cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14140332
title: Additional file 5 of Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour

description: Additional file 5: Table S4. ME10 genes associated with desiccation tolerance and ABI3 regulon
DOI: 10.6084/m9.figshare.14140320.v1
title: Additional file 2 of Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour

description: Additional file 2: Table S1. WGNCA module gene list
DOI: 10.6084/m9.figshare.14140323.v1
title: Additional file 3 of Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour

description: Additional file 3: Table S2. Overrepresentation analysis of biological function in the 21 genes modules
DOI: 10.6084/m9.figshare.14140338
title: Additional file 7 of Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour

description: Additional file 7: Table S6. Overrepresentation analysis of biological functions in specific or common genes positively associated with dormancy release (DR), germination under osmotic stress (G0.3MPa) and longevity (P50) in ME4.
DOI: 10.6084/m9.figshare.14140320
title: Additional file 2 of Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour

description: Additional file 2: Table S1. WGNCA module gene list
DOI: 10.6084/m9.figshare.23573868
title: nuccio_psych_project_data_june_2023

description: This data was used for analysis for an experiment examining the impact of seductive allure effect and trappings of science on how people evaluated information regarding alleged paranormal research.
DOI: 10.6084/m9.figshare.23573868.v1
title: nuccio_psych_project_data_june_2023

description: This data was used for analysis for an experiment examining the impact of seductive allure effect and trappings of science on how people evaluated information regarding alleged paranormal research.
DOI: 10.5281/zenodo.8068383
title: Breast_Cancer_DCE-MRI_Data

description: The dataset was specifically created for use in deep learning-aided segmentation tasks for breast cancer diagnosis. It comprises 100 cases obtained from Yunnan Cancer Hospital, each containing dynamic contrast-enhanced MRI (DCE-MRI) images with six phases, consisting of one pre-contrast image and five post-contrast images. Additionally, each case includes a breast tumor annotation (ground-truth image) and a whole breast annotation for accurate segmentation.
DOI: 10.5281/zenodo.8068382
title: Breast_Cancer_DCE-MRI_Data

description: The dataset was specifically created for use in deep learning-aided segmentation tasks for breast cancer diagnosis. It comprises 100 cases obtained from Yunnan Cancer Hospital, each containing dynamic contrast-enhanced MRI (DCE-MRI) images with six phases, consisting of one pre-contrast image and five post-contrast images. Additionally, each case includes a breast tumor annotation (ground-truth image) and a whole breast annotation for accurate segmentation.
DOI: 10.6084/m9.figshare.23573907.v1
title: The raw data for the paper

description: this data contains the HPLC and Mass spectrum for the pepride and MICs for the peptide
DOI: 10.6084/m9.figshare.23573907
title: The raw data for the paper

description: this data contains the HPLC and Mass spectrum for the pepride and MICs for the peptide
DOI: 10.6084/m9.figshare.23256965
title: The UHRF1 protein is a key regulator of retrotransposable elements and innate immune response to viral RNA in human cells

description: While epigenetic mechanisms such as DNA methylation and histone modification are known to be important for gene suppression, relatively little is still understood about the interplay between these systems. The UHRF1 protein can interact with both DNA methylation and repressive chromatin marks, but its primary function in humans has been unclear. To determine what that was, we first established stable UHRF1 knockdowns (KD) in normal, immortalized human fibroblasts using targeting shRNA, since CRISPR knockouts (KO) were lethal. Although these showed a loss of DNA methylation across the whole genome, transcriptional changes were dominated by the activation of genes involved in innate immune signalling, consistent with the presence of viral RNA from retrotransposable elements (REs). We confirmed using mechanistic approaches that 1) REs were demethylated and transcriptionally activated; 2) this was accompanied by activation of interferons and interferon-stimulated genes and 3) the pathway was conserved across other adult cell types. Restoring UHRF1 in either transient or stable KD systems could abrogate RE reactivation and the interferon response. Notably, UHRF1 itself could also re-impose RE suppression independent of DNA methylation, but not if the protein contained point mutations affecting histone 3 with trimethylated lysine 9 (H3K9me3) binding. Our results therefore show for the first time that UHRF1 can act as a key regulator of retrotransposon silencing independent of DNA methylation.
DOI: 10.6084/m9.figshare.23256965.v1
title: The UHRF1 protein is a key regulator of retrotransposable elements and innate immune response to viral RNA in human cells

