cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13670000
title: ATG5 in microglia does not contribute vitally to autoimmune neuroinflammation in mice

description: Microglia, resident myeloid immune cells of the central nervous system (CNS), actively shape the circuitry of the brain, maintain CNS homeostasis during the steady state and orchestrate immune responses upon CNS injury. Both canonical and non-canonical functions of the macroautophagy/autophagy-related protein ATG5 regulate myeloid cell survival and immune responses. Here, we report that loss of ATG5 in postnatal microglia does not perturb CNS tissue integrity, microglial cell survival, or immune activation. Learning task performances were unchanged in mutant mice. Furthermore, lack of ATG5 expression in microglia had no impact on the development of experimental autoimmune encephalomyelitis. These data indicate that, basal autophagy, identified to be essential for the survival and function of neuronal cells, is not required to maintain CNS homeostasis if absent in adult microglia and ATG5 expression is dispensable for the development of autoimmune neuroinflammation. <b>Abbreviations</b> Ag, antigen; APC, antigen presenting cell; ATG/<i>Atg</i>, autophagy-related; CD, cluster of differentiation; CNS, central nervous system; DC, dendritic cell; EAE, experimental autoimmune encephalomyelitis; fl, floxed; LAP, LC3-associated phagocytosis; LC3, microtubule-associated protein 1 light chain 3; MFI, median fluorescence intensity; MHCII, major histocompatibility complex class II; MOG, myelin oligodendrocyte glycoprotein; MS, multiple sclerosis
DOI: 10.6084/m9.figshare.13603058
title: Lipophagy confers a key metabolic advantage that ensures protective CD8A T-cell responses against HIV-1

description: Although macroautophagy/autophagy has been proposed as a critical defense mechanism against HIV-1 by targeting viral components for degradation, its contribution as a catabolic process in providing optimal anti-HIV-1 immunity has never been addressed. The failure to restore proper antiviral CD8A/CD8 T-cell immunity, especially against HIV-1, is still the major limitation of current antiretroviral therapies. Consequently, it is of clinical imperative to provide new strategies to enhance the function of HIV-1-specific CD8A T-cells in patients under antiretroviral treatments (ART). Here, we investigated whether targeting autophagy activity could be an optional solution to make this possible. Our data show that, after both polyclonal and HIV-1-specific activation, CD8A T-cells from ART displayed reduced autophagy-dependent degradation of lysosomal contents when compared to naturally HIV-1 protected elite controllers (EC). We further confirmed in EC, by using specific <i>BECN1</i> gene silencing and lysosomal inhibitors, the critical role of active autophagy in superior CD8A T-cell protection against HIV-1. More importantly, we found that an IL21 treatment was effective in rescuing the antiviral CD8A T-cell immunity from ART in an autophagy-dependent manner. Finally, we established that IL21-dependent rescue occurred due to the enhanced degradation of endogenous lipids via autophagy, referred to as lipophagy, which fueled the cellular rates of mitochondrial beta-oxidation. In summary, our data show that autophagy/lipophagy can be considered as a therapeutic tool to elicit functional antiviral CD8 T-cell responses. Our results also provide additional insights toward the development of improved T-cell-based prevention and cure strategies against HIV-1. <b>Abbreviations:</b> ART: patients under antiretroviral therapy; BaF: bafilomycin A<sub>1</sub>; BECN1: beclin 1; CEF: cytomegalo-, Epstein-Barr- and flu-virus peptide pool; Chloro.: chloroquine; EC: elite controllers; FAO: fatty acid beta-oxidation; HIV<sup>neg</sup>: HIV-1-uninfected control donors; IFNG/IFN-γ: interferon gamma; IL21: interleukin 21; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PBMC: peripheral blood mononuclear cells; SQSTM1: sequestosome 1; ULK1: unc-51 like autophagy activating kinase 1.
DOI: 10.6084/m9.figshare.13603058.v1
title: Lipophagy confers a key metabolic advantage that ensures protective CD8A T-cell responses against HIV-1

