cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5302957.v1
title: Proteomic analysis of protein phosphatase Z1 from Candida albicans

description: The project contains the raw data of a 2D electrophoresis experiment aiming to elucidate the role of CaPpZ1. Three biological replicates (numbered 1-3) of control (ctl) and PpZ1 KO (mut) Candida albicans samples were subjected to two dimensional electrophoresis. The gels were stained first by phosphoprotein-sensitive Pro-Q Diamond (denoted as p) scanned and then stained again with RuBPS (denoted as r) staining all the proteins. The gel images were recorded in all cases and subjected to image analysis using Delta2D (Decodon). The quantity table contains the values calculated by the software for Pro-Q Diamond and RuBPS-stained gels, respectively.<br>Control gel images:<br> Pro-Q Diamond stained gels: ctl1_p.jpg, ctl2_p.jpg, ctl3_p.jpg<br> RuBPS stained gels: ctl1_r.jpg, ctl2_r.jpg, ctl3_r.jpg<br>CaPpz1 KO gel images: Pro-Q Diamond stained gels: mut1_p.jpg, mut2_p.jpg, mut3_p.jpgRuBPS stained gels: mut1_r.jpg, mut2_r.jpg, mut3_r.jpgAnalysis results: quantity_table.xls<br>
DOI: 10.6084/m9.figshare.5302915
title: The cancer/testis-antigen PRAME supports the pluripotency network and represses somatic and germ cell differentiation programs in seminomas

description: Background: Cancer/testis-antigens (CTAs) are specifically expressed in human malignancies and testis tissue, but their molecular functions are poorly understood. CTAs serve as regulators of gene expression, cell cycle and spermatogenesis, as well as targets for immune-based therapies. The CTA PRAME is expressed in various cancers, antagonises retinoic acid signalling and is regulated by DNA methylation and histone acetylation.Methods: We analysed the molecular function of the CTA PRAME in primordial germ cells (PGC) and testicular germ cell cancers (GCC). GCCs arise from a common precursor lesion termed germ cell neoplasia in situ (GCNIS), which itself is thought to originate from a defective PGC. GCNIS cells eventually develop into unipotent seminomas or totipotent embryonal carcinomas (ECs), which are capable of differentiation into teratomas, yolk-sac tumours and choriocarcinomas. Results: PRAME is, like the master regulator of PGCs SOX17 expressed in human PGCs, GCNIS and seminomas but absent in ECs. shRNA-mediated knockdown of PRAME in seminomatous TCam-2 cells left SOX17 levels unchanged, but resulted in downregulation of pluripotency- and PGC-related genes (LIN28, PRDM14, ZSCAN10), whereas somatic and germ cell differentiation markers were upregulated. So, PRAME seems to act downstream of SOX17 by mediating the regulation of the germ cell differentiation and pluripotency programme. Endoderm differentiation is triggered in somatic cells by SOX17, suggesting that in PGCs, PRAME represses this programme and modulates SOX17 to function as a PGC-master regulator. Surprisingly, knockdown of PRAME in TCam-2 cells did not render the cells sensitive towards retinoic acid, despite the fact that PRAME has been described to antagonise retinoic acid signalling. Finally, we demonstrate that in non-seminomas PRAME expression is silenced by DNA methylation, which can be activated by formation of euchromatin via histone-deacetylase-inhibitors.Conclusions: We identified the CTA PRAME as a downstream factor of SOX17 and LIN28 in regulating pluripotency and suppressing somatic/germ cell differentiation in PGC, GCNIS and seminomas.<br>
DOI: 10.6084/m9.figshare.5302963.v2
title: Icelandic horses

description: Phenotypes and genotypes for Icelandic horses
DOI: 10.6084/m9.figshare.5302915.v1
title: The cancer/testis-antigen PRAME supports the pluripotency network and represses somatic and germ cell differentiation programs in seminomas

