cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15066183
title: Supplementary Material for: Characterization of Nucleotide Binding ­Site-Encoding Genes in Sweetpotato, <b><i>Ipomoea batatas</i></b>(L.) Lam., and Their Response to Biotic and Abiotic Stresses

description: Sweetpotato, <i>Ipomoea batatas</i> (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes’ expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that <i>IbNBS75</i>, <i>IbNBS219</i>, and <i>IbNBS256</i> respond to stem nematode infection; <i>Ib­NBS240</i>, <i>IbNBS90</i>, and <i>IbNBS80</i> respond to cold stress, while <i>IbNBS208</i>, <i>IbNBS71</i>, and <i>IbNBS159</i> respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.
DOI: 10.6084/m9.figshare.15066183.v1
title: Supplementary Material for: Characterization of Nucleotide Binding ­Site-Encoding Genes in Sweetpotato, <b><i>Ipomoea batatas</i></b>(L.) Lam., and Their Response to Biotic and Abiotic Stresses

description: Sweetpotato, <i>Ipomoea batatas</i> (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes’ expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that <i>IbNBS75</i>, <i>IbNBS219</i>, and <i>IbNBS256</i> respond to stem nematode infection; <i>Ib­NBS240</i>, <i>IbNBS90</i>, and <i>IbNBS80</i> respond to cold stress, while <i>IbNBS208</i>, <i>IbNBS71</i>, and <i>IbNBS159</i> respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.
DOI: 10.5281/zenodo.5140894
title: Chest x-ray in the COVID-19 pandemic: Radiologists real-world reader performance.

description: Dataset from the article Cozzi A, Schiaffino S, Arpaia F, Della Pepa G, Tritella S, Bertolotti P, Menicagli L, Monaco CG, Carbonaro LA, Spairani R, Babaei Paskeh B, Sardanelli F. Chest x-ray in the COVID-19 pandemic: Radiologists' real-world reader performance. Eur J Radiol. 2020 Nov;132:109272. doi: 10.1016/j.ejrad.2020.109272. Epub 2020 Sep 10. PMID: 32971326; PMCID: PMC7481070. <strong>Abstract</strong> <strong>Purpose: </strong>To report real-world diagnostic performance of chest x-ray (CXR) readings during the COVID-19 pandemic. <strong>Methods: </strong>In this retrospective observational study we enrolled all patients presenting to the emergency department of a Milan-based university hospital from February 24th to April 8th 2020 who underwent nasopharyngeal swab for reverse transcriptase-polymerase chain reaction (RT-PCR) and anteroposterior bedside CXR within 12 h. A composite reference standard combining RT-PCR results with phone-call-based anamnesis was obtained. Radiologists were grouped by CXR reading experience (Group-1, &gt;10 years; Group-2, &lt;10 years), diagnostic performance indexes were calculated for each radiologist and for the two groups. <strong>Results: </strong>Group-1 read 435 CXRs (77.0 % disease prevalence): sensitivity was 89.0 %, specificity 66.0 %, accuracy 83.7 %. Group-2 read 100 CXRs (73.0 % prevalence): sensitivity was 89.0 %, specificity 40.7 %, accuracy 76.0 %. During the first half of the outbreak (195 CXRs, 66.7 % disease prevalence), overall sensitivity was 80.8 %, specificity 67.7 %, accuracy 76.4 %, Group-1 sensitivity being similar to Group-2 (80.6 % versus 81.5 %, respectively) but higher specificity (74.0 % versus 46.7 %) and accuracy (78.4 % versus 69.0 %). During the second half (340 CXRs, 81.8 % prevalence), overall sensitivity increased to 92.8 %, specificity dropped to 53.2 %, accuracy increased to 85.6 %, this pattern mirrored in both groups, with decreased specificity (Group-1, 58.0 %; Group-2, 33.3 %) but increased sensitivity (92.7 % and 93.5 %) and accuracy (86.5 % and 81.0 %, respectively). <strong>Conclusions: </strong>Real-world CXR diagnostic performance during the COVID-19 pandemic showed overall high sensitivity with higher specificity for more experienced radiologists. The increase in accuracy over time strengthens CXR role as a first line examination in suspected COVID-19 patients.
DOI: 10.5281/zenodo.5140893
title: Chest x-ray in the COVID-19 pandemic: Radiologists real-world reader performance.

