cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5507983
title: Dataset of generated and evaluated Kuwaiti Public Authority for Housing Welfare building design program with lightweight steel framed construction elements

description: The geometric data was generated using the EPSAP algorithm; the construction elements physical properties were saved from the EPSAP algorithm database; and, the performance data was obtained using the FPOP algorithm coupled to the simulation engine EnergyPlus v8.7.0. The weather file used in the simulations was the KISR Kuwait International Airport - KWT data available at the Department of Energy (URL https://goo.gl/KauYMw).
DOI: 10.6084/m9.figshare.5508016.v1
title: Traits of tick species from the genus Ixodes

description: These data describe anatomical, life history, and ecological traits about tick species in the genus <i>Ixodes</i>.
DOI: 10.6084/m9.figshare.5505898
title: Nonlinear Analsis of Concrete Structures Using GFEM Enrichment Strategy with a Microplane Constitutive Model

description: The additional files to solve 2D solid mechanics problems using an OOP-based in-house code, called INSANE.<br>This files helps to reproduce the results shown in the paper: <b>Nonlinear Analsis of Concrete Structures Using GFEM Enrichment Strategy with a Microplane Constitutive Model</b>. IBRACON Structural and Materials Journal (under review), 2017.
DOI: 10.6084/m9.figshare.5505796
title: Data from: Functional compensation by insular scavengers: the relative contributions of vertebrates and invertebrates vary among islands

description: Sugiura, S. and Hayashi, M. Functional compensation by insular scavengers: the relative contributions of vertebrates and invertebrates vary among islands. Ecography (doi:10.1111/ecog.03226)
DOI: 10.6084/m9.figshare.5505856
title: Hair Dye Substance Database (HDSD)

description: Fully 2D-curated database of 313 QSAR-ready hair dye substances available for download as Excel spreadsheet or SDF (structure-data file). Includes information such as substance name, structure, CASRNs, DTXSIDs, classes, color (if applicable), and computed properties. SDF can be opened using chemical drawing software such as ChemDraw Professional or MarvinView. Marvin (ChemAxon) can be downloaded at: https://chemaxon.com/products/marvin/download<br>New with Version 3: Better defined structures for substances with HDSD ID: 91, 99 and 110 (aromaticity issues resolved).<br>For details regarding database development, analysis, and potential applications, see https://dx.doi.org/10.1021/acssuschemeng.7b03795. <br> We are seeking to improve the HDSD. Please contact Tova N. Williams at tovanwilliams@gmail.com for suggestions.
DOI: 10.6084/m9.figshare.5505796.v2
title: Data from: Functional compensation by insular scavengers: the relative contributions of vertebrates and invertebrates vary among islands

description: Sugiura, S. and Hayashi, M. Functional compensation by insular scavengers: the relative contributions of vertebrates and invertebrates vary among islands. Ecography (doi:10.1111/ecog.03226)
DOI: 10.6084/m9.figshare.5505898.v2
title: Nonlinear Analsis of Concrete Structures Using GFEM Enrichment Strategy with a Microplane Constitutive Model

description: The additional files to solve 2D solid mechanics problems using an OOP-based in-house code, called INSANE.<br>This files helps to reproduce the results shown in the paper: <b>Nonlinear Analsis of Concrete Structures Using GFEM Enrichment Strategy with a Microplane Constitutive Model</b>. IBRACON Structural and Materials Journal (under review), 2017.
DOI: 10.6084/m9.figshare.5505796.v1
title: Data from: Functional compensation by insular scavengers: the relative contributions of vertebrates and invertebrates vary among islands

description: Sugiura, S. and Hayashi, M. Functional compensation by insular scavengers: the relative contributions of vertebrates and invertebrates vary among islands. Ecography (doi:10.1111/ecog.03226)
DOI: 10.6084/m9.figshare.5505898.v1
title: Three-Point Bending and L-Shaped Panel Simulations

