cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1601992
title: Improvement of the adhesion between polyaniline and commercial carbon paper by acid treatment and its application in supercapacitor electrodes

description: Commercial carbon paper was coated with polyaniline (PANI) using <i>in situ</i> polymerization of aniline. Prior to the PANI coating, acid treatment was performed to carboxylate the surface of the carbon paper for enhancing PANI adhesion by sonication of the carbon paper in a mixture of concentrated sulfuric and nitric acids. The loading mass density of PANI on the acid-treated carbon paper increased more than three times compared to that on the carbon paper without acid treatment. The specific capacitance also increased from 112 to 174 F/g in a two-electrode system (calculated using a total mass of carbon paper and PANI) due to better PANI coating on the acid-treated carbon paper. The simple acid treatment provides good adhesion of PANI to the commercial carbon paper and can be applied to prepare supercapacitor electrodes.
DOI: 10.6084/m9.figshare.1601992.v1
title: Improvement of the adhesion between polyaniline and commercial carbon paper by acid treatment and its application in supercapacitor electrodes

description: Commercial carbon paper was coated with polyaniline (PANI) using <i>in situ</i> polymerization of aniline. Prior to the PANI coating, acid treatment was performed to carboxylate the surface of the carbon paper for enhancing PANI adhesion by sonication of the carbon paper in a mixture of concentrated sulfuric and nitric acids. The loading mass density of PANI on the acid-treated carbon paper increased more than three times compared to that on the carbon paper without acid treatment. The specific capacitance also increased from 112 to 174 F/g in a two-electrode system (calculated using a total mass of carbon paper and PANI) due to better PANI coating on the acid-treated carbon paper. The simple acid treatment provides good adhesion of PANI to the commercial carbon paper and can be applied to prepare supercapacitor electrodes.
DOI: 10.6084/m9.figshare.1601998
title: Casein kinases as potential therapeutic targets

description: <b><i>Introduction:</i></b> The conventional term ‘casein kinase’ (CK) denotes three classes of kinases – CK1, CK2 and Golgi-CK (G-CK)/Fam20C (family with sequence similarity 20, member C) – sharing the ability to phoshorylate casein <i>in vitro,</i> but otherwise unrelated to each other. All CKs have been reported to be implicated in human diseases, and reviews individually dealing with the druggability of CK1 and CK2 are available. Our aim is to provide a comparative analysis of the three classes of CKs as therapeutic targets. <b><i>Areas covered:</i></b> CK2 is the CK for which implication in neoplasia is best documented, with the survival of cancer cells often relying on its overexpression. An ample variety of cell-permeable CK2 inhibitors have been developed, with a couple of these now in clinical trials. Isoform-specific CK1 inhibitors that are expected to play a beneficial role in oncology and neurodegeneration have been also developed. In contrast, the pathogenic potential of G-CK/Fam20C is caused by its loss of function. Activators of Fam20C, notably sphingolipids and their analogs, may prove beneficial in this respect. <b><i>Expert opinion:</i></b> Optimization of CK2 and CK1 inhibitors will prove useful to develop new therapeutic strategies for treating cancer and neurodegenerative disorders, while the design of potent activators of G-CK/Fam20C will provide a new tool in the fields of bio-mineralization and hypophosphatemic diseases.
DOI: 10.6084/m9.figshare.1601998.v2
title: Casein kinases as potential therapeutic targets

description: <b><i>Introduction:</i></b> The conventional term ‘casein kinase’ (CK) denotes three classes of kinases – CK1, CK2 and Golgi-CK (G-CK)/Fam20C (family with sequence similarity 20, member C) – sharing the ability to phoshorylate casein <i>in vitro,</i> but otherwise unrelated to each other. All CKs have been reported to be implicated in human diseases, and reviews individually dealing with the druggability of CK1 and CK2 are available. Our aim is to provide a comparative analysis of the three classes of CKs as therapeutic targets. <b><i>Areas covered:</i></b> CK2 is the CK for which implication in neoplasia is best documented, with the survival of cancer cells often relying on its overexpression. An ample variety of cell-permeable CK2 inhibitors have been developed, with a couple of these now in clinical trials. Isoform-specific CK1 inhibitors that are expected to play a beneficial role in oncology and neurodegeneration have been also developed. In contrast, the pathogenic potential of G-CK/Fam20C is caused by its loss of function. Activators of Fam20C, notably sphingolipids and their analogs, may prove beneficial in this respect. <b><i>Expert opinion:</i></b> Optimization of CK2 and CK1 inhibitors will prove useful to develop new therapeutic strategies for treating cancer and neurodegenerative disorders, while the design of potent activators of G-CK/Fam20C will provide a new tool in the fields of bio-mineralization and hypophosphatemic diseases.
DOI: 10.6084/m9.figshare.1601988
title: DATA - Immigration rate in relation to density