description: Dataset from the article Cozzi A, Schiaffino S, Arpaia F, Della Pepa G, Tritella S, Bertolotti P, Menicagli L, Monaco CG, Carbonaro LA, Spairani R, Babaei Paskeh B, Sardanelli F. Chest x-ray in the COVID-19 pandemic: Radiologists' real-world reader performance. Eur J Radiol. 2020 Nov;132:109272. doi: 10.1016/j.ejrad.2020.109272. Epub 2020 Sep 10. PMID: 32971326; PMCID: PMC7481070. <strong>Abstract</strong> <strong>Purpose: </strong>To report real-world diagnostic performance of chest x-ray (CXR) readings during the COVID-19 pandemic. <strong>Methods: </strong>In this retrospective observational study we enrolled all patients presenting to the emergency department of a Milan-based university hospital from February 24th to April 8th 2020 who underwent nasopharyngeal swab for reverse transcriptase-polymerase chain reaction (RT-PCR) and anteroposterior bedside CXR within 12 h. A composite reference standard combining RT-PCR results with phone-call-based anamnesis was obtained. Radiologists were grouped by CXR reading experience (Group-1, &gt;10 years; Group-2, &lt;10 years), diagnostic performance indexes were calculated for each radiologist and for the two groups. <strong>Results: </strong>Group-1 read 435 CXRs (77.0 % disease prevalence): sensitivity was 89.0 %, specificity 66.0 %, accuracy 83.7 %. Group-2 read 100 CXRs (73.0 % prevalence): sensitivity was 89.0 %, specificity 40.7 %, accuracy 76.0 %. During the first half of the outbreak (195 CXRs, 66.7 % disease prevalence), overall sensitivity was 80.8 %, specificity 67.7 %, accuracy 76.4 %, Group-1 sensitivity being similar to Group-2 (80.6 % versus 81.5 %, respectively) but higher specificity (74.0 % versus 46.7 %) and accuracy (78.4 % versus 69.0 %). During the second half (340 CXRs, 81.8 % prevalence), overall sensitivity increased to 92.8 %, specificity dropped to 53.2 %, accuracy increased to 85.6 %, this pattern mirrored in both groups, with decreased specificity (Group-1, 58.0 %; Group-2, 33.3 %) but increased sensitivity (92.7 % and 93.5 %) and accuracy (86.5 % and 81.0 %, respectively). <strong>Conclusions: </strong>Real-world CXR diagnostic performance during the COVID-19 pandemic showed overall high sensitivity with higher specificity for more experienced radiologists. The increase in accuracy over time strengthens CXR role as a first line examination in suspected COVID-19 patients.
DOI: 10.5281/zenodo.5141069
title: MSVermet/Cell-Nuclei-Detection-And-Segmentation-CENet-UNet: Cell nuclei detection and segmentation

description: Fully automated nuclei detection and segmentation with CE-Net and U-Net on the PanNuke dataset. Repository includes code and dataset.
DOI: 10.5281/zenodo.5141068
title: MSVermet/Cell-Nuclei-Detection-And-Segmentation-CENet-UNet: Cell nuclei detection and segmentation

description: Fully automated nuclei detection and segmentation with CE-Net and U-Net on the PanNuke dataset. Repository includes code and dataset.
DOI: 10.5281/zenodo.5090531
title: Yes! We're open. Open science and the future of academic practices in translation and interpreting studies - Supplementary material