description: The additional files to solve 2D solid mechanics problems using an OOP-based in-house code, called INSANE.<br>This files helps to reproduce the results shown in the paper: <b>Nonlinear Analsis of Concrete Structures Using GFEM Enrichment Strategy with a Microplane Constitutive Model</b>. IBRACON Structural and Materials Journal (under review), 2017.
DOI: 10.6084/m9.figshare.5505661
title: The E3-ubiquitin ligase adaptor protein Skp1 is glycosylated by an evolutionarily conserved pathway that regulates protist growth and development.pdf

description: Toxoplasma gondii is a protist parasite of warm-blooded animals that causes disease by proliferating intracellularly in muscle and the central nervous system. Previous studies showed that a prolyl 4-hydroxylase related to animal HIFα prolyl hydroxylases is required for optimal parasite proliferation, especially at low O2. We also observed that Pro154 of Skp1, a subunit of the Skp1/Cullin-1/F-box protein (SCF)-class of E3-ubiquitin ligases, is a natural substrate of this enzyme. In an unrelated protist, Dictyostelium discoideum, Skp1 hydroxyproline is modified by 5 sugars via the action of three glycosyltransferases, Gnt1, PgtA and AgtA, which are required for optimal O2-dependent development. We show here that TgSkp1 hydroxyproline is modified by a similar pentasaccharide, based on mass spectrometry, and that assembly of the first three sugars is dependent on Toxoplasma homologs of Gnt1 and PgtA. Reconstitution of the glycosyltransferase reactions in extracts with radioactive sugar nucleotide substrates and appropriate Skp1 glycoforms, followed by chromatographic analysis of acid hydrolysates of the reaction products, confirmed the predicted sugar identities as GlcNAc, Gal and Fuc. Disruptions of gnt1 or pgtA resulted in decreased parasite growth. Off target effects were excluded based on restoration of the normal glycan chain and growth upon genetic complementation. By analogy to Dictyostelium Skp1, the mechanism may involve regulation of assembly of the SCF complex. Understanding the mechanism of Toxoplasma Skp1 glycosylation is expected to help develop it as a drug target for control of the pathogen, as the glycosyltransferases are absent from mammalian hosts.
DOI: 10.6084/m9.figshare.5505559
title: Digital-Assets-Webinar_UCWHRE-Turner.pptx

description: Showing one’s impact on their field is a complex and often subjective task. This webinar will introduce some of the more common indicators of impact and various tools that can be used to aid in improving one’s impact.<br>
DOI: 10.6084/m9.figshare.5505856.v2
title: Hair Dye Substance Database (HDSD)

description: Fully 2D-curated database of 313 QSAR-ready hair dye substances available for download as Excel spreadsheet or SDF (structure-data file). Includes information such as substance name, structure, CASRNs, DTXSIDs, classes, color (if applicable), and computed properties. SDF can be opened using chemical drawing software such as ChemDraw Professional or MarvinView. For details regarding database development, analysis, and potential applications, see https://dx.doi.org/10.1021/acssuschemeng.7b03795. <br> We are seeking to improve the HDSD. Please contact Tova N. Williams at tnwilli7@ncsu.edu for suggestions.
DOI: 10.6084/m9.figshare.5505661.v1
title: The E3-ubiquitin ligase adaptor protein Skp1 is glycosylated by an evolutionarily conserved pathway that regulates protist growth and development.pdf

description: Toxoplasma gondii is a protist parasite of warm-blooded animals that causes disease by proliferating intracellularly in muscle and the central nervous system. Previous studies showed that a prolyl 4-hydroxylase related to animal HIFα prolyl hydroxylases is required for optimal parasite proliferation, especially at low O2. We also observed that Pro154 of Skp1, a subunit of the Skp1/Cullin-1/F-box protein (SCF)-class of E3-ubiquitin ligases, is a natural substrate of this enzyme. In an unrelated protist, Dictyostelium discoideum, Skp1 hydroxyproline is modified by 5 sugars via the action of three glycosyltransferases, Gnt1, PgtA and AgtA, which are required for optimal O2-dependent development. We show here that TgSkp1 hydroxyproline is modified by a similar pentasaccharide, based on mass spectrometry, and that assembly of the first three sugars is dependent on Toxoplasma homologs of Gnt1 and PgtA. Reconstitution of the glycosyltransferase reactions in extracts with radioactive sugar nucleotide substrates and appropriate Skp1 glycoforms, followed by chromatographic analysis of acid hydrolysates of the reaction products, confirmed the predicted sugar identities as GlcNAc, Gal and Fuc. Disruptions of gnt1 or pgtA resulted in decreased parasite growth. Off target effects were excluded based on restoration of the normal glycan chain and growth upon genetic complementation. By analogy to Dictyostelium Skp1, the mechanism may involve regulation of assembly of the SCF complex. Understanding the mechanism of Toxoplasma Skp1 glycosylation is expected to help develop it as a drug target for control of the pathogen, as the glycosyltransferases are absent from mammalian hosts.
DOI: 10.6084/m9.figshare.5505406
title: Supplementary Material for: Hemodiafiltration Reduces All-Cause and Cardiovascular Mortality in Incident Hemodialysis Patients: A Propensity-Matched Cohort Study

