cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4121/18318644.v1
title: Data underlying the publication: Mucosal expression of Ca and P transporters and claudins in the small intestine of broilers is altered by dietary Ca:P in a limestone particle size dependent manner.

description: Effect of limestone particle size and inclusion level on duodenal and jejunal mucosal expression of Ca and P transporters and claudins in broilers was tested in a 2 × 3 factorial arrangement. Two limestone sources, coarse (mean particle size 1062 µm) vs. fine (mean particle size 160 µm), were separated from the same limestone limestone products via sieving. These two limestone sources were then added to a basal diet at three inclusion levels, resulting in Ca/P ratio 0.50, 1.00 and 1.75 in the experimental diets (dietary P content was fixed at 5.5 g/kg in the basal diet). Experimental diets were provided on day 14 onwards, and on day 20 and 21 three birds per replicate pen were randomly selected for collection of duodenal and jejunal mucosa. mRNA expression of Ca- and P-related transporters and claudins in the duodenal and jejunal mucosa were determined on individual bird level using RT-PCR. <br>For more details about the experimental design, please see the paper “Mucosal expression of Ca and P transporters and claudins in the small intestine of broilers is altered by dietary Ca:P in a limestone particle size dependent manner”.<br>
DOI: 10.6084/m9.figshare.11171342
title: Specific induction of the unique GPR15 expression in heterogeneous blood lymphocytes by tobacco smoking

description: <b>Purpose:</b> In the peripheral blood, it has been shown that smoking is, to date, the only specific condition leading to an increase in GPR15+ T cells. We, therefore, aimed to characterize GPR15-expressing blood T cells in more detail. <b>Materials and Methods:</b> The whole transcriptome by RNAseq as a proxy for protein expression was analyzed in GPR15+ and GPR15- T cells. A deep immuno-phenotyping was conducted for the identification of T cell subtypes. <b>Results:</b> The expression of GPR15 seemed to be unique, not concomitantly accompanied with the expression of another protein. According to different T cell subtypes, there is no single cell type prominently represented in GPR15+ T cells. The individually different proportions of GPR15+ cells among each GPR15-expressing T cell subtypes in blood were strongly associated with chronic smoking. Indeed, the frequency of GPR15+ T cell subtypes can be effectively used as a highly convincing biomarker for tobacco smoking. <b>Conclusions:</b> While the chronic smoking-induced enrichment of GPR15+ T cells in blood might indicate a systemic inflammation, by the widespread presence in different T cell subtypes, GPR15 could feature a general impact on maintaining the systemic homeostasis to putatively prevent harm from smoking.
DOI: 10.6084/m9.figshare.11171342.v1
title: Specific induction of the unique GPR15 expression in heterogeneous blood lymphocytes by tobacco smoking

description: <b>Purpose:</b> In the peripheral blood, it has been shown that smoking is, to date, the only specific condition leading to an increase in GPR15+ T cells. We, therefore, aimed to characterize GPR15-expressing blood T cells in more detail. <b>Materials and Methods:</b> The whole transcriptome by RNAseq as a proxy for protein expression was analyzed in GPR15+ and GPR15- T cells. A deep immuno-phenotyping was conducted for the identification of T cell subtypes. <b>Results:</b> The expression of GPR15 seemed to be unique, not concomitantly accompanied with the expression of another protein. According to different T cell subtypes, there is no single cell type prominently represented in GPR15+ T cells. The individually different proportions of GPR15+ cells among each GPR15-expressing T cell subtypes in blood were strongly associated with chronic smoking. Indeed, the frequency of GPR15+ T cell subtypes can be effectively used as a highly convincing biomarker for tobacco smoking. <b>Conclusions:</b> While the chronic smoking-induced enrichment of GPR15+ T cells in blood might indicate a systemic inflammation, by the widespread presence in different T cell subtypes, GPR15 could feature a general impact on maintaining the systemic homeostasis to putatively prevent harm from smoking.
DOI: 10.25403/upresearchdata.21717062
title: Electrochemical characterisation for layered double hydroxide materials synthesized using electrodeposition method

description: The presentation starts with the justification of the study by illustrating the challenges caused by fossil fuels. This is followed by showing the advantages of supercapacitors and the chosen electrode materials which are layered double hydroxides. The data consists of measurements of electrochemical measurements of cobalt nickel-layered double hydroxide composite materials. The figure illustrates how the synthesis of the electrode materials was carried out. Several other results after the characterization of the samples are also shown throughout the presentation. A comparison of the different samples is displayed in form of figures. The Ragone plot is used to compare the performance of the electrode materials and the assembled devices with the ones reported in published work.
DOI: 10.25403/upresearchdata.21717062.v1
title: Electrochemical characterisation for layered double hydroxide materials synthesized using electrodeposition method