description: Although macroautophagy/autophagy has been proposed as a critical defense mechanism against HIV-1 by targeting viral components for degradation, its contribution as a catabolic process in providing optimal anti-HIV-1 immunity has never been addressed. The failure to restore proper antiviral CD8A/CD8 T-cell immunity, especially against HIV-1, is still the major limitation of current antiretroviral therapies. Consequently, it is of clinical imperative to provide new strategies to enhance the function of HIV-1-specific CD8A T-cells in patients under antiretroviral treatments (ART). Here, we investigated whether targeting autophagy activity could be an optional solution to make this possible. Our data show that, after both polyclonal and HIV-1-specific activation, CD8A T-cells from ART displayed reduced autophagy-dependent degradation of lysosomal contents when compared to naturally HIV-1 protected elite controllers (EC). We further confirmed in EC, by using specific <i>BECN1</i> gene silencing and lysosomal inhibitors, the critical role of active autophagy in superior CD8A T-cell protection against HIV-1. More importantly, we found that an IL21 treatment was effective in rescuing the antiviral CD8A T-cell immunity from ART in an autophagy-dependent manner. Finally, we established that IL21-dependent rescue occurred due to the enhanced degradation of endogenous lipids via autophagy, referred to as lipophagy, which fueled the cellular rates of mitochondrial beta-oxidation. In summary, our data show that autophagy/lipophagy can be considered as a therapeutic tool to elicit functional antiviral CD8 T-cell responses. Our results also provide additional insights toward the development of improved T-cell-based prevention and cure strategies against HIV-1. <b>Abbreviations:</b> ART: patients under antiretroviral therapy; BaF: bafilomycin A<sub>1</sub>; BECN1: beclin 1; CEF: cytomegalo-, Epstein-Barr- and flu-virus peptide pool; Chloro.: chloroquine; EC: elite controllers; FAO: fatty acid beta-oxidation; HIV<sup>neg</sup>: HIV-1-uninfected control donors; IFNG/IFN-γ: interferon gamma; IL21: interleukin 21; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PBMC: peripheral blood mononuclear cells; SQSTM1: sequestosome 1; ULK1: unc-51 like autophagy activating kinase 1.
DOI: 10.6084/m9.figshare.13670000.v1
title: ATG5 in microglia does not contribute vitally to autoimmune neuroinflammation in mice

description: Microglia, resident myeloid immune cells of the central nervous system (CNS), actively shape the circuitry of the brain, maintain CNS homeostasis during the steady state and orchestrate immune responses upon CNS injury. Both canonical and non-canonical functions of the macroautophagy/autophagy-related protein ATG5 regulate myeloid cell survival and immune responses. Here, we report that loss of ATG5 in postnatal microglia does not perturb CNS tissue integrity, microglial cell survival, or immune activation. Learning task performances were unchanged in mutant mice. Furthermore, lack of ATG5 expression in microglia had no impact on the development of experimental autoimmune encephalomyelitis. These data indicate that, basal autophagy, identified to be essential for the survival and function of neuronal cells, is not required to maintain CNS homeostasis if absent in adult microglia and ATG5 expression is dispensable for the development of autoimmune neuroinflammation. <b>Abbreviations</b> Ag, antigen; APC, antigen presenting cell; ATG/<i>Atg</i>, autophagy-related; CD, cluster of differentiation; CNS, central nervous system; DC, dendritic cell; EAE, experimental autoimmune encephalomyelitis; fl, floxed; LAP, LC3-associated phagocytosis; LC3, microtubule-associated protein 1 light chain 3; MFI, median fluorescence intensity; MHCII, major histocompatibility complex class II; MOG, myelin oligodendrocyte glycoprotein; MS, multiple sclerosis
DOI: 10.6084/m9.figshare.13662235
title: The Epstein-Barr virus deubiquitinase BPLF1 targets SQSTM1/p62 to inhibit selective autophagy

