitions, each including 4 cell line, 3 PBMC and 2 tumor references samples (63 samples in total). – Used to asses reference sample cell yields in the current in comparison to previous runs.
DOI: 10.6084/m9.figshare.12661331.v1
title: ref_marker_levels.csv

description: A table of the 98th expression percentiles for each target (columns) across 7 previous acquisitions (rows). – Used to assess the staining efficiency of the current run.
DOI: 10.6084/m9.figshare.12661337.v1
title: spillover_matrix.csv

description: A spillover matrix calculated with CATALYST from beads single-stained with each of the 40 antibodies included in the panel used in this study. The matrix contains, for each measurement channel (rows), the percentage of signal received by all other channels (columns). – Used for correction of spillover.<br>
DOI: 10.6084/m9.figshare.12661319
title: sample_cell_counts.csv

description: A table of the number of cells measured in 7 previous acquisitions, each including 2 PBMC and 2 tumor samples each (28 samples in total). – Used to asses sample cell yields in the current in comparison to previous runs.
DOI: 10.6084/m9.figshare.12661322
title: normalization_beads.fcs

description: Beads identified using CATALYST during the normalization step of a previous CyTOF run. – Used as reference beads to correct for changes in signal sensitivity over time across multiple CyTOF runs.
DOI: 10.6084/m9.figshare.12661325.v1
title: ref_cell_counts.csv

description: A table of the number of cells measured in 7 previous acquisitions, each including 4 cell line, 3 PBMC and 2 tumor references samples (63 samples in total). – Used to asses reference sample cell yields in the current in comparison to previous runs.
DOI: 10.6084/m9.figshare.12661307
title: Supplementary Material for: Hemolysis Pathways during Storage of Erythrocytes and Inter-Donor Variability in Erythrocyte Morphology

description: <b><i>Background:</i></b> Red blood cells (RBCs) stored for transfusions can lyse over the course of the storage period. The lysis is traditionally assumed to occur via the formation of spiculated echinocyte forms, so that cells that appear smoother are assumed to have better storage quality. We investigate this hypothesis by comparing the morphological distribution to the hemolysis for samples from different donors. <b><i>Methods:</i></b> Red cell concentrates were obtained from a regional blood bank quality control laboratory. Out of 636 units processed by the laboratory, we obtained 26 high hemolysis units and 24 low hemolysis units for assessment of RBC morphology. The association between the morphology and the hemolysis was tested with the Wilcoxon-Mann-Whitney U test. <b><i>Results:</i></b> Samples with high stomatocyte counts (<i>p</i> = 0.0012) were associated with increased hemolysis, implying that cells can lyse via the formation of stomatocytes. <b><i>Conclusion:</i></b> RBCs can lyse without significant echinocyte formation. Lower degrees of spiculation are not a good indicator of low hemolysis when RBCs from different donors are compared.
DOI: 10.6084/m9.figshare.12661319.v1
title: sample_cell_counts.csv

description: A table of the number of cells measured in 7 previous acquisitions, each including 2 PBMC and 2 tumor samples each (28 samples in total). – Used to asses sample cell yields in the current in comparison to previous runs.
DOI: 10.6084/m9.figshare.12661322.v1
title: normalization_beads.fcs

description: Beads identified using CATALYST during the normalization step of a previous CyTOF run. – Used as reference beads to correct for changes in signal sensitivity over time across multiple CyTOF runs.
DOI: 10.6084/m9.figshare.12661217
title: unigene from PacBio sequencing of cucurbita ficifolia under fusarium oxysporum stress

description: The <i>cucurbita ficifolia</i> was used as the material, When the cotyledon occurs, each plant was inoculated with 10ml of 10<sup>8</sup> per ml preparation of F.<i> oxysporum</i> spores (fungal infection) or with 10 ml of sterile water (control) through the ways of root dipping and root irrigation. The leaves were harvested after 2d and 4d of inoculation and leaf samples from untreated plant were collected for sequencing.The sequencing was commissioned by Shanghai OEbiotech company.
DOI: 10.6084/m9.figshare.12661196
title: The Data of Deformed River Terraces in the Eastern Qilian Shan