description: <b><i>Background:</i></b> The majority of studies suggesting that online hemodiafiltration reduces the risk of mortality compared to hemodialysis (HD) have been performed in dialysis-prevalent populations. In this report, we conducted an epidemiologic study of mortality in incident dialysis patients, comparing post-dilution online hemodiafiltration and high-flux HD, with propensity score matching (PSM) used to correct indication bias. <b><i>Methods:</i></b> Our study cohort comprised 3,075 incident dialysis patients treated in 64 Spanish Fresenius Medical Care clinics between January 2009 and December 2012. The primary outcome of this study was to investigate the impact of the type of renal replacement on all-cause mortality. An analysis of cardiovascular mortality was defined as the secondary outcome. To achieve these objectives, patients were followed until December 2016. Patients were categorized as high-flux HD patients if they underwent this treatment exclusively. If &gt;90% of their treatment was with online hemodiafiltration, then the patient was grouped to that modality. <b><i>Results:</i></b> After PSM, a total of 1,012 patients were matched. Compared with patients on high-flux HD, those on online hemodiafiltration received a median replacement volume of 23.45 (interquartile range 21.27–25.51) L/session and manifested 24 and 33% reductions in all-cause and cardiovascular mortality (all-cause mortality hazards ratio [HR] 0.76, 95% CI 0.62–0.94 [<i>p</i> = 0.01]; and cardiovascular mortality HR 0.67, 95% CI 0.50–0.90 [<i>p</i> = 0.008]). <b><i>Conclusions:</i></b> This study shows that post-dilution online hemodiafiltration reduces all-cause and cardiovascular mortality compared to high-flux HD in an incident HD population.
DOI: 10.6084/m9.figshare.5505400
title: Supplementary Material for: Gene Microarray Integrated with High-Throughput Proteomics for the Discovery of Transthyretin in Rhabdomyolysis-Induced Acute Kidney Injury

description: <b><i>Background/Aims:</i></b> Rhabdomyolysis, one of the leading causes of acute kidney injury (AKI), develops after trauma, drug toxicity, infections, burns, and physical exertion. The aim of this study was to investigate differences in gene and protein expression to elucidate the pathogenesis of rhabdomyolysis (RM)-induced AKI. <b><i>Methods:</i></b> In this study, we used glycerol induced renal injury as a model of RM-induced AKI. Affymetrix U133 plus 2.0 microarrays were used to perform gene microarray analysis. Isobaric tagging with related and absolute quantitation (iTRAQ) labeling mass spectrometry (MS) was applied to screen and identify differentially expressed proteins between RM-induced AKI and normal murine renal tissue. Verification experiments included immunohistochemistry (IHC), real-time PCR, Western blotting, and the measurement of ATP and ROS production. HK-2 cells were incubated <i>in vitro</i> with ferrous myoglobin and pcDNA-TTR, followed by assays to detect cell proliferation, ROS and apoptosis. <b><i>Results:</i></b> According to gene microarray and iTRAQ-MS analysis, we screened 17 common elements. After multiple analyses, we selected transthyretin (TTR) as our focus and investigated TTR in the kidney. Verification experiments with IHC confirmed differential expression levels of TTR proteins. Furthermore, Western blotting showed a stepwise decrease in TTR in AKI renal tissues. Cell-based experiments showed that overexpression of TTR could improve HK-2 cell viability and inhibit apoptosis. TTR reduced apoptosis by decreasing the accumulation of reactive oxygen species (ROS). <b><i>Conclusion:</i></b> This study reports a possible mechanism for RM-induced AKI and suggests that reductions in TTR could increase the generation of ROS and induce apoptosis. TTR may be a potentially valuable target for RM-induced AKI.
DOI: 10.17028/rd.lboro.5505364
title: Survey for Study Habits and Attainment in Undergraduate Mathematics: A Social Network Analysis