description: Background: Cancer/testis-antigens (CTAs) are specifically expressed in human malignancies and testis tissue, but their molecular functions are poorly understood. CTAs serve as regulators of gene expression, cell cycle and spermatogenesis, as well as targets for immune-based therapies. The CTA PRAME is expressed in various cancers, antagonises retinoic acid signalling and is regulated by DNA methylation and histone acetylation.Methods: We analysed the molecular function of the CTA PRAME in primordial germ cells (PGC) and testicular germ cell cancers (GCC). GCCs arise from a common precursor lesion termed germ cell neoplasia in situ (GCNIS), which itself is thought to originate from a defective PGC. GCNIS cells eventually develop into unipotent seminomas or totipotent embryonal carcinomas (ECs), which are capable of differentiation into teratomas, yolk-sac tumours and choriocarcinomas. Results: PRAME is, like the master regulator of PGCs SOX17 expressed in human PGCs, GCNIS and seminomas but absent in ECs. shRNA-mediated knockdown of PRAME in seminomatous TCam-2 cells left SOX17 levels unchanged, but resulted in downregulation of pluripotency- and PGC-related genes (LIN28, PRDM14, ZSCAN10), whereas somatic and germ cell differentiation markers were upregulated. So, PRAME seems to act downstream of SOX17 by mediating the regulation of the germ cell differentiation and pluripotency programme. Endoderm differentiation is triggered in somatic cells by SOX17, suggesting that in PGCs, PRAME represses this programme and modulates SOX17 to function as a PGC-master regulator. Surprisingly, knockdown of PRAME in TCam-2 cells did not render the cells sensitive towards retinoic acid, despite the fact that PRAME has been described to antagonise retinoic acid signalling. Finally, we demonstrate that in non-seminomas PRAME expression is silenced by DNA methylation, which can be activated by formation of euchromatin via histone-deacetylase-inhibitors.Conclusions: We identified the CTA PRAME as a downstream factor of SOX17 and LIN28 in regulating pluripotency and suppressing somatic/germ cell differentiation in PGC, GCNIS and seminomas.<br>
DOI: 10.6084/m9.figshare.5302963.v1
title: Icelandic horses

description: Phenotypes and genotypes for Icelandic horses
DOI: 10.6084/m9.figshare.5302831
title: Somatosensory Focused Balance Training without cues can improve balance and gait in early Parkinson’s disease – a randomised pilot study

description: <b>Purpose:</b> To study the effect of Somatosensory Focused Balance Training without Cues, on gait and balance in people with early Parkinson’s disease. <b>Materials and methods:</b> This was a randomised pilot study. Twenty-eight community-dwelling people with early Parkinson’s disease were randomised to immediate or delayed start of a 8w-group training in a community fitness location. Outcomes were measured at preintervention and postintervention. In addition, the early start group performed a 6-month follow up. Clinical outcome measures included: Berg Balance Scale (BBS), BDL Balance Scale, Timed Up and Go, 10 m walk test and the motor part of Unified Parkinson’s disease Rating Scale. Nonparametric statistics was used for analysis. <b>Results:</b> Twenty-two participants (10 men, 12 female) were analysed (median age 69, Hoehn & Yahr 2.0). The participants improved significantly in performance of BBS (<i>p</i> = .007), BDL Balance Scale (<i>p</i> = .005), 10 m walk (<i>p</i> = .012) and mUPDRS (<i>p</i> = .027). At follow up, the improvement had declined. The small sample size restricts generalisability of the results. <b>Conclusions:</b> The intervention showed positive effects on balance, gait and mUPDRS, suggesting that this specific approach should be further explored as a rehabilitation method to delay balance decline in people in the early stages of Parkinson’s disease.
DOI: 10.6084/m9.figshare.5302831.v1
title: Somatosensory Focused Balance Training without cues can improve balance and gait in early Parkinson’s disease – a randomised pilot study

description: <b>Purpose:</b> To study the effect of Somatosensory Focused Balance Training without Cues, on gait and balance in people with early Parkinson’s disease. <b>Materials and methods:</b> This was a randomised pilot study. Twenty-eight community-dwelling people with early Parkinson’s disease were randomised to immediate or delayed start of a 8w-group training in a community fitness location. Outcomes were measured at preintervention and postintervention. In addition, the early start group performed a 6-month follow up. Clinical outcome measures included: Berg Balance Scale (BBS), BDL Balance Scale, Timed Up and Go, 10 m walk test and the motor part of Unified Parkinson’s disease Rating Scale. Nonparametric statistics was used for analysis. <b>Results:</b> Twenty-two participants (10 men, 12 female) were analysed (median age 69, Hoehn & Yahr 2.0). The participants improved significantly in performance of BBS (<i>p</i> = .007), BDL Balance Scale (<i>p</i> = .005), 10 m walk (<i>p</i> = .012) and mUPDRS (<i>p</i> = .027). At follow up, the improvement had declined. The small sample size restricts generalisability of the results. <b>Conclusions:</b> The intervention showed positive effects on balance, gait and mUPDRS, suggesting that this specific approach should be further explored as a rehabilitation method to delay balance decline in people in the early stages of Parkinson’s disease.
DOI: 10.6084/m9.figshare.5302801.v1
title: Molecular dynamics studies on the domain swapped <i>Salmonella typhimurium</i> survival protein SurE: insights on the possible reasons for catalytic cooperativity

