cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5468680.v1
title: Supplementary Material for: Vitamin D Receptor Activators Upregulate and Rescue Podocalyxin Expression in High Glucose-Treated Human Podocytes

description: <b><i>Background:</i></b> Vitamin D is beneficial in human and experimental chronic kidney disease, the leading cause of which is diabetic nephropathy. Vitamin D through its receptor, VDR, provides renal protection in diabetic nephropathy, but limited data exist about its effect on podocytes. Renal podocytes form the main filtration barrier possessing a unique phenotype maintained by proteins including podocalyxin and nephrin, the expression of which is suppressed in pathological conditions. <b><i>Methods:</i></b> We used immortalized human podocytes (human glomerular epithelial cells, HGEC) to assess podocalyxin and nephrin expression after treatment with 1,25-dihydroxyvitamin D<sub>3</sub> (calcitriol) and its analogue paricalcitol. The involvement of VDR was investigated by silencing with hVDR-siRNA and ChIP analysis. <b><i>Results:</i></b> HGEC exhibit high glucose-mediated downregulation of podocalyxin and nephrin, loss of which has been linked with loss of the permselective renal barrier and proteinuria. Calcitriol and paricalcitol reversed high glucose-induced decrease of nephrin and significantly enhanced podocalyxin expression in podocytes cultured in high glucose. HGEC express VDR and retinoid X receptor (RXR). In the presence of calcitriol and paricalcitol, VDR expression was upregulated and VDR colocalized with RXR in the nucleus. VDR knockdown abolished the protective action of calcitriol and paricalcitol on podocalyxin expression indicating that podocalyxin activation of expression is partly mediated by VDR. Furthermore, VDR specifically regulates podocalyxin expression by bounding to a site upstream of the podocalyxin promoter. <b><i>Conclusion:</i></b> Vitamin D analogues maintain and, furthermore, re-activate the expression of specialized components of podocytes including podocalyxin, hence they provide protection against loss of the permselective renal barrier, with molecular mechanisms elucidated herein.
DOI: 10.6084/m9.figshare.5468683
title: Norfolk Community Health and Care NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5468683.v1
title: Norfolk Community Health and Care NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5468665.v1
title: Supplementary Material for: Fluorescence Imaging of Intracellular Calcium Signals in Intact Kidney Tissue

description: <b><i>Background:</i></b> Intracellular calcium (Ca<sup>2+</sup>) plays an important role in normal renal physiology and in the pathogenesis of various kidney diseases; however, the study of Ca<sup>2+</sup> signals in intact tissue has been limited by technical difficulties, including achieving adequate loading of Ca<sup>2+</sup>-sensitive fluorescent dyes. The kidney slice preparation represents a model whereby three-dimensional tissue architecture is preserved and structures in both the cortex and medulla can be imaged using confocal or multiphoton microscopy. <b><i>Methods:</i></b> Ca<sup>2+</sup>-sensitive dyes Rhod-2, Fura-red and Fluo-4 were loaded into tubular and vascular cells in rat kidney slices using a re-circulating perfusion system and real-time imaging of Ca<sup>2+</sup> signals was recorded by confocal microscopy. Kidney slices were also obtained from transgenic mice expressing the GCaMP2 Ca<sup>2+</sup>-sensor in their endothelial cells and real time Ca<sup>2+</sup> transients stimulated by physiological stimuli. <b><i>Results:</i></b> Wide spread loading of Ca<sup>2+</sup> indicators was achieved in the tubular and vascular structures of both the medulla and cortex. Real time Ca<sup>2+</sup> signals were successfully recorded in different intracellular compartments of both rat and mouse cortical and medullary tubules in response to physiological stimuli (ATP and angiotensin II). Glomerular Ca<sup>2+</sup> transients were similarly recorded in kidney slices taken from the transgenic mouse expressing the GCaMP2 Ca<sup>2+</sup>-sensor. <b><i>Conclusion:</i></b> We present new approaches that can be adopted to image cytosolic and mitochondrial Ca<sup>2+</sup> signals within various cell types in intact kidney tissue. Moreover, techniques described in this study can be used to facilitate future detailed investigations of intracellular Ca<sup>2+</sup> homeostasis in renal health and disease.
DOI: 10.6084/m9.figshare.5468533
title: batch protocol

description: Icy protocol for automatic cell size count<br><br>
DOI: 10.6084/m9.figshare.5468536
title: figure.rar