description: The presentation starts with the justification of the study by illustrating the challenges caused by fossil fuels. This is followed by showing the advantages of supercapacitors and the chosen electrode materials which are layered double hydroxides. The data consists of measurements of electrochemical measurements of cobalt nickel-layered double hydroxide composite materials. The figure illustrates how the synthesis of the electrode materials was carried out. Several other results after the characterization of the samples are also shown throughout the presentation. A comparison of the different samples is displayed in form of figures. The Ragone plot is used to compare the performance of the electrode materials and the assembled devices with the ones reported in published work.
DOI: 10.6084/m9.figshare.19601583
title: Thus spoke peptides: SARS-CoV-2 spike gene evolved in humans and then shortly in rats while the rest of its genome in horseshoe bats and then in treeshrews

description: SARS-CoV-2 is suspected to be the product of a natural or artificial recombination of two viruses – one adapted to the horseshoe bat and the other, donor of the spike protein gene, adapted to an unknown species. Here we used a new method to search for the original host of the ancestor of the SARS-CoV-2 virus and for the donor of its gene for the spike protein, the molecule responsible for binding to and entering human cells. We computed immunological T-distances (the number of different peptides that are present in the viral proteins but absent in proteins of the host) between 11 species of coronaviruses and 38 representatives of the main mammal clades. Analyses of pentapeptides, the presumed principal targets of T-cell non-self recognition, showed the smallest T-distance of the spike protein of SARS-CoV-2 to humans, while the rest of SARS-CoV-2 proteome to the horseshoe bat. This suggests that the ancestor of SARS-CoV-2 was adapted to bats, but the spike gene donor was adapted to humans. Further analyses suggest that the ancestral coronavirus adapted to bats was shortly passaged in treeshrews, while the donor of the spike gene was shortly passaged in rats before the recombination event.
DOI: 10.6084/m9.figshare.19601583.v1
title: Thus spoke peptides: SARS-CoV-2 spike gene evolved in humans and then shortly in rats while the rest of its genome in horseshoe bats and then in treeshrews

description: SARS-CoV-2 is suspected to be the product of a natural or artificial recombination of two viruses – one adapted to the horseshoe bat and the other, donor of the spike protein gene, adapted to an unknown species. Here we used a new method to search for the original host of the ancestor of the SARS-CoV-2 virus and for the donor of its gene for the spike protein, the molecule responsible for binding to and entering human cells. We computed immunological T-distances (the number of different peptides that are present in the viral proteins but absent in proteins of the host) between 11 species of coronaviruses and 38 representatives of the main mammal clades. Analyses of pentapeptides, the presumed principal targets of T-cell non-self recognition, showed the smallest T-distance of the spike protein of SARS-CoV-2 to humans, while the rest of SARS-CoV-2 proteome to the horseshoe bat. This suggests that the ancestor of SARS-CoV-2 was adapted to bats, but the spike gene donor was adapted to humans. Further analyses suggest that the ancestral coronavirus adapted to bats was shortly passaged in treeshrews, while the donor of the spike gene was shortly passaged in rats before the recombination event.
DOI: 10.6084/m9.figshare.21723824
title: Beauveria bassiana experimental data.xls

description: <em>Beauverfdjndjbewufhusnjcnjbuhfudhfdsfjjjdjdjdj</em> Change of conc Changation with days Change of concentration with days entration with days rious media (i. Change of concentration with days e., water, soil, and cotton leaf surface) at 28 ºC
DOI: 10.26106/m4rv-px10
title: Data from Miniatura 5 fellowship - concept
DOI: 10.34740/kaggle/dsv/4721487
title: Elon Musk Tweets
DOI: 10.34943/f0f2b441-c654-4cd2-8e57-4e95a0479c92
title: Juan de Fuca Strait Acoustic Receiver Deployed 2021-08-07

description: The Vemco VR2W Single-Channel Acoustic Receiver 128570 was deployed on 2021-08-07 at Juan de Fuca Strait. Juan de Fuca Strait is a large body of water that connects the Salish Sea to the Pacific Ocean. This device is a Acoustic Receiver. Acoustic receivers detect and decode transmissions from acoustic tags. Receivers are categorized as passive or active which define how the receivers are used. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.34943/ce71927d-0f5b-47d5-aa1c-185aca463f42
title: Juan de Fuca Strait Acoustic Receiver Deployed 2021-12-17

