cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7097693
title: A simple in vitro assay for assessing the efficacy, mechanisms and kinetics of anti-prion fibril compounds

description: Prion diseases are caused by the conversion of normal cellular prion proteins (PrP) into lethal prion aggregates. These prion aggregates are composed of proteinase K (PK) resistant fibrils and comparatively PK-sensitive oligomers. Currently there are no anti-prion pharmaceuticals available to treat or prevent prion disease. Methods of discovering anti-prion molecules rely primarily on relatively complex cell-based, tissue slice or animal-model assays that measure the effects of small molecules on the formation of PK-resistant prion fibrils. These assays are difficult to perform and do not detect the compounds that directly inhibit oligomer formation or alter prion conversion kinetics. We have developed a simple cell-free method to characterize the impact of anti-prion fibril compounds on both the oligomer and fibril formation. In particular, this assay uses shaking-induced conversion (ShIC) of recombinant PrP in a 96-well format and resolution enhanced native acidic gel electrophoresis (RENAGE) to generate, assess and detect PrP fibrils in a high throughput fashion. The end-point PrP fibrils from this assay can be further characterized by PK analysis and negative stain transmission electron microscopy (TEM). This cell-free, gel-based assay generates metrics to assess anti-prion fibril efficacy and kinetics. To demonstrate its utility, we characterized the action of seven well-known anti-prion molecules: Congo red, curcumin, GN8, quinacrine, chloropromazine, tetracycline, and TUDCA (taurourspdeoxycholic acid), as well as four suspected anti-prion compounds: trans-resveratrol, rosmarinic acid, myricetin and ferulic acid. These findings suggest that this <i>in vitro</i> assay could be useful in identifying and comprehensively assessing novel anti-prion fibril compounds. <b>Abbreviations:</b> PrP, prion protein; PK, proteinase K; ShIC, shaking-induced conversion; RENAGE, resolution enhanced native acidic gel electrophoresis; TEM, transmission electron microscopy; TUDCA, taurourspdeoxycholic acid; BSE, bovine spongiform encephalopathy; CWD, chronic wasting disease; CJD, Creutzfeldt Jakob disease; GSS, Gerstmann–Sträussler–Scheinker syndrome; FFI, fatal familial insomnia; PrP<sup>c</sup>, cellular prion protein; recPrP<sup>C</sup>, recombinant monomeric prion protein; PrP<sup>Sc</sup>, infectious particle of misfolded prion protein; RT-QuIC, real-time quaking-induced conversion; PMCA, Protein Misfolding Cyclic Amplification; LPS, lipopolysaccharide; EGCG, epigallocatechin gallate; GN8, 2-pyrrolidin-1-yl-N-[4-[4-(2-pyrrolidin-1-yl-acetylamino)-benzyl]-phenyl]-acetamide; DMSO, dimethyl sulfoxide; ScN2A, scrapie infected neuroblastoma cells; IC50, inhibitory concentration for 50% reduction; recMoPrP <sup>23−231</sup>, recombinant full-length mouse prion protein residues 23-231; EDTA; PICUP, photo-induced cross-linking of unmodified protein; BSA, bovine serum albumin;; PMSF, phenylmethanesulfonyl fluoride.
DOI: 10.6084/m9.figshare.7097675
title: Data with Warming and Grazing.xlsx

description: Grazing buffers the effect of climatic change on species diversity of seedlings in an alpine meadow on the Tibetan Plateau
DOI: 10.6084/m9.figshare.7097693.v2
title: A simple in vitro assay for assessing the efficacy, mechanisms and kinetics of anti-prion fibril compounds