description: Prolonged culturing in vitro often leads to accumulation of genetic changes in cells. Although human multipotent mesenchymal stromal cells (hMSC) are considered as genetically stable, there is a risk of genomic instability and structural chromosome instability and, therefore, side effects of cell therapy associated with long-term effects. In this study, the karyotype, genetic variability and clone formation analyses have been carried out in the long-term culture MSC from human gingival mucosa.The immunophenotype and STR loci combination did not change during the process of cultivation. From passage 23 the proliferative activity of cultured MSCs was significantly reduced. From passage 12 of cultivation, clones of cells with stable chromosome aberrations have been identified and some of these (12%) are tetrasomy of chromosome 8. The random genetic and structural chromosomal aberrations and the spontaneous level of chromosomal aberrations in the hMSC long-term cultures were also described.
DOI: 10.6084/m9.figshare.5468527
title: Supplementary Material for: Innate Immunity Protein Tag7 Induces 3 Distinct Populations of Cytotoxic Cells That Use Different Mechanisms to Exhibit Their Antitumor Activity on Human Leukocyte Antigen-Deficient Cancer Cells

description: The search for new immune response mechanisms capable of controlling immune-evasive tumor cells devoid of the MHC antigen is a challenging task for immunologists. In this study, we found that the treatment of human peripheral blood lymphocytes with the innate immunity protein Tag7 (PGRP-S, PGLYRP1) induces differentiation of the populations of NK (natural killer) cells and CD8+ and CD4+ T lymphocytes that are cytotoxic for human leukocyte antigen-negative tumor cells. These populations employ different mechanisms of tumor cell lysis (based on the release of granzymes in the case of NK cells and on the FasL-Fas interaction in the case of CD8+ and CD4+ T lymphocytes) and induce different death pathways (apoptosis or necroptosis) in tumor cells. An analysis of genes activated in leukocyte populations after Tag7 treatment and experiments with specific inhibitors have shown that the TREM-1 receptor expressed on the monocyte cell surface is essential for activation of cytotoxic activity. Overall, the results of this study provide evidence for a novel role of the Tag7 protein in the immune response.
DOI: 10.6084/m9.figshare.5468527.v1
title: Supplementary Material for: Innate Immunity Protein Tag7 Induces 3 Distinct Populations of Cytotoxic Cells That Use Different Mechanisms to Exhibit Their Antitumor Activity on Human Leukocyte Antigen-Deficient Cancer Cells

description: The search for new immune response mechanisms capable of controlling immune-evasive tumor cells devoid of the MHC antigen is a challenging task for immunologists. In this study, we found that the treatment of human peripheral blood lymphocytes with the innate immunity protein Tag7 (PGRP-S, PGLYRP1) induces differentiation of the populations of NK (natural killer) cells and CD8+ and CD4+ T lymphocytes that are cytotoxic for human leukocyte antigen-negative tumor cells. These populations employ different mechanisms of tumor cell lysis (based on the release of granzymes in the case of NK cells and on the FasL-Fas interaction in the case of CD8+ and CD4+ T lymphocytes) and induce different death pathways (apoptosis or necroptosis) in tumor cells. An analysis of genes activated in leukocyte populations after Tag7 treatment and experiments with specific inhibitors have shown that the TREM-1 receptor expressed on the monocyte cell surface is essential for activation of cytotoxic activity. Overall, the results of this study provide evidence for a novel role of the Tag7 protein in the immune response.
DOI: 10.6084/m9.figshare.5468533.v2
title: batch protocol

description: Icy protocol for automatic cell size count<br><br>
DOI: 10.17045/sthlmuni.5468455
title: Open data for "Electrocortical N400 effects of semantic satiation" by Kim Ströberg, Lau M. Andersen, and Stefan Wiens

description: Contains the open data for "Electrocortical N400 Effects of Semantic Satiation" by Ströberg, Andersen, and Wiens (2017, Frontiers in Psychology)<br>NBS_Presentation.zip contains the scripts to run the experiment in Presentation. https://www.neurobs.com/ The folder also contains the logfiles of the behavioral data.<br><br>rawdata_bdf_*.zip contain the raw eeg data files (*.bdf) that were recorded with a biosemi system (www.biosemi.com). The files can be opened in matlab with the fieldtrip toolbox. http://www.fieldtriptoolbox.org/. https://doi.org/10.1155/2011/156869<br>fieldtrip_final_data_files.zip contains the preprocessed individual data files. They were generated with the fieldtrip toolbox in matlab. http://www.fieldtriptoolbox.org/, https://doi.org/10.1155/2011/156869<br>fieldtrip.zip contains all the matlab scripts that were used to process the ERP data with the toolbox fieldtrip. http://www.fieldtriptoolbox.org/, https://doi.org/10.1155/2011/156869. It also contains the r-scripts that were used to compute Bayes Factors. The r-files can be run with r (https://www.r-project.org/). Some files were generated with Aladins r scripts (https://doi.org/10.17045/sthlmuni.4981154). The folder also contains the main output files (csv, mat, tiff).
DOI: 10.17045/sthlmuni.5468455.v1
title: Open data for Electrocortical N400 Effects of Semantic Satiation