description: While epigenetic mechanisms such as DNA methylation and histone modification are known to be important for gene suppression, relatively little is still understood about the interplay between these systems. The UHRF1 protein can interact with both DNA methylation and repressive chromatin marks, but its primary function in humans has been unclear. To determine what that was, we first established stable UHRF1 knockdowns (KD) in normal, immortalized human fibroblasts using targeting shRNA, since CRISPR knockouts (KO) were lethal. Although these showed a loss of DNA methylation across the whole genome, transcriptional changes were dominated by the activation of genes involved in innate immune signalling, consistent with the presence of viral RNA from retrotransposable elements (REs). We confirmed using mechanistic approaches that 1) REs were demethylated and transcriptionally activated; 2) this was accompanied by activation of interferons and interferon-stimulated genes and 3) the pathway was conserved across other adult cell types. Restoring UHRF1 in either transient or stable KD systems could abrogate RE reactivation and the interferon response. Notably, UHRF1 itself could also re-impose RE suppression independent of DNA methylation, but not if the protein contained point mutations affecting histone 3 with trimethylated lysine 9 (H3K9me3) binding. Our results therefore show for the first time that UHRF1 can act as a key regulator of retrotransposon silencing independent of DNA methylation.
DOI: 10.6084/m9.figshare.23542884
title: <strong>Data Charting. </strong> All main data items that were extracted per record

description: Paper: <strong>Planning the analysis of routine mortality data: A methodological exploration using national data from Peru during the COVID-19 pandemic</strong> <strong>File: Data Charting. </strong> All main data items that were extracted per record
DOI: 10.6084/m9.figshare.23542884.v1
title: <strong>Data Charting. </strong> All main data items that were extracted per record

description: Paper: <strong>Planning the analysis of routine mortality data: A methodological exploration using national data from Peru during the COVID-19 pandemic</strong> <strong>File: Data Charting. </strong> All main data items that were extracted per record
DOI: 10.6084/m9.figshare.23542884.v2
title: <strong>Data Charting. </strong> All main data items that were extracted per record

description: Paper: <strong>Planning the analysis of routine mortality data: A methodological exploration using national data from Peru during the COVID-19 pandemic</strong> <strong>File: Data Charting. </strong> All main data items that were extracted per record
DOI: 10.5281/zenodo.8063124
title: Intergrated Multi-omics Sequencing Reveals Metabolic Reprograms in the Progression of ccRCC

description: ccRCC is a complex disease with remarkable immune and metabolic heterogeneity. Here, we present a TJ-RCC cohort, performing genomic, transcriptomic, proteomic, metabonomic and spatial multi-omic profiling on 100 ccRCC cases. Using the scRNA-seq-derived signature, we identify 4 subtypes. Multilevel profiling distinguishes a unique ccRCC subtype, De-clear cell differentiated (DCCD) -ccRCC, with distinctive metabolic features. DCCD cancer cells are characterized by fewer lipid droplets, extremely inhibited metabolic activity, enhanced nutrients uptake capability and a high proliferation rate, leading to poor prognosis. Using single-cell and spatial trajectory analysis, we demonstrate that DCCD is a common mode of ccRCC progression. Even among stage I patients, DCCD indicates worse outcomes and higher recurrence rate, indicating it cannot be cured by nephrectomy alone. This study provides a treatment strategy based on immune subtypes, which could enable precise clinical management of ccRCC.
DOI: 10.5281/zenodo.8063123
title: Intergrated Multi-omics Sequencing Reveals Metabolic Reprograms in the Progression of ccRCC