description: Stationary phase survival protein SurE from <i>Salmonella typhimurium</i> is a dimeric protein formed by the swapping of a tetramerization loop involved in the formation of a loose tetramer and a C-terminal helix. It functions as a phosphatase. The two-fold symmetry of the dimeric protein was lost in the mutants H234A and D230A/H234A in which a crucial hydrogen bond in the hinge involved in C-terminal helix swapping was eliminated. The catalytic activity of both mutants was drastically reduced. In contrast to the native protein, H234A exhibited positive cooperativity in its catalytic activity. In order to relate these observations to the dynamics of the native and distorted mutants, molecular dynamics (MD) simulations were carried out using GROMACS v4.0.7. In all the simulations, the swapped segments and a segment near the active site were found to be highly flexible. These segments exhibited distinct dynamic features in the two protomers (A and B) of the dimeric protein. The dimeric organization was more significantly affected in the mutants when compared to the native structure, suggesting that the mutations enhance the intrinsic flexibility of the protein. The larger flexibility of the mutants affects the relative movement between the loops near the two active sites. The positive cooperativity observed in H234A mutant is most likely due to this increased flexibility and loop movement.
DOI: 10.6084/m9.figshare.5302222
title: Classifying dermoscopic patterns of naevi in a case-control study of melanoma

description: This dataset contains the underlying data for our study comparing different classification systems for dermscopic patterns of naevi. It does not include image files in order to preserve participant privacy, as set out by the Human Research Ethics Committees of Princess Alexandra Hospital and The University of Queensland. Image files may be accessible to other research groups by arrangement with the corresponding author or the Metro South HREC Office (Ph: +61 7 3443 8049; email: EthicsResearch.PAH@health.qld.gov.au). <br>
DOI: 10.6084/m9.figshare.5302204
title: Patellofemoral Kinematic Characteristics in Anterior Cruciate Ligament Deficiency and Reconstruction

description: The dataset uploaded is supporting our result section in our manuscript.
DOI: 10.6084/m9.figshare.5302222.v1
title: Classifying dermoscopic patterns of naevi in a case-control study of melanoma

description: This dataset contains the underlying data for our study comparing different classification systems for dermscopic patterns of naevi. It does not include image files in order to preserve participant privacy, as set out by the Human Research Ethics Committees of Princess Alexandra Hospital and The University of Queensland. Image files may be accessible to other research groups by arrangement with the corresponding author or the Metro South HREC Office (Ph: +61 7 3443 8049; email: EthicsResearch.PAH@health.qld.gov.au). <br>
DOI: 10.6084/m9.figshare.5302201
title: California, amended death certificate no. 0190-047501 (1982), Bonita Williams

description: California, amended death certificate no. 0190-047501 (1982), Bonita Williams
DOI: 10.6084/m9.figshare.5302204.v1
title: Patellofemoral Kinematic Characteristics in Anterior Cruciate Ligament Deficiency and Reconstruction

description: The dataset uploaded is supporting our result section in our manuscript.
DOI: 10.6084/m9.figshare.5302141
title: Data for volatile organic compounds, amino acids and metals for multivariate analysis.xlsx

description: Quantitative profiles of metabolites (Volatile organic compounds (VOC), amino acids, minerals in earwax samples of heathy non-pregnant ewes (9 samples), healthy pregnant ewes (6 samples) and healthy lactating ewes (13 samples). These data were used for multivariate analysis by applying robust principal component analysis (RPCA) and hieraarchical cluster analysis (HCA) for discrimination between the three groups through the difference in quantitative profiles of metabolites in earwax samples obtained from the three groups.
DOI: 10.6084/m9.figshare.5302141.v1
title: Data for volatile organic compounds, amino acids and metals for multivariate analysis.xlsx

description: Quantitative profiles of metabolites (Volatile organic compounds (VOC), amino acids, minerals in earwax samples of heathy non-pregnant ewes (9 samples), healthy pregnant ewes (6 samples) and healthy lactating ewes (13 samples). These data were used for multivariate analysis by applying robust principal component analysis (RPCA) and hieraarchical cluster analysis (HCA) for discrimination between the three groups through the difference in quantitative profiles of metabolites in earwax samples obtained from the three groups.
DOI: 10.6084/m9.figshare.5298121
title: zebrafish ribosomal RNA genomic sequences

description: A subset of genomic DNA sequences of the zebrafish ribosomal RNA genes. Also included is a .sizes file, that contains the sequence names and lengths needed for use with bedtools.
DOI: 10.6084/m9.figshare.5301730
title: Costa-Paiva_HcM_pep