description: Contains the open data for "Electrocortical N400 Effects of Semantic Satiation" by Ströberg, Andersen, and Wiens (2017, Frontiers in Psychology)
DOI: 10.6084/m9.figshare.5467990
title: Victorian ornithopod NMV P221080: CT data of pes and tail

description: Raw DICOM data from CT scans of partial ornithopod postcranium, NMV P221080, from the Early Albian of Australia: data set 1, anterior region of tail and right distal crus, tarsus and pes; data set 2, remaining portion of the tail.<br>
DOI: 10.6084/m9.figshare.5467627
title: Fish encephalization figures

description: Figures representing relative average encephalization of different families of marine fishes. Encephalization was calculated as the residual from a log-log regression of brain mass on body mass. Data for these calculations was obtained from a combination of FishBase, peer-reviewed scientific papers, and new collections.
DOI: 10.6084/m9.figshare.5467627.v1
title: Fish encephalization figures

description: Figures representing relative average encephalization of different families of marine fishes. Encephalization was calculated as the residual from a log-log regression of brain mass on body mass. Data for these calculations was obtained from a combination of FishBase, peer-reviewed scientific papers, and new collections.
DOI: 10.5517/ccdc.csd.cc24sgt7
title: CCDC 1989729: Experimental Crystal Structure Determination

description: Related Article: Darko Vušak, Jelena Pejić, Mia Jurković, Gábor Szalontai, Jasmina Sabolović|2020|CrystEngComm|22|5587|doi:10.1039/D0CE00585A
DOI: 10.5517/ccdc.csd.cc259jrs
title: CCDC 2005165: Experimental Crystal Structure Determination

description: Related Article: Seulgi Kim, In-Hyeok Park, Shim Sung Lee, Wonbo Sim, Jai Young Lee|2020|CrystEngComm|22|5601|doi:10.1039/D0CE00864H
DOI: 10.5517/ccdc.csd.cc259jst
title: CCDC 2005166: Experimental Crystal Structure Determination

description: Related Article: Seulgi Kim, In-Hyeok Park, Shim Sung Lee, Wonbo Sim, Jai Young Lee|2020|CrystEngComm|22|5601|doi:10.1039/D0CE00864H
DOI: 10.5517/ccdc.csd.cc259jtv
title: CCDC 2005167: Experimental Crystal Structure Determination

description: Related Article: Seulgi Kim, In-Hyeok Park, Shim Sung Lee, Wonbo Sim, Jai Young Lee|2020|CrystEngComm|22|5601|doi:10.1039/D0CE00864H
DOI: 10.6084/m9.figshare.5467180.v2
title: Escarabajos Passalidae (Scarabaeoidea) del Perú

description: Especies de la familia Passalidae (Coleoptera: Scarabaeoidea) en el Perú, con base en recopilación bibliografica
DOI: 10.6084/m9.figshare.5467027
title: Porphyra umbilicalis Differential Expression database

description: The output from CLC workbench for the differential expression of genes/contigs from three libraries of Porphyra umbilicalis. The three libraries include: Fort Stark genotype 193 (FS193), Fort Stark genotype 211 (FS211), and Dover Point 193 (DP193). Genotypes from: Eriksen RL et al. Bot Mar. 2016;59(1):1-12.
DOI: 10.6084/m9.figshare.5467033
title: Effect of iron supplementation -- biom table

description: The biom table was generated using Qiime 1.8.0 using uclust reference based OTU picking against greengene database (gg_13_8). <br>otu_table_filtered.biom was filtered from the biom table by the following script:<br><i>filter_otus_from_otu_table.py -i otu_table.biom -o otu_table_filtered.biom -n 10 -s 2</i><br><br>n= The minimum total observation count of an otu for that otu to be retained,s = The minimum number of samples an OTU must be observed in for that otu to be retained<br>
DOI: 10.6084/m9.figshare.5467018
title: Effect of iron supplementation -- mapping file

description: Annotation on the mapping file:<br><br>Dietary treatment: control group (normal) and growth restricted (growth_restricted); <br>Iron supplementation: 0 ug/d iron, 30 ug/d iron and 150 ug/d iron daily.<br>Date: postnatal date 20 (PD20) and postnatal date 56 (PD56).
DOI: 10.6084/m9.figshare.5467027.v1
title: Porphyra umbilicalis Differential Expression database