description: Macroautophagy/autophagy plays an important role in the control of viral infections and viruses have evolved multiple strategies to interfere with autophagy to avoid destruction and promote their own replication and spread. Here we report that the deubiquitinase encoded in the N-terminal domain of the Epstein-Barr virus (EBV) large tegument protein, BPLF1, regulates selective autophagy. Mass spectrometry analysis identified several vesicular traffic and autophagy related proteins as BPLF1 interactors and potential substrates, suggesting that the viral protein targets this cellular defense during productive infection. Direct binding of BPLF1 to the autophagy receptor SQSTM1/p62 (sequestosome 1) was confirmed by co-immunoprecipitation of transfected BPLF1 and by <i>in vitro</i> affinity isolation of bacterially expressed proteins. Expression of the catalytically active BPLF1 was associated with decreased SQSTM1/p62 ubiquitination and failure to recruit LC3 to SQSTM1/p62-positive aggregates. Selective autophagy was inhibited as illustrated by the accumulation of large protein aggregates in BPLF1-positive cells co-transfected with an aggregate-prone HTT (huntingtin)-Q109 construct, and by a slower autophagy-dependent clearance of protein aggregates upon transfection of BPLF1 in cells expressing a tetracycline-regulated HTT-Q103. The inhibition of aggregate clearance was restored by overexpression of a SQSTM1/p62[E409A,K420R] mutant that does not require ubiquitination of Lys420 for cargo loading. These findings highlight a previously unrecognized role of the viral deubiquitinase in the regulation of selective autophagy, which may promote infection and the production of infectious virus. <b>Abbreviations:</b> BPLF1, BamH1 fragment left open reading frame-1; EBV, Epstein-Barr virus; GFP, green fluorescent protein; HTT, huntingtin; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; PB1, Phox and Bem1 domain; PE, phosphatidylethanolamine; SQSTM1/p62, sequestosome 1; UBA, ubiquitin-associated domain
DOI: 10.6084/m9.figshare.13662235.v1
title: The Epstein-Barr virus deubiquitinase BPLF1 targets SQSTM1/p62 to inhibit selective autophagy

description: Macroautophagy/autophagy plays an important role in the control of viral infections and viruses have evolved multiple strategies to interfere with autophagy to avoid destruction and promote their own replication and spread. Here we report that the deubiquitinase encoded in the N-terminal domain of the Epstein-Barr virus (EBV) large tegument protein, BPLF1, regulates selective autophagy. Mass spectrometry analysis identified several vesicular traffic and autophagy related proteins as BPLF1 interactors and potential substrates, suggesting that the viral protein targets this cellular defense during productive infection. Direct binding of BPLF1 to the autophagy receptor SQSTM1/p62 (sequestosome 1) was confirmed by co-immunoprecipitation of transfected BPLF1 and by <i>in vitro</i> affinity isolation of bacterially expressed proteins. Expression of the catalytically active BPLF1 was associated with decreased SQSTM1/p62 ubiquitination and failure to recruit LC3 to SQSTM1/p62-positive aggregates. Selective autophagy was inhibited as illustrated by the accumulation of large protein aggregates in BPLF1-positive cells co-transfected with an aggregate-prone HTT (huntingtin)-Q109 construct, and by a slower autophagy-dependent clearance of protein aggregates upon transfection of BPLF1 in cells expressing a tetracycline-regulated HTT-Q103. The inhibition of aggregate clearance was restored by overexpression of a SQSTM1/p62[E409A,K420R] mutant that does not require ubiquitination of Lys420 for cargo loading. These findings highlight a previously unrecognized role of the viral deubiquitinase in the regulation of selective autophagy, which may promote infection and the production of infectious virus. <b>Abbreviations:</b> BPLF1, BamH1 fragment left open reading frame-1; EBV, Epstein-Barr virus; GFP, green fluorescent protein; HTT, huntingtin; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; PB1, Phox and Bem1 domain; PE, phosphatidylethanolamine; SQSTM1/p62, sequestosome 1; UBA, ubiquitin-associated domain
DOI: 10.5281/zenodo.5729225
title: Information and results obtained from IoT Platform in Alba Iulia Pilot

description: The IoT platform allows the geolocation of the container, as well as manage the information of the filling level and traceability of trucks. The eco driving application on board of the truck sends the data from the truck (location, speed, RPM and engine load) t o the IoT platform where it is stored. At the same time sound alarms are emitted when driver excess the ecodriving parameters in the Android application. Besides this, the application receives from the IoT platform the position of the containers that must be collected. In this way the driver can see the position, order of collection of the containers and pathway to collect them, as explained above.<br> The IoT platform receives the information of the labels dispensed from the smart containers. The score of the characterized bags were registered in the platform as explained in the next section. Attached the different data sets generated during the project. For general info, follow the link: https://plasticircle.eu/home/
DOI: 10.5281/zenodo.5729224
title: Information and results obtained from IoT Platform in Alba Iulia Pilot