description: *Immigration data in response to a localized and experimental removal of two related damselfish species (<i>Stegastes diencaeus </i>and <i>S. adustus</i>). This dataset contains 12 columns. Data were collected in Barbados between 2005 and 2007 during summer.<br> Column 1; SITES: site in witch the experiment was performed. <br>Column 2; DATE_REMOVAL: Date at which the removal event was performed<br>Column3; REMOVAL: Sequential Removal event (0 = before the density manipulation). Column 4: DENSITY: Damselfish density on the site AFTER a given removal event. If REMOVAL = 0, no damselfish was removed so the number represents the initial population size<br>Column 5: NUMBER_HARVESTED_FISH: The number of harvested individual per removal eventColumn 6: IMMIGRANTS_PER_REMOVAL: The number of immigrants after a given removal event Column 7: IMMIGRANTS_PER_NEW_VACANCY: The number of immigrants per new vacancy created. Immigrants/vacancy; where vacancy = (DENSITY t-1)-(DENSITYt)<br> Column 8: IMMIGRANTS_PER_RESIDENT: Per capita immigration rate. IMMIGRANTS/DENSITYColumn 9: HARVESTED_STDI: Number of harvested <i>Stegastes diencaeus</i> (Longfin damselfish)<br>Column 10: HARVESTED_STAD Number of harvested <i>Stegastes adustus</i> (Dusky damselfish)Column 11: IMMIGRANTS_STDI Number of immigrants <i>Stegastes diencaeus</i> (Longfin damselfish)Column 12: IMMIGRANTS_STAD: Number of immigrants <i>Stegastes adustus</i> (Dusky damselfish)<br><br>
DOI: 10.6084/m9.figshare.1601968
title: Anvi'o pangenomic workflow

description: While multiple bioinformatics software are already available to generate and/or visualize pangenomes, interfaces do not necessary offer flexible analysis performances, limiting the user's capabilities interacting with their data. We recently have introduced a software platform, anvi'o, to bridge some of the gaps in our common bioinformatics toolkit. We are happy to announce that anvi'o can now process, visualize and manipulate pangenomic data in a user-friendly environment. Some modules are still under construction for a fully automatized workflow. Nevertheless, the current anvi'o interface already offers novel opportunities to combine pangenomes with a variety of contextual metadata and exports high-quality figures for publications. This blog describes original pangenomic investigations of publically available genomic collections. It is set to introduce the anvi'o pangenomic workflow to our enthusiastic users community.
DOI: 10.6084/m9.figshare.1601988.v1
title: DATA - Immigration rate in relation to density

description: *Immigration data in response to a localized and experimental removal of two related damselfish species (<i>Stegastes diencaeus </i>and <i>S. adustus</i>). This dataset contains 12 columns. Data were collected in Barbados between 2005 and 2007 during summer.<br> Column 1; SITES: site in witch the experiment was performed. <br>Column 2; DATE_REMOVAL: Date at which the removal event was performed<br>Column3; REMOVAL: Sequential Removal event (0 = before the density manipulation). Column 4: DENSITY: Damselfish density on the site AFTER a given removal event. If REMOVAL = 0, no damselfish was removed so the number represents the initial population size<br>Column 5: NUMBER_HARVESTED_FISH: The number of harvested individual per removal eventColumn 6: IMMIGRANTS_PER_REMOVAL: The number of immigrants after a given removal event Column 7: IMMIGRANTS_PER_NEW_VACANCY: The number of immigrants per new vacancy created. Immigrants/vacancy; where vacancy = (DENSITY t-1)-(DENSITYt)<br> Column 8: IMMIGRANTS_PER_RESIDENT: Per capita immigration rate. IMMIGRANTS/DENSITYColumn 9: HARVESTED_STDI: Number of harvested <i>Stegastes diencaeus</i> (Longfin damselfish)<br>Column 10: HARVESTED_STAD Number of harvested <i>Stegastes adustus</i> (Dusky damselfish)Column 11: IMMIGRANTS_STDI Number of immigrants <i>Stegastes diencaeus</i> (Longfin damselfish)Column 12: IMMIGRANTS_STAD: Number of immigrants <i>Stegastes adustus</i> (Dusky damselfish)<br><br>
DOI: 10.6084/m9.figshare.1601975
title: GSE37704 sample data