description: ccRCC is a complex disease with remarkable immune and metabolic heterogeneity. Here, we present a TJ-RCC cohort, performing genomic, transcriptomic, proteomic, metabonomic and spatial multi-omic profiling on 100 ccRCC cases. Using the scRNA-seq-derived signature, we identify 4 subtypes. Multilevel profiling distinguishes a unique ccRCC subtype, De-clear cell differentiated (DCCD) -ccRCC, with distinctive metabolic features. DCCD cancer cells are characterized by fewer lipid droplets, extremely inhibited metabolic activity, enhanced nutrients uptake capability and a high proliferation rate, leading to poor prognosis. Using single-cell and spatial trajectory analysis, we demonstrate that DCCD is a common mode of ccRCC progression. Even among stage I patients, DCCD indicates worse outcomes and higher recurrence rate, indicating it cannot be cured by nephrectomy alone. This study provides a treatment strategy based on immune subtypes, which could enable precise clinical management of ccRCC.
DOI: 10.5281/zenodo.5566712
title: Place name data for "Skeid – uncovering a fleeting meeting site"

description: The data contains the spatial distribution of 320 skeid (<em>skeið</em> n.) -names that are closer than two kilometres from a medieval church site, or one or more of the following place names: <em>hov/hof, ting</em>, or<em> leik/lek</em>. Through an examination of the landscape, archaeological finds and place names, 37 sites are highlighted as most likely to have hosted a skeid-type assembly. From these four case studies are discussed more in detail in the paper "Skeid – uncovering a fleeting meeting site"
DOI: 10.5281/zenodo.5566711
title: Place name data for "Skeid – uncovering a fleeting meeting site"

description: The data contains the spatial distribution of 320 skeid (<em>skeið</em> n.) -names that are closer than two kilometres from a medieval church site, or one or more of the following place names: <em>hov/hof, ting</em>, or<em> leik/lek</em>. Through an examination of the landscape, archaeological finds and place names, 37 sites are highlighted as most likely to have hosted a skeid-type assembly. From these four case studies are discussed more in detail in the paper "Skeid – uncovering a fleeting meeting site"
DOI: 10.5281/zenodo.7959115
title: Hourly air pollution data for Graz, Austria

description: The dataset spans from January 1, 2014, to March 15, 2020, with measurements recorded on an hourly basis. The environmental and pollutant data was provided by the Austrian government under the following license: CC-BY-4.0: Land Steiermark - data.steiermark.gv.at Air quality by means of NO2, NO, NOx, PM10 and O3 was measured at five sites in Graz, Austria (Süd (eng. South) - S, Nord (eng. North) - N, West (eng. West) - W, Don Bosco – D, Ost (eng. East) – O). Temperature, precipitation, relative humidity, pressure, and wind speed are among the weather conditions considered. To represent wind direction, the wind speed was multiplied by the sine and cosine of the wind direction. Lags were generated using weather data, considering the last 12 data points. The mean of these 12 values was then calculated to represent an hourly metric. The ERA5-Land data is subject to the Copernicus licence from following source https://cds.climate.copernicus.eu/cdsapp#!/dataset/10.24381/cds.e2161bac?tab=overview it includes following variables : Snowfall - sf Surface latent heat flux - slhf Snowmelt - smlt Snow cover - snowc Windspeed - speed Surface latent heat flux sshf Soil temperature level 4 - stl4 Skin temperature - str Surface thermal radiation downwards - strd Total precipitation - tp Temperature of snow layer - tsn 10m u-component of wind - u10 10m v-component of wind - v10 Surface net radiation - rsn Snow depth - sd Snow depth water equivalent - sde 2m dewpoint temperature - d2m Forecast albedo - fal Temporal values are also incorporated into this dataset, values such as holidays, weekdays, seasons, and months. The dataset includes Prophet values for all pollutants, which were determined by considering various metrics such as trend, seasonality (weekly, yearly, and daily), as well as yhat lower and upper bounds.
DOI: 10.6084/m9.figshare.23573963.v1
title: Relationship of residual feed intake with semen parameters and testicular ultrasound of Nellore bulls