description: The IoT platform allows the geolocation of the container, as well as manage the information of the filling level and traceability of trucks. The eco driving application on board of the truck sends the data from the truck (location, speed, RPM and engine load) t o the IoT platform where it is stored. At the same time sound alarms are emitted when driver excess the ecodriving parameters in the Android application. Besides this, the application receives from the IoT platform the position of the containers that must be collected. In this way the driver can see the position, order of collection of the containers and pathway to collect them, as explained above.<br> The IoT platform receives the information of the labels dispensed from the smart containers. The score of the characterized bags were registered in the platform as explained in the next section. Attached the different data sets generated during the project. For general info, follow the link: https://plasticircle.eu/home/
DOI: 10.5281/zenodo.5531917
title: Data and Code for Spin and Orbital Spectroscopy in the Absence of Coulomb Blockade in Lead Telluride Nanowire Quantum Dots

description: This repository contains combined data for two papers. Growth of PbTe nanowires by Molecular Beam Epitaxy<br> Authors: Sander G. Schellingerhout, Eline J. de Jong, Maksim Gomanko, Xin Guan, Yifan Jiang, Max S.M. Hoskam,<br> Sebastian Koelling, Oussama Moutanabbir, Marcel A. Verheijen, Sergey M. Frolov, Erik P.A.M. Bakkers <br> Spin and Orbital Spectroscopy in the Absence of Coulomb Blockade in Lead Telluride Nanowire Quantum Dots<br> Authors: M. Gomanko, E.J. de Jong, Y. Jiang, S.G. Schellingerhout, E.P.A.M. Bakkers, and S.M. Frolov <br> Content of this repository: Readme file. /RawData/<br> Original data obtained at the time of measurement separated into 3 folders from different chips/cooldowns<br> Data from devices 1,3 and 4 can be found in "RawData/PbTe_chip1", device 2 in "RawData/PbTe_chip2" and devices 5-8 in "RawData/PbTe_GBg" /Measurement notebooks/<br> OneNote notebook with 4 different sections for 3 chips (two sections for backgate chip). Pages in these sections contain the device number in the name.<br> Also, the same notebook is exported in pdf format for convenience. /Data processing/<br> Readme file, Jupiter notebooks, data files, and pictures, that were used to extract g-factors for different field orientations in device2. /Data summaries/<br> Powerpoints, that were used to overview data during the measurement stage.<br> Not all data from these powerpoints are present in the repository or paper (specifically excluding early data used in "additional backgate devices.pptx" and "PbTe 3rd device.pptx"). Data file types: data_NNN.dat - the original data file obtained at the time of the experiment<br> dataNNN.py - the original QTLab data acquisition script saved with data<br> data_NNN.set - settings of measurement instruments at the time of measurement<br> data_NNN.meta - auxillary file necessary for plotting data using SpyView (see below) <br> data_NNN.MTX - a simple 2D/3D matrix format developed for Spyview NNN stands for dataset number, automatically indexed by QTLab <br> How to plot data: 1) Spyview - a free data plotting program written by Gary Steele Data in this repository can be simply dropped into Spyview for plotting. Spyview also produces and can read .mtx files which are available for some of the data in this repository. https://nsweb.tn.tudelft.nl/~gsteele/spyview/ <br> 2) QTPlot - a Python plotter written by Ruben van Gulik Data in this repository can be directly opened with QTPlot, which will read axis labels. https://github.com/Rubenknex/qtplot Note: requires PyQT4
DOI: 10.5281/zenodo.5531916
title: Data and Code for Spin and Orbital Spectroscopy in the Absence of Coulomb Blockade in Lead Telluride Nanowire Quantum Dots