description: The Vemco VR2W Single-Channel Acoustic Receiver 125024 was deployed on 2021-12-17 at Juan de Fuca Strait. Juan de Fuca Strait is a large body of water that connects the Salish Sea to the Pacific Ocean. This device is a Acoustic Receiver. Acoustic receivers detect and decode transmissions from acoustic tags. Receivers are categorized as passive or active which define how the receivers are used. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.5281/zenodo.7436704
title: Dataset supporting publication: Design Framework and Laboratory Experiments for Helix and Slinky Type Ground Source Heat Exchangers for Retrofitting Projects

description: Dataset supporting publication: “Design Framework and Laboratory Experiments for Helix and Slinky Type Ground Source Heat Exchangers for Retrofitting Projects” (publication available for download: GEOFIT Zenodo). The focus of the experimental work was on shallow spiral geothermal heat exchanger configurations. Real-scale experiments were carried out for vertically oriented spiral collectors (helix) in sand and soil. One objective was to develop a measurement concept in laboratory environment to create a framework for a validated database. This database serves as the basis for further and new development of engineering design tools. To achieve the highest possible data-point density in the observed environment, temperature sensors and a fiber-optic temperature measurement system (DTS) were used. Soil probes were taken in situ before and after the measurements and analyzed at a thermophysical laboratory to determine material properties. The heat flow was controlled by an electric heating cable, which was installed in the form of a spiral-shaped heat exchanger in a 1 m³ container. To guarantee constant boundary conditions, the measurements were carried out in a climate chamber at a defined ambient temperature. The evaluation of the transient response behavior is spatially resolved. The results are coordinate-based temperature points, which describe temperature gradients in all axes of the container over time, which are combined with known soil properties. The collected data was used to develop computational fluid dynamic (CFD) models, which are used to extend the variety of geometry and soil configurations for developing new design tools.
DOI: 10.5281/zenodo.7436705
title: Dataset supporting publication: Design Framework and Laboratory Experiments for Helix and Slinky Type Ground Source Heat Exchangers for Retrofitting Projects

description: Dataset supporting publication: “Design Framework and Laboratory Experiments for Helix and Slinky Type Ground Source Heat Exchangers for Retrofitting Projects” (publication available for download: GEOFIT Zenodo). The focus of the experimental work was on shallow spiral geothermal heat exchanger configurations. Real-scale experiments were carried out for vertically oriented spiral collectors (helix) in sand and soil. One objective was to develop a measurement concept in laboratory environment to create a framework for a validated database. This database serves as the basis for further and new development of engineering design tools. To achieve the highest possible data-point density in the observed environment, temperature sensors and a fiber-optic temperature measurement system (DTS) were used. Soil probes were taken in situ before and after the measurements and analyzed at a thermophysical laboratory to determine material properties. The heat flow was controlled by an electric heating cable, which was installed in the form of a spiral-shaped heat exchanger in a 1 m³ container. To guarantee constant boundary conditions, the measurements were carried out in a climate chamber at a defined ambient temperature. The evaluation of the transient response behavior is spatially resolved. The results are coordinate-based temperature points, which describe temperature gradients in all axes of the container over time, which are combined with known soil properties. The collected data was used to develop computational fluid dynamic (CFD) models, which are used to extend the variety of geometry and soil configurations for developing new design tools.
DOI: 10.5281/zenodo.6761726
title: Supplementary data: "Revealing interactions between HVDC cross-area flows and frequency stability with explainable AI"

