cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12315212.v1
title: Phosphoproteomics of Aspergillus fumigatus exposed to the antifungal drug caspofungin, Supplementary files

description: <em>Aspergillus fumigatus</em> is an opportunistic and allergenic pathogenic fungus, responsible for fungal infections in humans. <em>A. fumigatus </em>infections are usually treated with polyenes, azoles, or echinocandins. Echinocandins, such as caspofungin, can inhibit the biosynthesis of the β-1,3-glucan polysaccharide, affecting the cell wall integrity and leading to fungal death. In some <em>A. fumigatus </em>strains, caspofungin treatment at high concentrations induces an increase of fungal growth, a phenomenon called Caspofungin Paradoxical Effect (CPE). Here, we analyze the proteome and phosphoproteome of <em>A. fumigatus</em> wild-type and the mitogen-activated protein kinases <em>mpkA</em> and <em>sakA </em>null mutant strains during CPE (2 µg/ml caspofungin for 1 hour). The wild-type proteome shows 75 proteins and 814 phosphopeptides (corresponding to 520 proteins) altered in abundance in response to caspofungin treatment. The <em>ΔmpkA </em>(<em>ΔmpkA </em>caspofungin/wild-type caspofungin) and <em>ΔsakA</em> (<em>ΔsakA </em>caspofungin/wild-type caspofungin) display 626 proteins and 1236 phosphopeptides (corresponding to 703 proteins) and 101 proteins and 1217 phosphopeptides (corresponding to 645 proteins), respectively, altered in abundance. Functional characterization of the phosphopeptides from the wild-type exposed to caspofungin show enrichment for transcription factors, protein kinases, and cytoskeleton proteins. Proteomic analysis for the Δ<em>mpkA</em> and Δ<em>sakA</em> mutants indicates that the control of proteins involved in metabolism, such as in secondary metabolites production, was highly represented in both mutants. Functional categorization of phosphopeptides from both mutants is very similar, and show a high number of proteins with decreased phosphorylation of proteins involved in transcriptional control, DNA/RNA binding, cell cycle control, and DNA processing. This study reveals novel transcription factors involved in caspofungin tolerance.
DOI: 10.6084/m9.figshare.12315230.v3
title: Aspergillus fumigatus transcription factors involved in the caspofungin paradoxical effect, supplementary files

description: <i>Aspergillus fumigatus </i>is the leading cause of pulmonary fungal diseases. Azoles have been used for many years as the main antifungal agents to treat and prevent invasive aspergillosis. However, in the last ten years there are several reports of azole resistance in <i>A. fumigatus</i> and new strategies are needed to combat invasive aspergillosis. Caspofungin is effective against other human fungal pathogens, but it is only fungistatic against <i>A. fumigatus</i>. Resistance to caspofungin in <i>A. fumigatus</i> have been linked to mutations in the <i>fksA</i> gene that encodes the target enzyme of the drug, β-1,3-glucan synthase. However, tolerance to high caspofungin concentrations, a phenomenon known as caspofungin paradoxical effect (CPE), is also important for subsequent adaptation and drug resistance evolution. Here, we have identified and characterized the transcription factors involved in the response to CPE by screening an <i>A. fumigatus</i> library of 484 null transcription factors (TFs) in CPE drug concentrations. We have identified eleven TFs that had reduced CPE encoding proteins involved in the basal modulation of the RNA polymerase II initiation sites, calcium metabolism and cell wall remodelling. One of theseTFs FhdA was important for mitochondrial respiratory function and iron metabolism. The Δ<i>fhdA</i> mutant had decreased growth when exposed to Congo Red or at high temperature. RNAseq analysis and further experimental validation indicate that the Δ<i>fhdA</i> mutant showed diminished respiratory capacity, probably affecting several pathways related to the caspofungin tolerance and resistance. Our results provide the foundation to understand signaling pathways that are important for caspofungin tolerance and resistance.
DOI: 10.6084/m9.figshare.12315107
title: Supplementary Table S2