description: The output from CLC workbench for the differential expression of genes/contigs from three libraries of Porphyra umbilicalis. The three libraries include: Fort Stark genotype 193 (FS193), Fort Stark genotype 211 (FS211), and Dover Point 193 (DP193). Genotypes from: Eriksen RL et al. Bot Mar. 2016;59(1):1-12.
DOI: 10.6084/m9.figshare.5467033.v1
title: Biom table

description: The biom table was generated using Qiime 1.8.0 using uclust reference based OTU picking against greengene database (gg_13_8). <br>otu_table_filtered.biom was filtered from the biom table by the following script:<br><i>filter_otus_from_otu_table.py -i otu_table.biom -o otu_table_filtered.biom -n 10 -s 2</i><br><br>n= The minimum total observation count of an otu for that otu to be retained,s = The minimum number of samples an OTU must be observed in for that otu to be retained<br>
DOI: 10.6084/m9.figshare.5467018.v2
title: Effect of iron supplementation -- mapping file

description: Annotation on the mapping file:<br><br>Dietary treatment: control group (normal) and growth restricted (growth_restricted); <br>Iron supplementation: 0 ug/d iron, 30 ug/d iron and 150 ug/d iron daily.<br>Date: postnatal date 20 (PD20) and postnatal date 56 (PD56).
DOI: 10.6084/m9.figshare.5467018.v1
title: Mapping file

description: Annotation on the mapping file:<br><br>Dietary treatment: control group (normal) and growth restricted (growth_restricted); <br>Iron supplementation: 0 ug/d iron, 30 ug/d iron and 150 ug/d iron daily.<br>Date: postnatal date 20 (PD20) and postnatal date 56 (PD56).
DOI: 10.6084/m9.figshare.5466895
title: Effect of iron supplementation -- forward reads (after demultiplexing)

description: This is the output after demultiplexing (qiime script: <i>split_libraries_fastq.py</i>).<br>Parameter used: <i>--barcode_type hamming_8 --max_barcode_errors 0</i>
DOI: 10.6084/m9.figshare.5466895.v2
title: Effect of iron supplementation -- forward reads (after demultiplexing)

description: This is the output after demultiplexing (qiime script: <i>split_libraries_fastq.py</i>).<br>Parameter used: <i>--barcode_type hamming_8 --max_barcode_errors 0</i>
DOI: 10.6084/m9.figshare.5466895.v1
title: Forward reads (after demultiplexing)

description: This is the output after demultiplexing (qiime script: <i>split_libraries_fastq.py</i>).<br>Parameter used: <i>--barcode_type hamming_8 --max_barcode_errors 0</i>
DOI: 10.6084/m9.figshare.5466838.v1
title: Lewis Frieman 2015 Bake Rings Rpt 3.pdf

description: <em>A Geophysical Survey of Bake Rings Enclosure, Pelynt, Cornwall</em><br>Lewis, J. & Frieman, C.J<br>Southeast Kernow Archaeological Survey Report No. 3
DOI: 10.24378/exe.1863
title: Implementing the branch-and-cut approach for a general purpose Benders’ decomposition framework - Computational results

description: Benders’ decomposition is a popular mathematical and constraint programming algorithm that is widely applied to exploit structure in mathematical and constraint programs arising from real-world applications. While useful for exploiting structure in mathematical and constraint programs, the use of Benders’ decomposition typically requires significant implementation effort to achieve an effective solution algorithm. Traditionally, Benders’ decomposition has been viewed as a problem specific algorithm, which has limited the development of general purpose algorithms and software solutions. This paper presents a general purpose Benders’ decomosition algorithm that is capable of handling many classes of mathematical and constraint prgrams and provides extensive flexibility in the implementation and use of this algorithm. A branch-and-cut approach for Benders’ decomposition has been implemented within the constraint integer programming solver SCIP using a plugin-based design to allow for a wide variety of extensions and customisations to the algorithm. The effectiveness of the Benders’ decomposition algorithm and available enhancement techniques is assessed in a comprehensive computational study.
description: Computational results from solving various instance using the Benders' decomposition framework within SCIP.
DOI: 10.17608/k6.auckland.5466595
title: The attributes of high achieving secondary school students and their teachers

description: This Excel spreadsheet contains a qualitative set of data collected from a questionnaire administered to 583 secondary school students across New Zealand in 2016. Students were surveyed about their perceptions of the attributes of academically successful students and their best and worst secondary school teachers. Demographic data were also collected which included (age, sex, ethnicity, parent education).<br><br>
DOI: 10.6084/m9.figshare.5466574
title: CeMEE supplementary data