description: Prion diseases are caused by the conversion of normal cellular prion proteins (PrP) into lethal prion aggregates. These prion aggregates are composed of proteinase K (PK) resistant fibrils and comparatively PK-sensitive oligomers. Currently there are no anti-prion pharmaceuticals available to treat or prevent prion disease. Methods of discovering anti-prion molecules rely primarily on relatively complex cell-based, tissue slice or animal-model assays that measure the effects of small molecules on the formation of PK-resistant prion fibrils. These assays are difficult to perform and do not detect the compounds that directly inhibit oligomer formation or alter prion conversion kinetics. We have developed a simple cell-free method to characterize the impact of anti-prion fibril compounds on both the oligomer and fibril formation. In particular, this assay uses shaking-induced conversion (ShIC) of recombinant PrP in a 96-well format and resolution enhanced native acidic gel electrophoresis (RENAGE) to generate, assess and detect PrP fibrils in a high throughput fashion. The end-point PrP fibrils from this assay can be further characterized by PK analysis and negative stain transmission electron microscopy (TEM). This cell-free, gel-based assay generates metrics to assess anti-prion fibril efficacy and kinetics. To demonstrate its utility, we characterized the action of seven well-known anti-prion molecules: Congo red, curcumin, GN8, quinacrine, chloropromazine, tetracycline, and TUDCA (taurourspdeoxycholic acid), as well as four suspected anti-prion compounds: trans-resveratrol, rosmarinic acid, myricetin and ferulic acid. These findings suggest that this <i>in vitro</i> assay could be useful in identifying and comprehensively assessing novel anti-prion fibril compounds. <b>Abbreviations:</b> PrP, prion protein; PK, proteinase K; ShIC, shaking-induced conversion; RENAGE, resolution enhanced native acidic gel electrophoresis; TEM, transmission electron microscopy; TUDCA, taurourspdeoxycholic acid; BSE, bovine spongiform encephalopathy; CWD, chronic wasting disease; CJD, Creutzfeldt Jakob disease; GSS, Gerstmann–Sträussler–Scheinker syndrome; FFI, fatal familial insomnia; PrP<sup>c</sup>, cellular prion protein; recPrP<sup>C</sup>, recombinant monomeric prion protein; PrP<sup>Sc</sup>, infectious particle of misfolded prion protein; RT-QuIC, real-time quaking-induced conversion; PMCA, Protein Misfolding Cyclic Amplification; LPS, lipopolysaccharide; EGCG, epigallocatechin gallate; GN8, 2-pyrrolidin-1-yl-N-[4-[4-(2-pyrrolidin-1-yl-acetylamino)-benzyl]-phenyl]-acetamide; DMSO, dimethyl sulfoxide; ScN2A, scrapie infected neuroblastoma cells; IC50, inhibitory concentration for 50% reduction; recMoPrP <sup>23−231</sup>, recombinant full-length mouse prion protein residues 23-231; EDTA; PICUP, photo-induced cross-linking of unmodified protein; BSA, bovine serum albumin;; PMSF, phenylmethanesulfonyl fluoride.
DOI: 10.6084/m9.figshare.7097693.v1
title: A Simple In Vitro Assay for Assessing the Efficacy, Mechanisms and Kinetics of Anti-Prion Fibril Compounds

description: Prion diseases are caused by the conversion of normal cellular prion proteins (PrP) into lethal prion aggregates. These prion aggregates are composed of proteinase K (PK) resistant fibrils and comparatively PK-sensitive oligomers. Currently there are no anti-prion pharmaceuticals available to treat or prevent prion disease. Methods of discovering anti-prion molecules rely primarily on relatively complex cell-based, tissue slice or animal-model assays that measure the effects of small molecules on the formation of PK-resistant prion fibrils. These assays are difficult to perform and do not detect the compounds that directly inhibit oligomer formation or alter prion conversion kinetics. We have developed a simple cell-free method to characterize the impact of anti-prion fibril compounds on both the oligomer and fibril formation. In particular, this assay uses shaking-induced conversion (ShIC) of recombinant PrP in a 96-well format and resolution enhanced native acidic gel electrophoresis (RENAGE) to generate, assess and detect PrP fibrils in a high throughput fashion. The end-point PrP fibrils from this assay can be further characterized by PK analysis and negative stain transmission electron microscopy (TEM). This cell-free, gel-based assay generates metrics to assess anti-prion fibril efficacy and kinetics. To demonstrate its utility, we characterized the action of seven well-known anti-prion molecules: Congo red, curcumin, GN8, quinacrine, chloropromazine, tetracycline, and TUDCA (taurourspdeoxycholic acid), as well as four suspected anti-prion compounds: trans-resveratrol, rosmarinic acid, myricetin and ferulic acid. These findings suggest that this <i>in vitro</i> assay could be useful in identifying and comprehensively assessing novel anti-prion fibril compounds.
DOI: 10.6084/m9.figshare.7097624
title: Supplementary Material for: High Enhancement Settings for White Light Observation Improves Colorectal Polyp Visibility in Color Difference Value and an Endoscopist’s Visibility