description: This repository contains processed data and result files for the paper Revealing interactions between HVDC cross-area flows and frequency stability with explainable AI. The code for producing the processed data and the results is available at github. <strong>Data</strong> The data folder contains the feature and target data used to train the ML model: stability_input: A Folder containing training and test sets for the stability model for each area. flow_input: A Folder containing training and test sets for the flow model for each link. <em>raw_input_data.h5</em><strong> </strong>:<strong> </strong>The aggregated external features without additional engineered features. <em>input_forecast.h5 </em>and<em> input_actual.h5: </em>The day-ahead available (forecast) and ex-post available (actual) data of external features including the engineered features. <em>indicators.h5 </em>: The grid frequency stability indicators. <em>documentation_of_data_download</em>: Information files concerning the ENTSO-E raw data and its aggregation. HVDClinks: A Folder containing preprocessed time series for scheduled and unscheduled HVDC flows <strong>Data sources</strong> Most of the data is derived from ENTSO-E Transparency Platform data [1]. The grid stability indicators (indicators<em>.h5</em>) are based on publicly available data from the German Transmission System Operators (TSOs) [2]. <strong>Results</strong> The stability_results and the flow_results folder contain the results of hyperparameter optimization, model prediction and interpretation via SHAP for the respective models. <em>cv_results_gtb_full.csv</em> : Performance results for each combination in the hyperparameter optimization. <em>cv_best_params_gtb_full.csv</em> : Hyperparameters used in the final (optimized) model. <em>shap_values_gtb_full.npy</em> : First-order SHAP values calculated on different data sets: The train set, the randomized test set and the continuous test set. <em>y_pred.h5/y_pred_links.h5</em> : Predictions of daily profile predictor and Machine Learning models. <strong>Disclaimer</strong> The data might be subject to copyright or related rights. Please consult the primary data owner.
description: {"references": ["[1] ENTSO-E Transparency Platform. https://transparency.entsoe.eu/", "[2] 50Hertz Transmission GmbH, Amprion GmbH, TransnetBW GmbH and TenneT TSO GmbH, \"Regelleistung.Net\", https://www.regelleistung.net/ext/"]}
DOI: 10.5281/zenodo.7436699
title: Clinicopathological characteristics and genomic profile of primary sinonasal tract diffuse large B cell lymphoma (DLBCL) reveals gain at 1q31 and RGS1 encoding protein; high RGS1 immunohistochemical expression associates with poor overall survival in DLBCL not otherwise specified (NOS)

description: Raw annonymized data, OncoScan CEL files of the manuscript. PMID: 27775850 DOI: 10.1111/his.13106 ABSTRACT: <strong>Aims: </strong> We aimed to define the clinicopathological characteristics of 29 primary sinonasal diffuse large B cell lymphoma (DLBCL<sup>sn</sup> ) in a series of 240 cases of DLBCL not otherwise specified [DLBCL<sup>all (</sup><sup>NOS</sup><sup>)</sup> ], including DLBCL<sup>sn</sup> training set (n = 11) and validation set (n = 18), and DLBCL<sup>non-sn</sup> (n = 211). <strong>Methods and results: </strong> In the training set, 82% had a non-germinal center B-cell-like (Hans' Classifier) (non-GCB) phenotype and 18% were Epstein-Barr virus-encoded small RNAs (EBER)<sup>+</sup> . The genomic profile showed gains<sup>(+)</sup> of 1q21.3q31.2 (55%), 10q24.1 (46%), 11q14.1 (46%) and 18q12.1q23 (46%); losses<sup>(-)</sup> of 6q26q27 (55%) and 9p21.3 (64%); and copy number neutral loss of heterozygosity (LOH) (acquired uniparental disomy, UPD) at 6p25.3p21.31 (36%). This profile is comparable to DLBCL<sup>NOS</sup> (GSE11318, n = 203.) and closer to non-GCB/activated B-cell-like subtype (ABC). Nevertheless, +1q31, -9p21.3 and -10q11.1q26.2 were more characteristic of DLBCL<sup>sn</sup> (P &lt; 0.001). Array results were verified successfully by fluorescence in situ hybridization (FISH) on +1q21.3 (CKS1B), -6q26 (PARK2), +8q24.21 (MYC), -9p21.3 (MTAP, CDKN2A/B), -17p13.1 (TP53) and +18q21.33 (BCL2) with 82-91% agreement. Minimal common regions included biologically relevant genes of MNDA (+1q23.1), RGS1 and RGS13 (+1q31.2), FOXP1 (+3p13), PRDM1 (BLIMP1) and PARK2 (-6q21q26), MYC (+8q24.21), CDKN2A (-9p21.3), PTEN (-10q23.31), MDM2 (+12q15), TP53 (-17p13.1) and BCL2 (+18q21.33). Correlation between DNA copy number and protein immunohistochemistry was confirmed for RGS1, RGS13, FOXP1, PARK2 and BCL2. The microenvironment had high infiltration of M2-like tumour associated macrophages (TAMs) and CD8<sup>+</sup> T lymphocytes that associated with higher genomic instability. The DLBCL<sup>sn</sup> validation set confirmed the clinicopathological characteristics, all FISH loci and immunohistochemistry (IHC) for RGS1. RGS1, one of the most frequently altered genes, was analysed by IHC in DLBCL<sup>all</sup> and high RGS1 expression associated with non-GCB, EBER<sup>+</sup> and unfavourable overall survival (hazard ratio = 1.794; P = 0.016). <strong>Conclusions: </strong> DLBCL<sup>sn</sup> has a characteristic genomic profile. High RGS1 IHC expression associates with poor overall survival in DLBCL<sup>all (</sup><sup>NOS</sup><sup>)</sup> .
DOI: 10.5281/zenodo.7436698
title: Clinicopathological characteristics and genomic profile of primary sinonasal tract diffuse large B cell lymphoma (DLBCL) reveals gain at 1q31 and RGS1 encoding protein; high RGS1 immunohistochemical expression associates with poor overall survival in DLBCL not otherwise specified (NOS)