description: Supplementary material to the article "<em>Yes! We’re open</em>. Open science and the future of academic practices in translation and interpreting studies" by Christian Olalla-Soler. Sheet 1: Translation and Interpreting Studies journals and bibliometric indicators. Sheet 2: Translation and Interpreting Studies articles in Scopus. Sheet 3: Pre-registrations related to translation and interpreting. Reference: Olalla-Soler, Christian (2021). "<em>Yes! We’re open</em>. Open science and the future of academic practices in translation and interpreting studies". <em>Translation & Interpreting</em> 13 (2): 1-28. https://doi.org/10.12807/ti.113202.2021.a01
DOI: 10.5281/zenodo.5090530
title: Yes! We're open. Open science and the future of academic practices in translation and interpreting studies - Supplementary material

description: Supplementary material to the article "<em>Yes! We’re open</em>. Open science and the future of academic practices in translation and interpreting studies" by Christian Olalla-Soler. Sheet 1: Translation and Interpreting Studies journals and bibliometric indicators. Sheet 2: Translation and Interpreting Studies articles in Scopus. Sheet 3: Pre-registrations related to translation and interpreting. Reference: Olalla-Soler, Christian (2021). "<em>Yes! We’re open</em>. Open science and the future of academic practices in translation and interpreting studies". <em>Translation & Interpreting</em> 13 (2): 1-28. https://doi.org/10.12807/ti.113202.2021.a01
DOI: 10.6084/m9.figshare.14680659
title: Overall prediction tool performances

description: Overall performance measures from the different AMP prediction tools.<br>
DOI: 10.6084/m9.figshare.14680659.v2
title: Overall prediction tool performances

description: Overall performance measures from the different AMP prediction tools.<br>
DOI: 10.6084/m9.figshare.14680659.v1
title: Overall prediction tool performances

description: Overall performance measures from the different AMP prediction tools.<br>
DOI: 10.6084/m9.figshare.14680653
title: Per-taxon AMP prediction tool performances

description: Performance measures from the AMP prediction tools, separately for each taxa within each prediction tool.<br>
DOI: 10.6084/m9.figshare.14680653.v2
title: Per-taxon AMP prediction tool performances

description: Performance measures from the AMP prediction tools, separately for each taxa within each prediction tool.<br>
DOI: 10.6084/m9.figshare.14680653.v1
title: Per-taxon AMP prediction tool performances

description: Performance measures from the AMP prediction tools, separately for each taxa within each prediction tool.<br>
DOI: 10.5281/zenodo.5141195
title: jsPerf Sampling Data

description: SCAM 2021
DOI: 10.5281/zenodo.5141194
title: jsPerf Sampling Data

description: SCAM 2021
DOI: 10.5281/zenodo.4741875
title: jsPerf Sampling Data

description: ESEC/FSE 2021
DOI: 10.5281/zenodo.4741874
title: jsPerf Sampling Data

description: ESEC/FSE 2021
DOI: 10.21227/y0t4-hr09
title: Data for: Leveraging Deep Learning Techniques to Improve P300-Based Brain Computer Interfaces

description: Brain-Computer Interface (BCI) has become an established technology to interconnect a human brain and an external device. One of the most popular protocols for BCI is based on the extraction of the so-called P300 wave from EEG recordings. P300 wave is an event-related potential with a latency of 300 ms after the onset of a rare stimulus. In this paper, we used deep learning architectures, namely convolutional neural networks (CNNs), to improve P300-based BCIs. We propose a novel BCI classifier, called P3CNET, that improved P300 classification accuracy performances of the best state-of-the-art classifier. In addition, we explored pre-processing and training choices that improved the usability of BCI systems. For the pre-processing of EEG data, we explored the optimal signal interval that would improve classification accuracies. Then, we explored the minimum number of calibration sessions to balance higher accuracy and shorter calibration time. To improve the explainability of deep learning architectures, we analyzed the saliency maps of the input EEG signal leading to a correct P300 classification and we observed that the elimination of less informative electrode channels from the data did not result in better accuracy. All the methodologies and explorations were performed and validated on two different CNN classifiers, demonstrating the generalizability of the obtained results. Finally, we showed the advantages given by transfer learning when using the proposed novel architecture on other P300 data sets. The presented architectures and practical suggestions can be used by BCI practitioners to improve its effectiveness.
DOI: 10.48420/14635917
title: Ncounter Fibrosis panel gene expression analysis