description: <b>Proteome (A) and Phosphoproteome (B) profile of proteins modulated in<i> ΔmpkA</i> strain during caspofungin stress </b>(2µg/ml, 1 h; <i>t</i>-Student test, p &lt; 0.05). <b>A.</b> Table was obtained from Maxquant output file *Proteingroup. The <i>t-</i>Student test was performed between LFQ intensity values for <i>ΔmpkA</i> versus WT treated with caspofungin. <b>B.</b> Table was obtained from Maxquant output file *Phospho(STY)sites. The <i>t-</i>Student<i> </i>test<i> </i>was performed between Phosphosite intensity values for <i>ΔmpkA</i> versus WT treated with caspofungin. <b> </b>
DOI: 10.6084/m9.figshare.12315113
title: Supplementary Table S3

description: <b>Proteome (A) and Phosphoproteome (B) profile of proteins modulated in<i> ΔsakA</i> strain during Caspofungin stress </b>(2µg/mL, 1 h; <i>t</i>-Student test, p &lt; 0.05). <b>A.</b> Table was obtained from Maxquant output file *Proteingroup. The <i>t-</i>Student<i> </i>test was performed between LFQ intensity values for <i>ΔsakA</i> versus WT treated with caspofungin. <b>B.</b> Table was obtained from Maxquant output file *Phospho(STY)sites. The <i>t-</i>Student test<i> </i>was performed between Phosphosite intensity values for <i>ΔsakA</i> versus WT treated with caspofungin
DOI: 10.6084/m9.figshare.12315101
title: Comparison of Pre-Treatment vs. Post-Treatment Retinal Vessel Density in Children with Amblyopia

description: Prior studies have reported a lower retinal vessel density (RVD) in amblyopic vs. non-amblyopic eyes. No studies have shown if amblyopic eye RVD changes following patching therapy. We assessed for RVD differences between pre-treatment vs. post-treatment amblyopic eyes. Participants were included if they were &lt;10 years old with unilateral amblyopia. All subjects were required to visit the pediatric eye clinic for examination. Exclusion criteria included: deprivation amblyopia, bilateral amblyopia, nystagmus, media opacity, intraocular inflammation, or any retinal disease. All participants underwent optical coherence tomography angiography (OCTA) before and after refraction and patching treatment. Outcomes included superficial (SCP) and deep (DCP) capillary plexus RVD. 12 patients (12 amblyopic eyes) were included. Mean (SD) age, gestational age (GA), birth weight (BW), and follow-up time were: 6.5 (1.7) years, 39.4 weeks (1.4 w), 3271 g (262 g), and 114 days (46d), respectively. There was a significant increase in the RVD of the DCP in 3 × 3-mm scans after treatment, specifically in the whole image (52.6 ± 5.75 vs 56.5 ± 2.48%, <i>p</i> = .046) and superior hemisphere regions (52.47 ± 6.17 vs 56.73 ± 2.27%, <i>p</i> = .048). Amblyopic eye RVD potentially increases after amblyopia treatment in specific regions of the retina. Further research is required to refine this clinical parameter.
DOI: 10.6084/m9.figshare.12315101.v1
title: Comparison of Pre-Treatment vs. Post-Treatment Retinal Vessel Density in Children with Amblyopia

description: Prior studies have reported a lower retinal vessel density (RVD) in amblyopic vs. non-amblyopic eyes. No studies have shown if amblyopic eye RVD changes following patching therapy. We assessed for RVD differences between pre-treatment vs. post-treatment amblyopic eyes. Participants were included if they were &lt;10 years old with unilateral amblyopia. All subjects were required to visit the pediatric eye clinic for examination. Exclusion criteria included: deprivation amblyopia, bilateral amblyopia, nystagmus, media opacity, intraocular inflammation, or any retinal disease. All participants underwent optical coherence tomography angiography (OCTA) before and after refraction and patching treatment. Outcomes included superficial (SCP) and deep (DCP) capillary plexus RVD. 12 patients (12 amblyopic eyes) were included. Mean (SD) age, gestational age (GA), birth weight (BW), and follow-up time were: 6.5 (1.7) years, 39.4 weeks (1.4 w), 3271 g (262 g), and 114 days (46d), respectively. There was a significant increase in the RVD of the DCP in 3 × 3-mm scans after treatment, specifically in the whole image (52.6 ± 5.75 vs 56.5 ± 2.48%, <i>p</i> = .046) and superior hemisphere regions (52.47 ± 6.17 vs 56.73 ± 2.27%, <i>p</i> = .048). Amblyopic eye RVD potentially increases after amblyopia treatment in specific regions of the retina. Further research is required to refine this clinical parameter.
DOI: 10.6084/m9.figshare.12315089
title: Supplementary Table S1