description: ABSTRACT The objective of this study was to evaluate characteristics of the testicular parenchyma and vascular parameters of the pampiniform plexus obtained by ultrasound, semen quality parameters, and sperm freezability in Nellore bulls classified based on residual feed intake (RFI). Twenty-seven bulls (21.82±0.88 months of age) evaluated for feed efficiency were sampled for the study, including 15 with low RFI (−0.592±0.09 kg dry matter/day) and 12 with high RFI (0.792±0.10 kg dry matter/day). In ultrasound and Doppler assessment, the most efficient animals (low RFI) showed higher pulsatility and resistive indexes, as well as a tendency towards greater heterogeneity of the testicular parenchyma (0.625±0.032 vs. 0.508±0.032, 1.012±0.072 vs. 0.802±0.072, and 12.9±0.96 vs. 10.2±0.96, respectively, for low vs. high RFI). However, these animals tended to have lower peak diastolic velocity (5.19±0.50 for low RFI vs. 6.54±0.50 for high RFI). Analysis of fresh semen showed a lower percentage of minor defects in low RFI animals (2.67±1.19%) compared with high RFI animals (8.10±1.19%), without differences in the other parameters in fresh or thawed semen and after thermoresistance testing. Evaluation of flow cytometry parameters showed a higher quality of mitochondrial respiration in semen samples of low RFI animals (22.04±2.50%) compared with high RFI animals (12.29±2.71%). Therefore, although RFI exerts an effect on the Doppler parameters of the pampiniform plexus, it is not sufficient to affect the quality of fresh or thawed semen.
DOI: 10.6084/m9.figshare.23573963
title: Relationship of residual feed intake with semen parameters and testicular ultrasound of Nellore bulls

description: ABSTRACT The objective of this study was to evaluate characteristics of the testicular parenchyma and vascular parameters of the pampiniform plexus obtained by ultrasound, semen quality parameters, and sperm freezability in Nellore bulls classified based on residual feed intake (RFI). Twenty-seven bulls (21.82±0.88 months of age) evaluated for feed efficiency were sampled for the study, including 15 with low RFI (−0.592±0.09 kg dry matter/day) and 12 with high RFI (0.792±0.10 kg dry matter/day). In ultrasound and Doppler assessment, the most efficient animals (low RFI) showed higher pulsatility and resistive indexes, as well as a tendency towards greater heterogeneity of the testicular parenchyma (0.625±0.032 vs. 0.508±0.032, 1.012±0.072 vs. 0.802±0.072, and 12.9±0.96 vs. 10.2±0.96, respectively, for low vs. high RFI). However, these animals tended to have lower peak diastolic velocity (5.19±0.50 for low RFI vs. 6.54±0.50 for high RFI). Analysis of fresh semen showed a lower percentage of minor defects in low RFI animals (2.67±1.19%) compared with high RFI animals (8.10±1.19%), without differences in the other parameters in fresh or thawed semen and after thermoresistance testing. Evaluation of flow cytometry parameters showed a higher quality of mitochondrial respiration in semen samples of low RFI animals (22.04±2.50%) compared with high RFI animals (12.29±2.71%). Therefore, although RFI exerts an effect on the Doppler parameters of the pampiniform plexus, it is not sufficient to affect the quality of fresh or thawed semen.
DOI: 10.6084/m9.figshare.23573968
title: Photochemical Pre-Treatment to Quantify Iron in Thin Films

description: Metal-based catalysts are indispensable in modern chemistry and one of the biggest challenges for industrial applications is to quantify their performance and stability. The metrics of performance can be obtained in terms of the turnover number and turnover frequency, and the stability might be associated with the leaching of the heterogeneous catalysts. Thus, metal quantification is the starting point to understand and evaluate the features of catalysts. Among the technologies for metal determination, spectrophotometric analysis stands out for being cheap and easy to perform. However, the challenge is the sample preparation to direct quantification from the heterogeneous materials. Herein, it is shown how important is the photochemical pre-treatment for the quantification of the total iron from heterogeneous thin films composed of iron-based materials. The photochemical approach was used to ensure a full dissociation of iron ions before the quantification. This method was revealed to be highly effective and precise, having a wide range of applications for different iron-based catalysts.
DOI: 10.6084/m9.figshare.23573968.v1
title: Photochemical Pre-Treatment to Quantify Iron in Thin Films