description: zip. folders containing the raw data files (.rcc) from the Ncounter Flex system as well as<br>the associated nSolver advanced analysis. <br><br>Mice were injected with peritoneal dialysis fluid (Physioneal 40, 3.86% glucose, Baxter Healthcare) or dialysis fluid supplemented with 40 mM Methylglyoxal once daily, 5 times a week for a total of 14 injections and whole PEC isolated and subjected to RNA-isolation and Ncounter-transcript analysis. As control naive, uninjected mice were used.<br>Groups of samples:<br>1-3: naive<br>4-6: Physioneal<br>7-9: Physioneal + Methylglyoxal
DOI: 10.48420/14635917.v1
title: Ncounter Fibrosis panel gene expression analysis

description: zip. folders containing the raw data files (.rcc) from the Ncounter Flex system as well as<br>the associated nSolver advanced analysis. <br><br>Mice were injected with peritoneal dialysis fluid (Physioneal 40, 3.86% glucose, Baxter Healthcare) or dialysis fluid supplemented with 40 mM Methylglyoxal once daily, 5 times a week for a total of 14 injections and whole PEC isolated and subjected to RNA-isolation and Ncounter-transcript analysis. As control naive, uninjected mice were used.<br>Groups of samples:<br>1-3: naive<br>4-6: Physioneal<br>7-9: Physioneal + Methylglyoxal
DOI: 10.5281/zenodo.4570565
title: Veillon et al. (2020), Geoscientific Model Development : data and development

description: F.Veillon, M.Dumont, C.Amory, M.Fructus : A versatile method for computing optimized snow albedo from spectrally fixed radiative variables : VALHALLA v1.0, Geoscientific Model Development, in review, 2020. See README for a full description of the dataset content Please contact me at marie.dumont@meteo.fr if you need more details on the dataset
DOI: 10.25345/c5hc33
title: MassIVE MSV000087894 - Piper_Plants_LC-HRMS_Screening
title: Twenty-seven (n=27) Piper species. Leaf tissues extracted with EtOH/Water (75:25) and profiled with LC-HRMS in dd-MS2 acquisition mode.
DOI: 10.15151/esrf-dc-514708283
title: Thaumatin data sets for mini-kappa calibration

description: Data sets collected on MASSIF-1 for calibration of the mini-kappa goniometer
DOI: 10.5281/zenodo.5141175
title: Dataset related to article "Acetaldehyde in polyethylene terephthalate (PET) bottledwater: assessment and mitigation of health risk for consumers"

description: <em>The file contains the raw data related to the manuscript: "Acetaldehyde in Polyethylene Terephthalate (PET) Bottled Water: Assessment and Mitigation of Health Risk for Consumers"</em> <strong>Abstract</strong>: This study was designed to investigate the levels of acetaldehyde residues in polyethylene terephthalate bottled water and its significance in terms of consumer health. We analyzed 104 samples collected throughout Italy, so as to be representative of the national market. Parameters such as CO<sub>2</sub> level, shelf life, weight of the empty bottle and distance from the production sites to the point of sale were also collected. Although the levels of acetaldehyde complied with the limits established by Italian legislation, they varied widely, with concentrations ranging from 0.41 to 76.2 µg/L. An assessment of safety for human health, using the margin of exposure approach, showed that the amount of acetaldehyde in bottled water is unlikely to be of any safety concern for human health. The acetaldehyde residues were mainly due to CO<sub>2</sub> levels which influence solubility of acetaldehyde in water. They are also related to the size of the bottle and the distance from the store, but not to the shelf life, at least for 40 days. The findings suggest some good practices for a better product from the point of view of public health, like polymer quality and limitation of transport distances. <strong>Funding</strong>: This research was funded by Mineracqua.
description: {"references": ["Re Depaolini, Andrea, Elena Fattore, Giancarlo Bianchi, Roberto Fanelli, and Enrico Davoli. 2020. \"Acetaldehyde in Polyethylene Terephthalate (PET) Bottled Water: Assessment and Mitigation of Health Risk for Consumers\" Applied Sciences 10, no. 12: 4321. https://doi.org/10.3390/app10124321"]}
DOI: 10.5281/zenodo.5141174
title: Dataset related to article "Acetaldehyde in polyethylene terephthalate (PET) bottledwater: assessment and mitigation of health risk for consumers"