description: This is the survey used in the research for the associated paper "Study Habits and Attainment in Undergraduate Mathematics: A Social Network Analysis".
DOI: 10.17028/rd.lboro.5505364.v1
title: Survey for Study Habits and Attainment in Undergraduate Mathematics: A Social Network Analysis

description: This is the survey used in the research for the associated paper "Study Habits and Attainment in Undergraduate Mathematics: A Social Network Analysis".
DOI: 10.6084/m9.figshare.5505241
title: Supplementary Material for: Wilms' Tumor Gene 1 (WT1) Peptide Vaccine Therapy for Hematological Malignancies: From CTL Epitope Identification to Recent Progress in Clinical Studies Including a Cure-Oriented Strategy

description: The identification of human Wilms’ tumor gene 1 (WT1) protein-derived cytotoxic T lymphocyte (CTL) epitopes and the in vivo efficacy of WT1 peptide-based immunotherapy in a mouse model were reported in 2000. This successful basic research led to clinical studies of a WT1 peptide vaccine, and a positive impact on clinical response was first demonstrated in 2003 in the form of a reduction in blast cells of vaccine-treated patients with myelodysplastic syndromes (MDS). Since then, data on WT1 peptide vaccine-treated patients with immunological and/or clinical response have been accumulated. MDS and acute myeloid leukemia were the major target diseases to provide proof of concept for the therapeutic potential of the WT1 peptide vaccine. WT1 vaccination-induced clinical responses or usefulness were also shown for chronic myeloid leukemia, multiple myeloma, and acute lymphoblastic leukemia, as well as various types of solid cancers. Non-Hodgkin’s lymphoma and myeloproliferative neoplasms may also be target diseases because of their WT1 expression. Of note, recent clinical studies have demonstrated that patients with hematological malignancies who have minimal residual disease after chemotherapy or allogeneic hematopoietic stem cell transplantation may be cured by WT1 Peptide vaccination. Further enhancement of the efficacy and usefulness of the WT1 peptide vaccine is expected.
DOI: 10.6084/m9.figshare.5505340.v1
title: WeichselbaumLederAnsorge2017

description: Data include: data for the expertise questionnaire, the explicit rating scale, and the implicit association test.<br>
DOI: 10.6084/m9.figshare.5505241.v1
title: Supplementary Material for: Wilms' Tumor Gene 1 (WT1) Peptide Vaccine Therapy for Hematological Malignancies: From CTL Epitope Identification to Recent Progress in Clinical Studies Including a Cure-Oriented Strategy

description: The identification of human Wilms’ tumor gene 1 (WT1) protein-derived cytotoxic T lymphocyte (CTL) epitopes and the in vivo efficacy of WT1 peptide-based immunotherapy in a mouse model were reported in 2000. This successful basic research led to clinical studies of a WT1 peptide vaccine, and a positive impact on clinical response was first demonstrated in 2003 in the form of a reduction in blast cells of vaccine-treated patients with myelodysplastic syndromes (MDS). Since then, data on WT1 peptide vaccine-treated patients with immunological and/or clinical response have been accumulated. MDS and acute myeloid leukemia were the major target diseases to provide proof of concept for the therapeutic potential of the WT1 peptide vaccine. WT1 vaccination-induced clinical responses or usefulness were also shown for chronic myeloid leukemia, multiple myeloma, and acute lymphoblastic leukemia, as well as various types of solid cancers. Non-Hodgkin’s lymphoma and myeloproliferative neoplasms may also be target diseases because of their WT1 expression. Of note, recent clinical studies have demonstrated that patients with hematological malignancies who have minimal residual disease after chemotherapy or allogeneic hematopoietic stem cell transplantation may be cured by WT1 Peptide vaccination. Further enhancement of the efficacy and usefulness of the WT1 peptide vaccine is expected.
DOI: 10.6084/m9.figshare.5505199
title: Bedrock geology of DFDP-2B, central Alpine Fault, New Zealand