description: Alignment of HcM sequences
DOI: 10.6084/m9.figshare.5301754
title: Crumley_Sproles_ESIP_Final_220dpi.pdf

description: Results from ESIP Lab competition.
DOI: 10.6084/m9.figshare.5301691
title: Costa-Paiva_HcA_pep

description: Alignment of HcA sequences
DOI: 10.6084/m9.figshare.5301730.v1
title: Costa-Paiva_HcM_pep

description: Alignment of HcM sequences
DOI: 10.6084/m9.figshare.5301691.v1
title: Costa-Paiva_HcA_pep

description: Alignment of HcA sequences
DOI: 10.6084/m9.figshare.5301754.v1
title: Crumley_Sproles_ESIP_Final_220dpi.pdf

description: Results from ESIP Lab competition.
DOI: 10.6084/m9.figshare.5297833
title: DavidFaecal_Ananke.h5

description: HDF5 file for use with Ananke-UI (https://github.com/beiko-lab/ananke-ui). Contains time-series clusters of 16S rRNA gene abundances from faecal samples taken almost daily for one year, as well as taxonomic classifications and sequence identity-based clusters.
DOI: 10.6084/m9.figshare.5297866
title: 20MeSeq Deduplicated FASTQ Sequences

description: This archive contains gzipped fasta files that contain the deduplicated fastq sequences from the other 2OMeSeq datasets hosted in this collection.
DOI: 10.6084/m9.figshare.5298121.v2
title: zebrafish ribosomal RNA genomic sequences

description: A subset of genomic DNA sequences of the zebrafish ribosomal RNA genes. Also included is a .sizes file, that contains the sequence names and lengths needed for use with bedtools.
DOI: 10.6084/m9.figshare.5297797
title: <i>Cedrus atlantica</i> pollen morphology and investigation of grain size variability using laser diffraction granulometry

description: The morphology and size variability of pollen grains of <i>Cedrus atlantica</i> were investigated using a novel approach employing laser diffraction granulometry. We provide new insights into size variability and present high-quality light microscopy (LM) and scanning electron microscopy (SEM) imagery of <i>Cedrus atlantica</i> pollen. Grains have an average size of 59.1 ± 4.0 µm, measured on millions of grains from 91 samples. Analysis showed there is high variability of grain size within individual samples, although variability between samples is not significant. We found no significant relationships between grain size and climate (including temperature, precipitation and aridity), and suggest that grain size of fossil <i>Cedrus</i> pollen would not be a good proxy for climate reconstruction. Grain size may be influenced by a number of complex factors such as genome size or adaptations to support wind pollination, while variability within individual samples may result from the irregular development of pollen. The laser diffraction method produced repeatable, robust measurements on millions of pollen grains which are highly correlated with measurements taken using LM (<i>r</i> = 0.91, p = 0.002). Where grain size information is crucial for pollen identification, for developing isolation techniques for geochemical analysis, for investigating climatic and environmental influence, or for investigating links between genomes and grain size, particle size analysis by laser diffraction provides a reproducible and robust method for quickly determining pollen grain size on many samples.
DOI: 10.6084/m9.figshare.5297833.v1
title: DavidFaecal_Ananke.h5

description: HDF5 file for use with Ananke-UI (https://github.com/beiko-lab/ananke-ui). Contains time-series clusters of 16S rRNA gene abundances from faecal samples taken almost daily for one year, as well as taxonomic classifications and sequence identity-based clusters.
DOI: 10.6084/m9.figshare.5297866.v1
title: 20MeSeq Deduplicated FASTQ Sequences

description: This archive contains gzipped fasta files that contain the deduplicated fastq sequences from the other 2OMeSeq datasets hosted in this collection.
DOI: 10.6084/m9.figshare.5297758
title: Bird Use of Organic Apple Orchards in Colorado

description: We examined bird use of organic apple orchards as well as how birds influence fruit production positively through control of an economically important insect pest (codling moth (<i>Cydia pomonella</i>)) and negatively through fruit damage. We conducted transect surveys, observed bird frugivory and assessed bird and insect damage with an exclosure experiment. We found that organic apple orchards in our study region provide habitat for a large number of both human-adapted and human-sensitive species and that the species in orchards were relatively similar to adjacent hedgerow habitats. Habitat use did not vary as a function of orchard characteristics, and apple damage by both birds and <i>C. pomonella</i> was consistent within and across apple blocks that varied in size. A small subset of bird species was observed foraging on apples yet the effect of birds as agents of fruit damage appeared rather minor and birds did not reduce <i>C. pomonella</i> damage.
DOI: 10.6084/m9.figshare.5298121.v1
title: zebrafish ribosomal RNA genomic sequences