description: <b>Proteome (A) and Phosphoproteome (B) profile of proteins modulated in wildt-ype strain during caspofungin stress </b>(2µg/ml, 1 h; <i>t</i>-Student test, p &lt; 0.05). <b>A.</b> Table was obtained from Maxquant output file *Proteingroup. The <i>t</i>-Student test was performed between LFQ intensity values for WT not treated (0) or treated with caspofungin. <b>B.</b> Table was obtained from Maxquant output file *Phospho(STY)sites. The <i>t</i>-Student test was performed between Phosphosite intensity values for WT not treated (0) or treated with caspofungin.
DOI: 10.6084/m9.figshare.12315113.v2
title: Supplementary Table S3

description: <b>Proteome (A) and Phosphoproteome (B) profile of proteins modulated in<i> ΔsakA</i> strain during Caspofungin stress </b>(2µg/mL, 1 h; <i>t</i>-Student test, p &lt; 0.05). <b>A.</b> Table was obtained from Maxquant output file *Proteingroup. The <i>t-</i>Student<i> </i>test was performed between LFQ intensity values for <i>ΔsakA</i> versus WT treated with caspofungin. <b>B.</b> Table was obtained from Maxquant output file *Phospho(STY)sites. The <i>t-</i>Student test<i> </i>was performed between Phosphosite intensity values for <i>ΔsakA</i> versus WT treated with caspofungin
DOI: 10.6084/m9.figshare.12315113.v1
title: Untitled Item

description: <b>Proteome (A) and Phosphoproteome (B) profile of proteins modulated in<i> ΔsakA</i> strain during Caspofungin stress </b>(2µg/mL, 1 h; <i>t</i>-Student test, p &lt; 0.05). <b>A.</b> Table was obtained from Maxquant output file *Proteingroup. The <i>t-</i>Student<i> </i>test was performed between LFQ intensity values for <i>ΔsakA</i> versus WT treated with caspofungin. <b>B.</b> Table was obtained from Maxquant output file *Phospho(STY)sites. The <i>t-</i>Student test<i> </i>was performed between Phosphosite intensity values for <i>ΔsakA</i> versus WT treated with caspofungin
DOI: 10.6084/m9.figshare.12312497
title: Granite State Poll #69 (Client Poll) - Technical Report

description: Granite State Poll is a quarterly poll conducted by the University of New Hampshire Survey Center. The poll sample consists of about 500 New Hampshire adults with a working telephone across the state. Each poll contains a series of basic demographic questions that are repeated in future polls, as well as a set of unique questions that are submitted by clients. This poll includes four questions related to preferences about dams. These questions were designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>This Technical Report was written by the UNH Survey Center and describes the protocols and standards of the Granite State Poll #69 (Client Poll), which includes questions related to preferences about dams, designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>The first file is a screenshot of the Technical Report to provide a preview for Figshare. The second file is the Technical Report in Microsoft Word format.
DOI: 10.6084/m9.figshare.12313577
title: Granite State Poll #70 (Political Poll) - Technical Report

description: Granite State Poll is a quarterly poll conducted by the University of New Hampshire Survey Center. The poll sample consists of about 500 New Hampshire adults with a working telephone across the state. Each poll contains a series of basic demographic questions that are repeated in future polls, as well as a set of unique questions that are submitted by clients. This poll includes four questions related to preferences about dams. These questions were designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>This Technical Report was written by the UNH Survey Center and describes the protocols and standards of the Granite State Poll #68 (Client Poll), which includes questions related to preferences about dams, designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>The first file is a screenshot of the Technical Report to provide a preview for Figshare. The second file is the Technical Report in Microsoft Word format.
DOI: 10.6084/m9.figshare.12312497.v1
title: Granite State Poll #69 (Client Poll) - Technical Report

description: Granite State Poll is a quarterly poll conducted by the University of New Hampshire Survey Center. The poll sample consists of about 500 New Hampshire adults with a working telephone across the state. Each poll contains a series of basic demographic questions that are repeated in future polls, as well as a set of unique questions that are submitted by clients. This poll includes four questions related to preferences about dams. These questions were designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>This Technical Report was written by the UNH Survey Center and describes the protocols and standards of the Granite State Poll #69 (Client Poll), which includes questions related to preferences about dams, designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>The first file is a screenshot of the Technical Report to provide a preview for Figshare. The second file is the Technical Report in Microsoft Word format.
DOI: 10.6084/m9.figshare.12313577.v1
title: Granite State Poll #70 (Political Poll) - Technical Report