description: River terrace and related datasupporting Deformed River Terraces in the Eastern Qilian Shan
DOI: 10.6084/m9.figshare.12661217.v1
title: unigene from PacBio sequencing of cucurbita ficifolia under fusarium oxysporum stress

description: The <i>cucurbita ficifolia</i> was used as the material, When the cotyledon occurs, each plant was inoculated with 10ml of 10<sup>8</sup> per ml preparation of F.<i> oxysporum</i> spores (fungal infection) or with 10 ml of sterile water (control) through the ways of root dipping and root irrigation. The leaves were harvested after 2d and 4d of inoculation and leaf samples from untreated plant were collected for sequencing.The sequencing was commissioned by Shanghai OEbiotech company.
DOI: 10.6084/m9.figshare.12661196.v1
title: The Data of Deformed River Terraces in the Eastern Qilian Shan

description: River terrace and related datasupporting Deformed River Terraces in the Eastern Qilian Shan
DOI: 10.6084/m9.figshare.12661157
title: Supplementary Material for: A Novel SEMA3G Mutation in Two Siblings Affected by Syndromic GnRH Deficiency

description: <b><i>Introduction:</i></b> Gonadotropin-releasing hormone (GnRH) deficiency causes hypogonadotropic hypogonadism (HH), a rare genetic disorder that impairs sexual reproduction. HH can be due to defective GnRH-secreting neuron development or function and may be associated with other clinical signs in overlapping genetic syndromes. With most of the cases being idiopathic, genetics underlying HH is still largely unknown. <b><i>Objective:</i></b> To assess the contribution of mutated Semaphorin 3G (<i>SEMA3G</i>) in the onset of a syndromic form of HH, characterized by intellectual disability and facial dysmorphic features. <b><i>Method:</i></b> By combining homozygosity mapping with exome sequencing, we identified a novel variant in the <i>SEMA3G</i> gene. We then applied mouse as a model organism to examine <i>SEMA3G</i>expression and its functional requirement in vivo. Further, we applied homology modelling in silico and cell culture assays in vitro to validate the pathogenicity of the identified gene variant. <b><i>Results:</i></b> We found that (i) SEMA3G is expressed along the migratory route of GnRH neurons and in the developing pituitary, (ii) SEMA3G affects GnRH neuron development, but is redundant in the adult hypothalamic-pituitary-gonadal axis, and (iii) mutated SEMA3G alters binding properties in silico and in vitro to its PlexinA receptors and attenuates its effect on the migration of immortalized GnRH neurons. <b><i>Conclusion:</i></b> In silico, in vitro, and in vivo models revealed that SEMA3G regulates GnRH neuron migration and that its mutation affecting receptor selectivity may be responsible for the HH-related defects.
DOI: 10.6084/m9.figshare.12661145
title: Plantation mask for the Hansen maps of Global Forest Loss

description: This repository includes the raster datasets which mask plantations—mainly oil palm and rubber—in the Hansen's data of forest loss during the period 2001–2015. The pixel values representing plantations are encoded as 1.<br>The plantation mask covers the main production countries of oil palm (Malaysia, Nigeria, and Indonesia) and rubber (Indonesia, Thailand, Malaysia, and Vietnam) in 2000.
DOI: 10.6084/m9.figshare.12661157.v1
title: Supplementary Material for: A Novel SEMA3G Mutation in Two Siblings Affected by Syndromic GnRH Deficiency