description: Six samples from GSE37704, mapped with STAR to GRCh38, counted with featureCounts, restricted to protein-coding genes only.
DOI: 10.6084/m9.figshare.1601968.v1
title: Anvi'o pangenomic workflow tutorial

description: While multiple bioinformatics software are already available to generate and/or visualize pangenomes, interfaces do not necessary offer flexible analysis performances, limiting the user's capabilities interacting with their data. We recently have introduced a software platform, anvi'o, to bridge some of the gaps in our common bioinformatics toolkit. We are happy to announce that anvi'o can now process, visualize and manipulate pangenomic data in a user-friendly environment. Some modules are still under construction for a fully automatized workflow. Nevertheless, the current anvi'o interface already offers novel opportunities to combine pangenomes with a variety of contextual metadata and exports high-quality figures for publications. This blog describes original pangenomic investigations of publically available genomic collections. It is set to introduce the anvi'o pangenomic workflow to our enthusiastic users community.
DOI: 10.6084/m9.figshare.1601938.v2
title: Autophagy contributes to regulation of the hypoxia response during submergence in <i>Arabidopsis thaliana</i>

description: Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In mammals, hypoxia rapidly stimulates autophagy as a cell survival response. Here, we examine the function of autophagy in the regulation of the plant response to submergence, an abiotic stress that leads to hypoxia and anaerobic respiration in plant cells. In <i>Arabidopsis thaliana</i>, submergence induces the transcription of autophagy-related (<i>ATG</i>) genes and the formation of autophagosomes. Consistent with this, the autophagy-defective (<i>atg</i>) mutants are hypersensitive to submergence stress and treatment with ethanol, the end product of anaerobic respiration. Upon submergence, the <i>atg</i> mutants have increased levels of transcripts of anaerobic respiration genes (<i>alcohol dehydrogenase 1, ADH1</i> and <i>pyruvate decarboxylase 1, PDC1</i>), but reduced levels of transcripts of other hypoxia- and ethylene-responsive genes. Both submergence and ethanol treatments induce the accumulation of reactive oxygen species (ROS) in the rosettes of <i>atg</i> mutants more than in the wild type. Moreover, the production of ROS by the nicotinamide adenine dinucleotide phosphate (NADPH) oxidases is necessary for plant tolerance to submergence and ethanol, submergence-induced expression of <i>ADH1</i> and <i>PDC1</i>, and activation of autophagy. The submergence- and ethanol-sensitive phenotypes in the <i>atg</i> mutants depend on a complete salicylic acid (SA) signaling pathway. Together, our findings demonstrate that submergence-induced autophagy functions in the hypoxia response in <i>Arabidopsis</i> by modulating SA-mediated cellular homeostasis.
DOI: 10.6084/m9.figshare.1601983
title: Getting Funded Supplements

description: Supplements for Book, Getting Funded by Chandra S. Mishra, Palgrave Macmillan, 2015
DOI: 10.6084/m9.figshare.1601938.v1
title: Autophagy contributes to regulation of the hypoxia response during submergence in <i>Arabidopsis thaliana</i>