description: Granite State Poll is a quarterly poll conducted by the University of New Hampshire Survey Center. The poll sample consists of about 500 New Hampshire adults with a working telephone across the state. Each poll contains a series of basic demographic questions that are repeated in future polls, as well as a set of unique questions that are submitted by clients. This poll includes four questions related to preferences about dams. These questions were designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>This Technical Report was written by the UNH Survey Center and describes the protocols and standards of the Granite State Poll #68 (Client Poll), which includes questions related to preferences about dams, designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>The first file is a screenshot of the Technical Report to provide a preview for Figshare. The second file is the Technical Report in Microsoft Word format.
DOI: 10.25375/uct.12315092.v1
title: Using the Epps effect to detect discrete data generating processes: Dataset

description: Data consists of Trade and Quote data for 10 equities from the Johannesburg Stock Exchange. The data consists of 40 days of trading data starting from 2019-05-02 to 2019-06-28. The data has been processed to contain only the Automated Trade (AT) types. Furthermore, trades with the same time-stamp have been aggregated using a volume weighted average so that there is only one trade per time-stamp. Missing data is indicated with NaN's. <br><br>The 10 equities included are: FirstRand Limited (FSR), Shoprite Holdings Ltd (SHP), Absa Group Ltd (ABG), Nedbank Group Ltd (NED), Standard Bank Group Ltd (SBK), Sasol Ltd (SOL), Mondi Plc (MNP), Anglo American Plc (AGL), Naspers Ltd (NPN) and British American Tobacco Plc (BTI).<br><br>The data structure in each csv file is 11 columns, with the first being the times at which the assets have traded. The remaining 10 columns are the trade information of the tickers. The values in these columns are the trading price (aggregated). NaN means the asset did not trade at that time stamp.<br>The data should only be used to aid the reproducibility for the paper: Using the Epps effect to detect discrete data generating processes. The steps to reproduce our results can be found in our GitHub site: https://github.com/CHNPAT005/PCEPTG-EC. <br>The research focuses on empirically determining if correlations are an emerging property in high frequency finance. <br>The work is funded by the South African Statistical Association. The original data was sourced from Bloomberg Pro. The code for the research is done using Julia Pro.<br>DOI for the code: 10.25375/uct.12315167
DOI: 10.6084/m9.figshare.12315089.v1
title: Untitled Item

description: <b>Proteome (A) and Phosphoproteome (B) profile of proteins modulated in wildt-ype strain during caspofungin stress </b>(2µg/ml, 1 h; <i>t</i>-Student test, p &lt; 0.05). <b>A.</b> Table was obtained from Maxquant output file *Proteingroup. The <i>t</i>-Student test was performed between LFQ intensity values for WT not treated (0) or treated with caspofungin. <b>B.</b> Table was obtained from Maxquant output file *Phospho(STY)sites. The <i>t</i>-Student test was performed between Phosphosite intensity values for WT not treated (0) or treated with caspofungin.
DOI: 10.6084/m9.figshare.12315089.v2
title: Untitled Item

description: <b>Proteome (A) and Phosphoproteome (B) profile of proteins modulated in wildt-ype strain during caspofungin stress </b>(2µg/ml, 1 h; <i>t</i>-Student test, p &lt; 0.05). <b>A.</b> Table was obtained from Maxquant output file *Proteingroup. The <i>t</i>-Student test was performed between LFQ intensity values for WT not treated (0) or treated with caspofungin. <b>B.</b> Table was obtained from Maxquant output file *Phospho(STY)sites. The <i>t</i>-Student test was performed between Phosphosite intensity values for WT not treated (0) or treated with caspofungin.
DOI: 10.6084/m9.figshare.12312278
title: Blue tit fecal microbiota sequences (part 3)