description: <b><i>Introduction:</i></b> Gonadotropin-releasing hormone (GnRH) deficiency causes hypogonadotropic hypogonadism (HH), a rare genetic disorder that impairs sexual reproduction. HH can be due to defective GnRH-secreting neuron development or function and may be associated with other clinical signs in overlapping genetic syndromes. With most of the cases being idiopathic, genetics underlying HH is still largely unknown. <b><i>Objective:</i></b> To assess the contribution of mutated Semaphorin 3G (<i>SEMA3G</i>) in the onset of a syndromic form of HH, characterized by intellectual disability and facial dysmorphic features. <b><i>Method:</i></b> By combining homozygosity mapping with exome sequencing, we identified a novel variant in the <i>SEMA3G</i> gene. We then applied mouse as a model organism to examine <i>SEMA3G</i>expression and its functional requirement in vivo. Further, we applied homology modelling in silico and cell culture assays in vitro to validate the pathogenicity of the identified gene variant. <b><i>Results:</i></b> We found that (i) SEMA3G is expressed along the migratory route of GnRH neurons and in the developing pituitary, (ii) SEMA3G affects GnRH neuron development, but is redundant in the adult hypothalamic-pituitary-gonadal axis, and (iii) mutated SEMA3G alters binding properties in silico and in vitro to its PlexinA receptors and attenuates its effect on the migration of immortalized GnRH neurons. <b><i>Conclusion:</i></b> In silico, in vitro, and in vivo models revealed that SEMA3G regulates GnRH neuron migration and that its mutation affecting receptor selectivity may be responsible for the HH-related defects.
DOI: 10.6084/m9.figshare.12661145.v1
title: Plantation mask for the Hansen maps of Global Forest Loss

description: This repository includes the dataset of the plantation mask which masks plantations—mainly oil palm and rubber—in the Hansen's data of forest loss during the period 2001–2015. The pixel values representing plantations are encoded as 1.
DOI: 10.6084/m9.figshare.12660971
title: Additional file 3 of Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance

description: Additional file 3. Supplemental Table S2. Contains summary data for each low-pass WGS library sequenced and reported in the main text.
DOI: 10.6084/m9.figshare.12660968
title: Additional file 2 of Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance

description: Additional file 2. Supplemental Table S1. Contains summary data (e.g., number of reads, number of barcodes, top barcode ID and prevalence, etc.) from each lineage barcode gDNA library sequenced and reported in the main text.
DOI: 10.6084/m9.figshare.12660971.v1
title: Additional file 3 of Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance

description: Additional file 3. Supplemental Table S2. Contains summary data for each low-pass WGS library sequenced and reported in the main text.
DOI: 10.6084/m9.figshare.12660968.v1
title: Additional file 2 of Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance

description: Additional file 2. Supplemental Table S1. Contains summary data (e.g., number of reads, number of barcodes, top barcode ID and prevalence, etc.) from each lineage barcode gDNA library sequenced and reported in the main text.
DOI: 10.6084/m9.figshare.12660925
title: Additional file 6 of ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

description: Additional file 6: Table S5. Super enhancers that are co-occupied by both ASXL3 and BRD4.
DOI: 10.6084/m9.figshare.12660928
title: Additional file 7 of ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

description: Additional file 7: Table S6. Genes that are co-regulated by BAP1 and ASXL3.
DOI: 10.6084/m9.figshare.12660922
title: Additional file 5 of ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

description: Additional file 5: Table S4. ASXL3 target genes that are occupied by ASXL3 at TSS or NonTSS regions.
DOI: 10.6084/m9.figshare.12660928.v1
title: Additional file 7 of ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

description: Additional file 7: Table S6. Genes that are co-regulated by BAP1 and ASXL3.
DOI: 10.6084/m9.figshare.12660916
title: Additional file 3 of ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

description: Additional file 3: Table S2. Genes significantly enriched in the ASXL3-high and ASXL3-low expressed group of SCLC cells.
DOI: 10.6084/m9.figshare.12660919
title: Additional file 4 of ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

description: Additional file 4: Table S3. Mass spectrometry results for ASXL3 purification.
DOI: 10.6084/m9.figshare.12660922.v1
title: Additional file 5 of ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

description: Additional file 5: Table S4. ASXL3 target genes that are occupied by ASXL3 at TSS or NonTSS regions.
DOI: 10.6084/m9.figshare.12660925.v1
title: Additional file 6 of ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

description: Additional file 6: Table S5. Super enhancers that are co-occupied by both ASXL3 and BRD4.
DOI: 10.6084/m9.figshare.12660916.v1
title: Additional file 3 of ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

description: Additional file 3: Table S2. Genes significantly enriched in the ASXL3-high and ASXL3-low expressed group of SCLC cells.