description: During the second phase of the Alpine Fault, Deep Fault Drilling Project (DFDP) in the Whataroa River, South Westland, New Zealand, bedrock was encountered in the DFDP-2B borehole from 238.5–893.2 m Measured Depth (MD). Continuous sampling and meso- to microscale characterisation of whole rock cuttings established that, in sequence, the borehole sampled amphibolite facies, Torlesse Composite Terrane-derived schists, protomylonites and mylonites, terminating 200–400 m above an Alpine Fault Principal Slip Zone (PSZ) with a maximum dip of 62°. The most diagnostic structural features of increasing PSZ proximity were the occurrence of shear bands and reduction in mean quartz grain sizes. A change in composition to greater mica:quartz + feldspar, most markedly below c. 700 m MD, is inferred to result from either heterogeneous sampling or a change in lithology related to alteration. Major oxide variations suggest the fault-proximal Alpine Fault alteration zone, as previously defined in DFDP-1 core, was not sampled.
DOI: 10.6084/m9.figshare.5505199.v1
title: Bedrock geology of DFDP-2B, central Alpine Fault, New Zealand

description: During the second phase of the Alpine Fault, Deep Fault Drilling Project (DFDP) in the Whataroa River, South Westland, New Zealand, bedrock was encountered in the DFDP-2B borehole from 238.5–893.2 m Measured Depth (MD). Continuous sampling and meso- to microscale characterisation of whole rock cuttings established that, in sequence, the borehole sampled amphibolite facies, Torlesse Composite Terrane-derived schists, protomylonites and mylonites, terminating 200–400 m above an Alpine Fault Principal Slip Zone (PSZ) with a maximum dip of 62°. The most diagnostic structural features of increasing PSZ proximity were the occurrence of shear bands and reduction in mean quartz grain sizes. A change in composition to greater mica:quartz + feldspar, most markedly below c. 700 m MD, is inferred to result from either heterogeneous sampling or a change in lithology related to alteration. Major oxide variations suggest the fault-proximal Alpine Fault alteration zone, as previously defined in DFDP-1 core, was not sampled.
DOI: 10.6084/m9.figshare.5505088
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This repository provides data generated using a novel internal control as well as data generated using a xenogenic spike-in method.
DOI: 10.6084/m9.figshare.5505088.v1
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This data includes the use of a novel internal control, CTCF binding, to normalise.
DOI: 10.6084/m9.figshare.5505070
title: XRD raw data from Silver–palladium catalysts for the direct synthesis of hydrogen peroxide

description: This contains the raw data for the XRD figures
DOI: 10.6084/m9.figshare.5505070.v1
title: XRD raw data from Silver–palladium catalysts for the direct synthesis of hydrogen peroxide

description: This contains the raw data for the XRD figures
DOI: 10.6084/m9.figshare.5505088.v2
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This data includes the use of a novel internal control, CTCF binding, to normalise.
DOI: 10.6084/m9.figshare.5505067
title: XPS raw data from Silver–palladium catalysts for the direct synthesis of hydrogen peroxide

description: This contains the raw data for the XPS figures
DOI: 10.6084/m9.figshare.5505061
title: TPR raw data from Silver–palladium catalysts for the direct synthesis of hydrogen peroxide

description: This contains the raw data for the TPR figures
DOI: 10.6084/m9.figshare.5505088.v3
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This data includes the use of a novel internal control, CTCF binding, to normalise.
DOI: 10.6084/m9.figshare.5505061.v1
title: TPR raw data from Silver–palladium catalysts for the direct synthesis of hydrogen peroxide

description: This contains the raw data for the TPR figures
DOI: 10.6084/m9.figshare.5505067.v1
title: XPS raw data from Silver–palladium catalysts for the direct synthesis of hydrogen peroxide

description: This contains the raw data for the XPS figures