description: Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In mammals, hypoxia rapidly stimulates autophagy as a cell survival response. Here, we examine the function of autophagy in the regulation of the plant response to submergence, an abiotic stress that leads to hypoxia and anaerobic respiration in plant cells. In <i>Arabidopsis thaliana</i>, submergence induces the transcription of autophagy-related (<i>ATG</i>) genes and the formation of autophagosomes. Consistent with this, the autophagy-defective (<i>atg</i>) mutants are hypersensitive to submergence stress and treatment with ethanol, the end product of anaerobic respiration. Upon submergence, the <i>atg</i> mutants have increased levels of transcripts of anaerobic respiration genes (<i>alcohol dehydrogenase 1, ADH1</i> and <i>pyruvate decarboxylase 1, PDC1</i>), but reduced levels of transcripts of other hypoxia- and ethylene-responsive genes. Both submergence and ethanol treatments induce the accumulation of reactive oxygen species in the rosettes of <i>atg</i> mutants more than in the wild type. Moreover, the production of reactive oxygen species by the nicotinamide adenine dinucleotide phosphate (NADPH) oxidases is necessary for plant tolerance to submergence and ethanol, submergence-induced expression of <i>ADH1</i> and <i>PDC1</i>, and activation of autophagy. The submergence- and ethanol-sensitive phenotypes in the <i>atg</i> mutants depend on a complete salicylic acid (SA) signaling pathway. Together, our findings demonstrate that submergence-induced autophagy functions in the hypoxia response in <i>Arabidopsis</i> by modulating SA-mediated cellular homeostasis.
DOI: 10.6084/m9.figshare.1601968.v2
title: Anvi'o pangenomic workflow tutorial

description: While multiple bioinformatics software are already available to generate and/or visualize pangenomes, interfaces do not necessary offer flexible analysis performances, limiting the user's capabilities interacting with their data. We recently have introduced a software platform, anvi'o, to bridge some of the gaps in our common bioinformatics toolkit. We are happy to announce that anvi'o can now process, visualize and manipulate pangenomic data in a user-friendly environment. Some modules are still under construction for a fully automatized workflow. Nevertheless, the current anvi'o interface already offers novel opportunities to combine pangenomes with a variety of contextual metadata and exports high-quality figures for publications. This blog describes original pangenomic investigations of publically available genomic collections. It is set to introduce the anvi'o pangenomic workflow to our enthusiastic users community.
DOI: 10.6084/m9.figshare.1601968.v3
title: Anvi

description: While multiple bioinformatics software are already available to generate and/or visualize pangenomes, interfaces do not necessary offer flexible analysis performances, limiting the user's capabilities interacting with their data. We recently have introduced a software platform, anvi'o, to bridge some of the gaps in our common bioinformatics toolkit. We are happy to announce that anvi'o can now process, visualize and manipulate pangenomic data in a user-friendly environment. Some modules are still under construction for a fully automatized workflow. Nevertheless, the current anvi'o interface already offers novel opportunities to combine pangenomes with a variety of contextual metadata and exports high-quality figures for publications. This blog describes original pangenomic investigations of publically available genomic collections. It is set to introduce the anvi'o pangenomic workflow to our enthusiastic users community.
DOI: 10.6084/m9.figshare.1601913
title: Atg41/Icy2 regulates autophagosome formation

description: Macroautophagy (hereafter autophagy) is one of the major degradation systems in eukaryotic cells, and its dysfunction may result in diseases ranging from neurodegeneration to cancer. Although most of the autophagy-related (Atg) proteins that function in this pathway were first identified in yeast, many were subsequently shown to have homologs in higher eukaryotes including humans, and the overall mechanism of autophagy is highly conserved. The most prominent feature of autophagy is the formation of a double-membrane sequestering compartment, the phagophore; this transient organelle surrounds part of the cytoplasm and matures into an autophagosome, which subsequently fuses with the vacuole or lysosome to allow degradation of the cargo. Much attention has focused on the process involved in phagophore nucleation and expansion, but many questions remain. Here, we identified the yeast protein Icy2, which we now name Atg41, as playing a role in autophagosome formation. Atg41 interacts with the transmembrane protein Atg9, a key component involved in autophagosome biogenesis, and both proteins display a similar localization profile. Under autophagy-inducing conditions the expression level of Atg41 increases dramatically and is regulated by the transcription factor Gcn4. This work provides further insight into the mechanism of Atg9 function and the dynamics of sequestering membrane formation during autophagy.
DOI: 10.6084/m9.figshare.1601915
title: Reactivation of autophagy by spermidine ameliorates the myopathic defects of collagen VI-null mice