description: <b><i>Background/Aims:</i></b> Settings of structure and color enhancement (CE) change view of white light imaging and a preset low enhancement setting is used regularly. The aim of this study was to investigate whether higher enhancement settings increased colorectal lesions’ visibility with endoscopists’ visibility scoring and objective color difference (CD) value. <b><i>Methods:</i></b> From April 2015 to September 2015, we analyzed 27 pictures and 100 videos of colorectal lesions. Combinations of structure enhancement (B3, A3, A5) and CE (CE 0, 1, 3) were evaluated and CD values of 2 corresponding modes (high enhancement: A5 + CE3, preset low enhancement: A3 + CE0) were calculated using marketed software. In the video, these 2 modes were evaluated. All pictures and movies were graded by 4 endoscopists using visibility scores: score 4 (excellent) to score 1 (poor). <b><i>Results:</i></b> The scores of A3 + CE0 (2.74 ± 1.09) were significantly lower than those of all other higher enhancement settings such as B3 + CE1 (3.11 ± 1.08), A3 + CE1 (3.33 ± 0.91), and A5 + CE3 (3.56 ± 0.74; <i>p</i> &lt; 0.001). The CD value of A5 + CE3 was significantly higher than A3 + CE0 (20.2 ± 6.9 vs. 12.9 ± 5.6, <i>p</i> &lt; 0.001). In the video, the scores for A5 + CE3 were significantly higher than A3 + CE0 (3.27 ± 0.83 vs. 2.53 ± 1.05, <i>p</i> &lt; 0.001). <b><i>Conclusions:</i></b> Higher enhancement settings increased visibility of colorectal lesions.
DOI: 10.6084/m9.figshare.7097603
title: Nutritional mutualism in a pitcher plant supports the monotonic rather than the hump-shaped stress-gradient hypothesis model

description: Data underlying:Leong, F. W. S., Lam, W. N., & Tan, H. T. W. (2019) Nutritional mutualism in a pitcher plant supports the monotonic rather than the hump-shaped stress-gradient hypothesis model. Oecologia<br>Nitrogen.csvData of total pitcher-available nitrogen in the form of ammonia and fluid protein, in each tube in the experiment of the cited study<br>Pupation.csvData of pupation success and date of each inquiline used in the experiment of the cited study.
DOI: 10.6084/m9.figshare.7097603.v1
title: Nutritional mutualism in a pitcher plant supports the monotonic rather than the hump-shaped stress-gradient hypothesis model

description: Data underlying:Leong, F. W. S., Lam, W. N., & Tan, H. T. W. (2019) Nutritional mutualism in a pitcher plant supports the monotonic rather than the hump-shaped stress-gradient hypothesis model. Oecologia<br>Nitrogen.csvData of total pitcher-available nitrogen in the form of ammonia and fluid protein, in each tube in the experiment of the cited study<br>Pupation.csvData of pupation success and date of each inquiline used in the experiment of the cited study.
DOI: 10.6084/m9.figshare.7097480
title: Kurczyn, J.A., P. Pérez-Brunius, M. López, J. Candela, F. Delgadillo-Hinojosa, and E. García. “Water masses and ocean currents along the continental slope off Todos Santos Bay, Baja California.”, submitted to JGR-Oceans (Paper #2018JC013962R), 2018.

description: See readme.pdf file
DOI: 10.6084/m9.figshare.7097132
title: Questionnaire to professors about ICT in the classroom

description: This is an instrument applied to teachers to determine if they use ICT in the classroom.<br>Este es un instrumento se aplica a los profesores para determinar si ellos usan las TIC en el aula.<br>
DOI: 10.6084/m9.figshare.7097132.v1
title: Questionnaire to professors about ICT in the classroom

description: This is an instrument applied to teachers to determine if they use ICT in the classroom.<br>Este es un instrumento se aplica a los profesores para determinar si ellos usan las TIC en el aula.<br>
DOI: 10.6084/m9.figshare.7097108
title: Additional file 5: of ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