description: <em>The file contains the raw data related to the manuscript: "Acetaldehyde in Polyethylene Terephthalate (PET) Bottled Water: Assessment and Mitigation of Health Risk for Consumers"</em> <strong>Abstract</strong>: This study was designed to investigate the levels of acetaldehyde residues in polyethylene terephthalate bottled water and its significance in terms of consumer health. We analyzed 104 samples collected throughout Italy, so as to be representative of the national market. Parameters such as CO<sub>2</sub> level, shelf life, weight of the empty bottle and distance from the production sites to the point of sale were also collected. Although the levels of acetaldehyde complied with the limits established by Italian legislation, they varied widely, with concentrations ranging from 0.41 to 76.2 µg/L. An assessment of safety for human health, using the margin of exposure approach, showed that the amount of acetaldehyde in bottled water is unlikely to be of any safety concern for human health. The acetaldehyde residues were mainly due to CO<sub>2</sub> levels which influence solubility of acetaldehyde in water. They are also related to the size of the bottle and the distance from the store, but not to the shelf life, at least for 40 days. The findings suggest some good practices for a better product from the point of view of public health, like polymer quality and limitation of transport distances. <strong>Funding</strong>: This research was funded by Mineracqua.
description: {"references": ["Re Depaolini, Andrea, Elena Fattore, Giancarlo Bianchi, Roberto Fanelli, and Enrico Davoli. 2020. \"Acetaldehyde in Polyethylene Terephthalate (PET) Bottled Water: Assessment and Mitigation of Health Risk for Consumers\" Applied Sciences 10, no. 12: 4321. https://doi.org/10.3390/app10124321"]}
DOI: 10.6084/m9.figshare.15066348
title: Global study on Flying Foxes (Pteropus livingstonii): A bibliometric analysis and knowledge mapping

description: The purpose of the study is to know the various aspects of research publications on flying foxes, including types of documents, annual scientific productivity, top contributing authors and their impact, authorship and collaboration pattern, top contributing countries and organizations, most important source publication, most cited papers, commonly used keywords in the area of flying foxes.
DOI: 10.6084/m9.figshare.15066348.v1
title: Global study on Flying Foxes (Pteropus livingstonii): A bibliometric analysis and knowledge mapping

description: The purpose of the study is to know the various aspects of research publications on flying foxes, including types of documents, annual scientific productivity, top contributing authors and their impact, authorship and collaboration pattern, top contributing countries and organizations, most important source publication, most cited papers, commonly used keywords in the area of flying foxes.
DOI: 10.6084/m9.figshare.15063213
title: Mycorrhizal responsiveness predicts plant community changes in response to long term N and P fertilization

description: It includes data of plant species percentage cover and species with the mycorrhizal responsiveness reported.
DOI: 10.15468/dl.g8rseg
title: Occurrence Download

description: A dataset containing 71919 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pelophylax ridibundus (Pallas, 1771)"
 ]
}

 The dataset includes 71919 records from 1582 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088846-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gkcped
title: Occurrence Download

description: A dataset containing 1734 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Coccinella transversoguttata Faldermann, 1835",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 1734 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088867-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dkk8qj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dendrotriton bromeliacius (Schmidt, 1936))",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088868-240626123714530/datasets/export for details.