description: Raw annonymized data, OncoScan CEL files of the manuscript. PMID: 27775850 DOI: 10.1111/his.13106 ABSTRACT: <strong>Aims: </strong> We aimed to define the clinicopathological characteristics of 29 primary sinonasal diffuse large B cell lymphoma (DLBCL<sup>sn</sup> ) in a series of 240 cases of DLBCL not otherwise specified [DLBCL<sup>all (</sup><sup>NOS</sup><sup>)</sup> ], including DLBCL<sup>sn</sup> training set (n = 11) and validation set (n = 18), and DLBCL<sup>non-sn</sup> (n = 211). <strong>Methods and results: </strong> In the training set, 82% had a non-germinal center B-cell-like (Hans' Classifier) (non-GCB) phenotype and 18% were Epstein-Barr virus-encoded small RNAs (EBER)<sup>+</sup> . The genomic profile showed gains<sup>(+)</sup> of 1q21.3q31.2 (55%), 10q24.1 (46%), 11q14.1 (46%) and 18q12.1q23 (46%); losses<sup>(-)</sup> of 6q26q27 (55%) and 9p21.3 (64%); and copy number neutral loss of heterozygosity (LOH) (acquired uniparental disomy, UPD) at 6p25.3p21.31 (36%). This profile is comparable to DLBCL<sup>NOS</sup> (GSE11318, n = 203.) and closer to non-GCB/activated B-cell-like subtype (ABC). Nevertheless, +1q31, -9p21.3 and -10q11.1q26.2 were more characteristic of DLBCL<sup>sn</sup> (P &lt; 0.001). Array results were verified successfully by fluorescence in situ hybridization (FISH) on +1q21.3 (CKS1B), -6q26 (PARK2), +8q24.21 (MYC), -9p21.3 (MTAP, CDKN2A/B), -17p13.1 (TP53) and +18q21.33 (BCL2) with 82-91% agreement. Minimal common regions included biologically relevant genes of MNDA (+1q23.1), RGS1 and RGS13 (+1q31.2), FOXP1 (+3p13), PRDM1 (BLIMP1) and PARK2 (-6q21q26), MYC (+8q24.21), CDKN2A (-9p21.3), PTEN (-10q23.31), MDM2 (+12q15), TP53 (-17p13.1) and BCL2 (+18q21.33). Correlation between DNA copy number and protein immunohistochemistry was confirmed for RGS1, RGS13, FOXP1, PARK2 and BCL2. The microenvironment had high infiltration of M2-like tumour associated macrophages (TAMs) and CD8<sup>+</sup> T lymphocytes that associated with higher genomic instability. The DLBCL<sup>sn</sup> validation set confirmed the clinicopathological characteristics, all FISH loci and immunohistochemistry (IHC) for RGS1. RGS1, one of the most frequently altered genes, was analysed by IHC in DLBCL<sup>all</sup> and high RGS1 expression associated with non-GCB, EBER<sup>+</sup> and unfavourable overall survival (hazard ratio = 1.794; P = 0.016). <strong>Conclusions: </strong> DLBCL<sup>sn</sup> has a characteristic genomic profile. High RGS1 IHC expression associates with poor overall survival in DLBCL<sup>all (</sup><sup>NOS</sup><sup>)</sup> .
DOI: 10.5281/zenodo.7432183
title: URInary peptidomic patterns of Long-COVID syndrome "UriCoV"

description: Post acute sequelae of SARS-CoV-2 infection (PASC), also referred to as long COVID, is the most frequent, yet poorly characterized sequelae of COVID-19. It has tremendous, unpredictable consequences on personal health and socioeconomic status of affected individuals, and on global economic issues. UriCov is a multidisciplinary, comprehensive project with the aim to investigate in depth the molecular phenotype(s) of individual patients previously infected by SARS-CoV-2 and identify patients at risk of PASC. This will be achieved through multi-disciplinary research based on omics and clinical data in a bioinformatics framework, based on the hypothesis that endothelial damage is a key event in PASC. The developed molecular tools may allow patient stratification to initiate personalized treatment for prevention of PASC prior to symptoms and to decrease the PASC incidence. UriCoV will also provide missing fundamental knowledge on the molecular pathophysiology of PASC.