description: Metal-based catalysts are indispensable in modern chemistry and one of the biggest challenges for industrial applications is to quantify their performance and stability. The metrics of performance can be obtained in terms of the turnover number and turnover frequency, and the stability might be associated with the leaching of the heterogeneous catalysts. Thus, metal quantification is the starting point to understand and evaluate the features of catalysts. Among the technologies for metal determination, spectrophotometric analysis stands out for being cheap and easy to perform. However, the challenge is the sample preparation to direct quantification from the heterogeneous materials. Herein, it is shown how important is the photochemical pre-treatment for the quantification of the total iron from heterogeneous thin films composed of iron-based materials. The photochemical approach was used to ensure a full dissociation of iron ions before the quantification. This method was revealed to be highly effective and precise, having a wide range of applications for different iron-based catalysts.
DOI: 10.6084/m9.figshare.23573969
title: Dispersive Liquid Phase Microextraction (DLPME) as a Strategy for CdII Separation and Determination in High-Salinity Produced Waters by Graphite Furnace Atomic Absorption Spectrometry

description: In this study, we propose a microextraction method for the determination of CdII in produced waters. The process is based on the conversion of CdII ions into a hydrophobic diethyldithiocarbamate (DDTC) complex with its subsequent dispersive liquid phase microextraction (DLPME) from the aqueous medium with chloroform. The organic phase was then diluted with ethanol and Cd absorbance was measured by graphite furnace atomic absorption spectrometry (GF AAS). The experimental conditions related to the DLPME process were investigated, and the best microextraction conditions were achieved at pH = 6.0 (acetate buffer), 7.5 × 10-6 mol L-1 of DDTC, and when using 200 µL of chloroform as the extracting solvent. No dispersing solvent was needed, which allowed the recovery of approximately 140 µL of chloroform extract. Pyrolysis and atomization temperatures of the GF AAS program were determined through the construction of the respective curves. The estimated limits of detection (LOD) and quantification (LOQ) were 5 and 17 ng L-1, respectively, whereas the enrichment factor for the method was 17. Six samples of seawater and five samples of produced waters with salinities between 30 and 270‰ were analyzed as well as two certified reference materials of saline waters.
DOI: 10.6084/m9.figshare.23573969.v1
title: Dispersive Liquid Phase Microextraction (DLPME) as a Strategy for CdII Separation and Determination in High-Salinity Produced Waters by Graphite Furnace Atomic Absorption Spectrometry

description: In this study, we propose a microextraction method for the determination of CdII in produced waters. The process is based on the conversion of CdII ions into a hydrophobic diethyldithiocarbamate (DDTC) complex with its subsequent dispersive liquid phase microextraction (DLPME) from the aqueous medium with chloroform. The organic phase was then diluted with ethanol and Cd absorbance was measured by graphite furnace atomic absorption spectrometry (GF AAS). The experimental conditions related to the DLPME process were investigated, and the best microextraction conditions were achieved at pH = 6.0 (acetate buffer), 7.5 × 10-6 mol L-1 of DDTC, and when using 200 µL of chloroform as the extracting solvent. No dispersing solvent was needed, which allowed the recovery of approximately 140 µL of chloroform extract. Pyrolysis and atomization temperatures of the GF AAS program were determined through the construction of the respective curves. The estimated limits of detection (LOD) and quantification (LOQ) were 5 and 17 ng L-1, respectively, whereas the enrichment factor for the method was 17. Six samples of seawater and five samples of produced waters with salinities between 30 and 270‰ were analyzed as well as two certified reference materials of saline waters.
DOI: 10.6084/m9.figshare.22714921
title: III-nitride heteroepitaxial films approaching bulk-class quality

description: AlN growth on nano-patterned AlN template
DOI: 10.6084/m9.figshare.22714921.v1
title: III-nitride heteroepitaxial films approaching bulk-class quality

description: AlN growth on nano-patterned AlN template