description: Autophagy is a self-degradative process responsible for the clearance of damaged or unnecessary cellular components. We have previously found that persistence of dysfunctional organelles due to autophagy failure is a key event in the pathogenesis of COL6/collagen VI-related myopathies, and have demonstrated that reactivation of a proper autophagic flux rescues the muscle defects of <i>Col6a1</i>-null (<i>col6a1</i><sup><i>−/−</i></sup>) mice. Here we show that treatment with spermidine, a naturally occurring nontoxic autophagy inducer, is beneficial for <i>col6a1</i><sup><i>−/−</i></sup> mice. Systemic administration of spermidine in <i>col6a1</i><sup><i>−/−</i></sup> mice reactivated autophagy in a dose-dependent manner, leading to a concurrent amelioration of the histological and ultrastructural muscle defects. The beneficial effects of spermidine, together with its being easy to administer and the lack of overt side effects, open the field for the design of novel nutraceutical strategies for the treatment of muscle diseases characterized by autophagy impairment.
DOI: 10.6084/m9.figshare.1601912
title: Analysis of the native conformation of the LIR/AIM motif in the Atg8/LC3/GABARAP-binding proteins

description: The Atg8/LC3/GABARAP family of proteins, a group that has structural homology with ubiquitin, connects with a large set of binding partners to function in macroautophagy (hereafter autophagy). This interaction occurs primarily via a conserved motif termed the LC3-interacting region (LIR), or the Atg8-interacting motif (AIM). The consensus sequence for this motif, [W/F/Y]xx[L/I/V], can be found in many proteins, but only some of them are physiological partners containing a functional LIR/AIM. Because the structure of many full-length partners has not been, or cannot be, solved, the structural context of the LIR/AIM within the native protein conformation is not obvious. Here we suggest that the functional LIR/AIM is a short linear motif (SLiM) protein-binding module, arising from an intrinsically disordered region. This finding enables the rapid elimination of some false Atg8/LC3/GABARAP-binding proteins, and connects the exponentially growing knowledge on disordered SLiMs with autophagy.
DOI: 10.6084/m9.figshare.1601968.v4
title: Anvi

description: While multiple bioinformatics software are already available to generate and/or visualize pangenomes, interfaces do not necessary offer flexible analysis performances, limiting the user's capabilities interacting with their data. We recently have introduced a software platform, anvi'o, to bridge some of the gaps in our common bioinformatics toolkit. We are happy to announce that anvi'o can now process, visualize and manipulate pangenomic data in a user-friendly environment. Some modules are still under construction for a fully automatized workflow. Nevertheless, the current anvi'o interface already offers novel opportunities to combine pangenomes with a variety of contextual metadata and exports high-quality figures for publications. This blog describes original pangenomic investigations of publically available genomic collections. It is set to introduce the anvi'o pangenomic workflow to our enthusiastic users community.
DOI: 10.6084/m9.figshare.1601911
title: Autophagy positively regulates DNA damage recognition by nucleotide excision repair

description: Macroautophagy (hereafter autophagy) is a cellular catabolic process that is essential for maintaining tissue homeostasis and regulating various normal and pathologic processes in human diseases including cancer. One cancer-driving process is accumulation of genetic mutations due to impaired DNA damage repair, including nucleotide excision repair. Here we show that autophagy positively regulates nucleotide excision repair through enhancing DNA damage recognition by the DNA damage sensor proteins XPC and DDB2 <i>via</i> 2 pathways. First, autophagy deficiency downregulates the transcription of <i>XPC</i> through TWIST1-dependent activation of the transcription repressor complex E2F4-RBL2. Second, autophagy deficiency impairs the recruitment of DDB2 to ultraviolet radiation (UV)-induced DNA damage sites through TWIST1-mediated inhibition of EP300. In mice, the pharmacological autophagy inhibitor Spautin-1 promotes UVB-induced tumorigenesis, whereas the autophagy inducer rapamycin reduces UVB-induced tumorigenesis. These findings demonstrate the crucial role of autophagy in maintaining proper nucleotide excision repair in mammalian cells and suggest a previously unrecognized tumor-suppressive mechanism of autophagy in cancer.
DOI: 10.6084/m9.figshare.1601910
title: Tom August - Workflow number #1

description: In this workflow I demonstrate the powers of the ZOON R package