description: This data set contains the compress folder “BlueTitFecalMicobiotaSequences_part3” which contains 124 raw sequence data in FASTQ format, produced by a sequencing run using Illumina MiSeq sequencing technology. The sequences came from blue tit fecal microbiota samples that were part of the same sequencing run (see in the same project the dataset “Metadata – Microbiota sequences form a blue tit trophic network, file “trophicLevel_microbiota_metadata.txt”; run blueTit3). The file names are composed of the sample_names which correspond to the metadata first column, followed by a variable part, and by the extension fastq.gz:<b> “sample-names_S<i>XXX</i>_L001_R1_001.fastq.gz” </b>and <b>“sample-names_S<i>XXX</i>_L001_R2_001.fastq.gz”</b>, respectively for the forward and reverse sequences. Data collection procedures and information on barcode sequences are described in the manuscript "Microbiota similarity between predators and prey in a blue tit trophic network" by Dion-Phénix et al. (manuscript submitted at <i>The ISME Journal</i>).
DOI: 10.6084/m9.figshare.12312257
title: data.csv

description: Macroeconomic and tax data for Greece<br>
DOI: 10.6084/m9.figshare.12312257.v1
title: data.csv

description: Macroeconomic and tax data for Greece<br>
DOI: 10.6084/m9.figshare.12312278.v1
title: Blue tit fecal microbiota sequences (part 3)

description: This data set contains the compress folder “BlueTitFecalMicobiotaSequences_part3” which contains 124 raw sequence data in FASTQ format, produced by a sequencing run using Illumina MiSeq sequencing technology. The sequences came from blue tit fecal microbiota samples that were part of the same sequencing run (see in the same project the dataset “Metadata – Microbiota sequences form a blue tit trophic network, file “trophicLevel_microbiota_metadata.txt”; run blueTit3). The file names are composed of the sample_names which correspond to the metadata first column, followed by a variable part, and by the extension fastq.gz:<b> “sample-names_S<i>XXX</i>_L001_R1_001.fastq.gz” </b>and <b>“sample-names_S<i>XXX</i>_L001_R2_001.fastq.gz”</b>, respectively for the forward and reverse sequences. Data collection procedures and information on barcode sequences are described in the manuscript "Microbiota similarity between predators and prey in a blue tit trophic network" by Dion-Phénix et al. (manuscript submitted at <i>The ISME Journal</i>).
DOI: 10.6084/m9.figshare.12312284
title: Granite State Poll #68 (Client Poll) - Technical Report

description: Granite State Poll is a quarterly poll conducted by the University of New Hampshire Survey Center. The poll sample consists of about 500 New Hampshire adults with a working telephone across the state. Each poll contains a series of basic demographic questions that are repeated in future polls, as well as a set of unique questions that are submitted by clients. This poll includes two questions related to preferences about dams. These questions were designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>This Technical Report was written by the UNH Survey Center and describes the protocols and standards of the Granite State Poll #68 (Client Poll), which includes questions related to preferences about dams, designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>The first file is a screenshot of the Technical Report to provide a preview for Figshare. The second file is the Technical Report in Microsoft Word format.<br>
DOI: 10.6084/m9.figshare.12315089.v3
title: Supplementary Table S1

description: <b>Proteome (A) and Phosphoproteome (B) profile of proteins modulated in wildt-ype strain during caspofungin stress </b>(2µg/ml, 1 h; <i>t</i>-Student test, p &lt; 0.05). <b>A.</b> Table was obtained from Maxquant output file *Proteingroup. The <i>t</i>-Student test was performed between LFQ intensity values for WT not treated (0) or treated with caspofungin. <b>B.</b> Table was obtained from Maxquant output file *Phospho(STY)sites. The <i>t</i>-Student test was performed between Phosphosite intensity values for WT not treated (0) or treated with caspofungin.
DOI: 10.6084/m9.figshare.12312284.v1
title: Granite State Poll #68 (Client Poll) - Technical Report

description: Granite State Poll is a quarterly poll conducted by the University of New Hampshire Survey Center. The poll sample consists of about 500 New Hampshire adults with a working telephone across the state. Each poll contains a series of basic demographic questions that are repeated in future polls, as well as a set of unique questions that are submitted by clients. This poll includes two questions related to preferences about dams. These questions were designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>This Technical Report was written by the UNH Survey Center and describes the protocols and standards of the Granite State Poll #68 (Client Poll), which includes questions related to preferences about dams, designed by Natallia Leuchanka Diessner, Catherine M. Ashcraft, Kevin H. Gardner, and Lawrence C. Hamilton as part of the "Future of Dams" project.<br>The first file is a screenshot of the Technical Report to provide a preview for Figshare. The second file is the Technical Report in Microsoft Word format.<br>