description: A subset of genomic DNA sequences of the zebrafish ribosomal RNA genes
DOI: 10.6084/m9.figshare.5297674
title: Stochastic multi-attribute acceptability analysis (SMAA): an application to the ranking of Italian regions

description: We consider the issue of ranking regions with respect to a range of economic and social variables. Departing from the current practice of aggregating different dimensions via a composite index, usually based on an arithmetic mean, we instead use stochastic multi-attribute acceptability analysis (SMAA). SMAA considers the ‘whole space’ of weights for the considered dimensions. The methodology is applied to the ranking of Italian regions, showing that although the north–south divide is definitely wider than the one measured simply in terms of gross domestic product. There are southern regions that perform generally better than those belonging to their broad region: a kind of ‘northern regions within the southern broad region’. This result poses interesting questions about the uneven development of Italian regions.
DOI: 10.6084/m9.figshare.5297677
title: What does PIA stand for

description: List of synonyms and antonyms for "PIA" and terms related to privacy impact assessment. Compiled as part of a systematic review into publicly available privacy impact assessments (PIAs) and data protection impact assessments (DPIAs).<br>Could be of use to others considering bibliographic searches with the abbreviation PIA
DOI: 10.6084/m9.figshare.5297674.v1
title: Stochastic multi-attribute acceptability analysis (SMAA): an application to the ranking of Italian regions

description: We consider the issue of ranking regions with respect to a range of economic and social variables. Departing from the current practice of aggregating different dimensions via a composite index, usually based on an arithmetic mean, we instead use stochastic multi-attribute acceptability analysis (SMAA). SMAA considers the ‘whole space’ of weights for the considered dimensions. The methodology is applied to the ranking of Italian regions, showing that although the north–south divide is definitely wider than the one measured simply in terms of gross domestic product. There are southern regions that perform generally better than those belonging to their broad region: a kind of ‘northern regions within the southern broad region’. This result poses interesting questions about the uneven development of Italian regions.
DOI: 10.6084/m9.figshare.5297677.v1
title: What does PIA stand for

description: List of synonyms and antonyms for "PIA" and terms related to privacy impact assessment. Compiled as part of a systematic review into publicly available privacy impact assessments (PIAs) and data protection impact assessments (DPIAs).<br>Could be of use to others considering bibliographic searches with the abbreviation PIA
DOI: 10.6084/m9.figshare.5297647
title: PSets

description: GDSC: Genomics of Drug Sensitivity in CancerCCLE:Cancer Cell Line Encyclopedia<br>gCSI: genentech Cell Screening InitiativeGRAY: A pharmacogenomic dataset of 70 breast cancer cell line from Joe Gray labUHN: A pharmacogenomic dataset of 84 breast cancer cell line from University Health Network
DOI: 10.6084/m9.figshare.5297656
title: Processing of hybrid wood plastic composite reinforced with short PET fibers

description: Poly(ethylene terephthalate) (PET) fibers (virgin, waste, and mixed) were incorporated in the composite poly(methyl methacrylate) (PMMA)–wood. Hybrid composite panels were prepared by pressure molding. Toluene-2,4-diisocyanate (TDI) and (3-mercaptopropyl)trimethoxysilane (MPTMS) were used as cross-linking bonding agents for modification of wood fibers. Influence of cross-linking bonding agents, structure, and composition of PET fibers was examined by studying thermomechanical properties as well as moisture absorption. Moisture absorption was lower for composites with bonding agents. Mechanical testing revealed that the addition of PET fibers drastically enhances properties of the composites. Covalent and hydrogen bonds formed with the addition of bonding agents have also improved mechanical properties compared to the untreated composites.
DOI: 10.6084/m9.figshare.5297620
title: RAW_DataBlock_by_parameters_all_2018_10_24.mat

description: S. Cinciute, A. Daktariunas, and O. Ruksenas, “Hemodynamic effects of sex and handedness on the Wisconsin Card Sorting Test: the contradiction between neuroimaging and behavioural results” PeerJ [Internet], 2018.<br><br>Data for MATLAB
DOI: 10.6084/m9.figshare.5297647.v1
title: PSets

description: GDSC: Genomics of Drug Sensitivity in CancerCCLE:Cancer Cell Line Encyclopedia<br>gCSI: genentech Cell Screening InitiativeGRAY: A pharmacogenomic dataset of 70 breast cancer cell line from Joe Gray labUHN: A pharmacogenomic dataset of 84 breast cancer cell line from University Health Network