description: This repository contains combined data for two papers. Growth of PbTe nanowires by Molecular Beam Epitaxy<br> Authors: Sander G. Schellingerhout, Eline J. de Jong, Maksim Gomanko, Xin Guan, Yifan Jiang, Max S.M. Hoskam,<br> Sebastian Koelling, Oussama Moutanabbir, Marcel A. Verheijen, Sergey M. Frolov, Erik P.A.M. Bakkers <br> Spin and Orbital Spectroscopy in the Absence of Coulomb Blockade in Lead Telluride Nanowire Quantum Dots<br> Authors: M. Gomanko, E.J. de Jong, Y. Jiang, S.G. Schellingerhout, E.P.A.M. Bakkers, and S.M. Frolov <br> Content of this repository: Readme file. /RawData/<br> Original data obtained at the time of measurement separated into 3 folders from different chips/cooldowns<br> Data from devices 1,3 and 4 can be found in "RawData/PbTe_chip1", device 2 in "RawData/PbTe_chip2" and devices 5-8 in "RawData/PbTe_GBg" /Measurement notebooks/<br> OneNote notebook with 4 different sections for 3 chips (two sections for backgate chip). Pages in these sections contain the device number in the name.<br> Also, the same notebook is exported in pdf format for convenience. /Data processing/<br> Readme file, Jupiter notebooks, data files, and pictures, that were used to extract g-factors for different field orientations in device2. /Data summaries/<br> Powerpoints, that were used to overview data during the measurement stage.<br> Not all data from these powerpoints are present in the repository or paper (specifically excluding early data used in "additional backgate devices.pptx" and "PbTe 3rd device.pptx"). Data file types: data_NNN.dat - the original data file obtained at the time of the experiment<br> dataNNN.py - the original QTLab data acquisition script saved with data<br> data_NNN.set - settings of measurement instruments at the time of measurement<br> data_NNN.meta - auxillary file necessary for plotting data using SpyView (see below) <br> data_NNN.MTX - a simple 2D/3D matrix format developed for Spyview NNN stands for dataset number, automatically indexed by QTLab <br> How to plot data: 1) Spyview - a free data plotting program written by Gary Steele Data in this repository can be simply dropped into Spyview for plotting. Spyview also produces and can read .mtx files which are available for some of the data in this repository. https://nsweb.tn.tudelft.nl/~gsteele/spyview/ <br> 2) QTPlot - a Python plotter written by Ruben van Gulik Data in this repository can be directly opened with QTPlot, which will read axis labels. https://github.com/Rubenknex/qtplot Note: requires PyQT4
DOI: 10.24339/82896eee-7e08-4a6a-97ca-640e098c4cbd
title: Child-UP Focus Groups with Children, Greater London Primary Schools

description: Focus Groups with Children, EU Horizon 2020 Child-UP, Transcriptions
DOI: 10.5281/zenodo.5729308
title: List of promoters

description: These are annotated lists of potential promoters identified by the novel method proposed on the article <strong>Machine learning and statistics shape a novel path in archaeal genome annotation</strong>.
DOI: 10.5281/zenodo.5729307
title: List of promoters

description: These are annotated lists of potential promoters identified by the novel method proposed on the article <strong>Machine learning and statistics shape a novel path in archaeal genome annotation</strong>.
DOI: 10.5255/ukda-sn-855294
title: Learning Outcomes and Teacher Effectiveness for Children Facing Multiple Disadvantages in India and Pakistan, 2015-2018

description: The quantitative data from the TEACh project allows us to identify the characteristics of children not learning, and factors associated with disparities in educational outcomes in India and Pakistan. Information was collected from households and schools, at the beginning of the school year (in April). Assessments were made in school again at the end of the school year to identify what learning gains have been made, and the role of teacher and other factors (such as related parental support) in these gains for children with different characteristics. The first stage of the quantitative data collection required us to identify the children whose learning we want to assess. Cross-sectional data was collected from households to enumerate key household and individual characteristics. This included information such as household size and socio-economic status, as well as individual information on all of the children within the household (irrespective of their schooling participation). The household survey provides the first step towards quantifying whether children with different characteristics are in school. For those in school, it identifies the type of school they are attending (whether a mainstream or special school, and whether run by government, private sector, or NGOs). We also assessed learning of children aged 8-12 (approximately equivalent to grades 3-5) in the selected households. The second stage was to identify primary schools within the vicinity that are accessed by a majority of the children in the sample community or village. Children in grades 3-5 were tested both at the beginning and end of the school year in order to identify learning gains, using the same instruments as used in the households. These classes contained some children from the sampled households which allows us to link them back to the household information that has been gathered. Some basic household level information was also collected from all sampled children in the school (such as parental education and household size) to ensure this information is available for all children. Questionnaires were also administered to teachers to identify their background and other characteristics commonly associated with teacher effectiveness. Existing instruments such asSchoolTELLS in India and Pakistan, were adapted to draft the teacher surveys. The teacher instruments were designed to capture the extent to which teachers are aware of, and respond to, children’s diverse learning needs, their perceptions and attitudes towards these children, and the extent to which they feel prepared to teach children of different abilities, including related to training and other forms of support that they receive. As with SchoolTELLS, teachers were also asked to mark student tests to identify teachers’ content knowledge of subjects they are teaching.