description: See data_documentation for details.
DOI: 10.6084/m9.figshare.5466574.v1
title: CeMEE supplementary data

description: See data_documentation for details.
DOI: 10.6084/m9.figshare.5466556
title: Sum of residuals squared - VZV model

description: This file contains sums of residuals squared used to determine scenario selection in VZV model calibration and experimentation. It accompanies the scientific paper entitled "Evaluation of the effect of chickenpox vaccination on shingles epidemiology using agent-based modeling"
DOI: 10.17608/k6.auckland.5466595.v1
title: The attributes of high achieving secondary school students and their teachers dataset.xlsx

description: This Excel spreadsheet contains a qualitative set of data collected from a questionnaire administered to 583 secondary school students across New Zealand in 2016. Students were surveyed about their perceptions of the attributes of academically successful students and their best and worst secondary school teachers. Demographic data were also collected which included (age, sex, ethnicity, parent education).<br><br>
DOI: 10.6084/m9.figshare.5466556.v1
title: Sum of residuals squared - VZV model

description: This file contains sums of residuals squared used to determine scenario selection in VZV model calibration and experimentation. It accompanies the scientific paper entitled "Evaluation of the effect of chickenpox vaccination on shingles epidemiology using agent-based modeling"
DOI: 10.6084/m9.figshare.5466487
title: Infant rhesus monkey -- stool microbiome -- reverse reads (16s V4)

description: This reverse read sequence does contain data from other studies. Please use the mapping file for demultiplexing.
DOI: 10.15161/oar.it/30659
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.6084/m9.figshare.5466355
title: RatHeadFixRestraintSystem

description: Dimensions of head holder, arms, and restraint frames for headfix behavioral experiments with rats.<br>Files with .stl extension are for 3D printing with for example Form lab 2 of Formlabs.<br>Files with .rsdoc extension are for 3D CAD with the DesignSpark Mecanical software.<br>Files with .vsdx extension are for MS Visio software.
DOI: 10.6084/m9.figshare.5466487.v2
title: Infant rhesus monkey -- stool microbiome -- reverse reads (16s V4)

description: This reverse read sequence does contain data from other studies. Please use the mapping file for demultiplexing.
DOI: 10.6084/m9.figshare.5466355.v1
title: RatHeadFixRestraintSystem

description: Dimensions of head holder, arms, and restraint frames for headfix behavioral experiments with rats.<br>Files with .stl extension are for 3D printing with for example Form lab 2 of Formlabs.<br>Files with .rsdoc extension are for 3D CAD with the DesignSpark Mecanical software.<br>Files with .vsdx extension are for MS Visio software.
DOI: 10.6084/m9.figshare.5466487.v1
title: Infant rhesus monkey -- stool microbiome -- Reverse reads (16s V4)

description: This reverse read sequence does contain data from other studies. Please use the mapping file for demultiplexing.
DOI: 10.6084/m9.figshare.5465029
title: Percentage change in limb length

description: Percentage change in limb length from week 0 to week 12 by experimental group
DOI: 10.6084/m9.figshare.5466331
title: From patches to richness: Assessing the potential impact of landscape transformation on biodiversity - Dataset and codes

description: Eight Tropical Andean biomes described as their patch sizes and distance between them. The associated codes allow to estimate different fragmentation metrics and to explore the effect of turnover on regional species richness for each biome (Arnillas et al. <i>in press</i>).<br>Each biome map used to produce these tables has been obtained from Tovar et al. (2013, http://dx.doi.org/10.1371/journal.pone.0063634).<br>Codes also available in: https://github.com/carlos-arnillas/fragmentation-ecosphere2017<br><br><br>
DOI: 10.6084/m9.figshare.5465029.v1
title: Percentage change in limb length

description: Percentage change in limb length from week 0 to week 12 by experimental group
DOI: 10.6084/m9.figshare.5466331.v1
title: From patches to richness: Assessing the potential impact of landscape transformation on biodiversity - Dataset and codes

description: Eight Tropical Andean biomes described as their patch sizes and distance between them. The associated codes allow to estimate different fragmentation metrics and to explore the effect of turnover on regional species richness for each biome (Arnillas et al. <i>in press</i>).<br>Each biome map used to produce these tables has been obtained from Tovar et al. (2013, http://dx.doi.org/10.1371/journal.pone.0063634).<br>Codes also available in: https://github.com/carlos-arnillas/fragmentation-ecosphere2017<br><br><br>