description: LTPs peaks. Detected peaks and annotation related with LTPs genes. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.7097108.v1
title: Additional file 5: of ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

description: LTPs peaks. Detected peaks and annotation related with LTPs genes. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.7097102
title: Additional file 4: of ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

description: ABCG peaks. Detected peaks and annotation related with ABCG genes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7097096
title: Additional file 3: of ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

description: Enzyme peaks. Detected peaks and annotation related with enzyme coding genes. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7097102.v1
title: Additional file 4: of ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

description: ABCG peaks. Detected peaks and annotation related with ABCG genes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7097096.v1
title: Additional file 3: of ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

description: Enzyme peaks. Detected peaks and annotation related with enzyme coding genes. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7097090
title: Additional file 2: of ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

description: Types of transcriptional regulators. Families and number of transcriptional regulators targeted by QsMYB1. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.7097090.v1
title: Additional file 2: of ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

description: Types of transcriptional regulators. Families and number of transcriptional regulators targeted by QsMYB1. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.7097072
title: Additional file 1: of Comparative genotyping and phenotyping of Aspergillus fumigatus isolates from humans, dogs and the environment

description: Table S1. Excel file with detailed phenotypic and genetic data .n.d, not determined (no PCR product or sequence obtained) (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.7097072.v1
title: Additional file 1: of Comparative genotyping and phenotyping of Aspergillus fumigatus isolates from humans, dogs and the environment

description: Table S1. Excel file with detailed phenotypic and genetic data .n.d, not determined (no PCR product or sequence obtained) (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.7097036
title: Additional file 7: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Table S5. Comparison of the glycoside hydrolase (GH) profiles of A. vulgare, termite, snail, slug, human, panda, HF cross, jersey cow, cow, reindeer, and macropod gut metagenomes, showing GH groups that are involved in the breakdown/modification of plant cell wall polysaccharides. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.7097036.v1
title: Additional file 7: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Table S5. Comparison of the glycoside hydrolase (GH) profiles of A. vulgare, termite, snail, slug, human, panda, HF cross, jersey cow, cow, reindeer, and macropod gut metagenomes, showing GH groups that are involved in the breakdown/modification of plant cell wall polysaccharides. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.7097024
title: Additional file 6: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Table S4. List of predicted enzymatic functions of CAZymes identified in metagenomes and host transcriptome. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.7097018
title: Additional file 9: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Tables showing all genes in the regions spanned by significant SNPs for each peak. Gene information was obtained from the Phytomine tool in Phytozome v3.0. (ZIP 8760 kb)
DOI: 10.6084/m9.figshare.7097021
title: MOESM3 of Complex delay dynamics on railway networks from universal laws to realistic modelling

description: Supplementary data (ZIP 480 kB)
DOI: 10.6084/m9.figshare.7097024.v1
title: Additional file 6: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Table S4. List of predicted enzymatic functions of CAZymes identified in metagenomes and host transcriptome. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.7097018.v1
title: Additional file 9: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Tables showing all genes in the regions spanned by significant SNPs for each peak. Gene information was obtained from the Phytomine tool in Phytozome v3.0. (ZIP 8760 kb)
DOI: 10.6084/m9.figshare.7097021.v1
title: MOESM3 of Complex delay dynamics on railway networks from universal laws to realistic modelling

description: Supplementary data (ZIP 480 kB)
DOI: 10.6084/m9.figshare.7097012
title: Additional file 5: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Table S3. RPKM values for CAZymes identified in the transcriptome of A. vulgare. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.7097012.v1
title: Additional file 5: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Table S3. RPKM values for CAZymes identified in the transcriptome of A. vulgare. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.7097015
title: Additional file 2: of A novel Rice QTL qOPW11 Associated with Panicle Weight Affects Panicle and Plant Architecture

description: Table S1. Genotypes of RILs. Table S2. Additional markers using genotypes of RILs. Table S3Â Days to heading of CSSLs and parents. (XLSX 212 kb)
DOI: 10.6084/m9.figshare.7097015.v1
title: Additional file 2: of A novel Rice QTL qOPW11 Associated with Panicle Weight Affects Panicle and Plant Architecture

description: Table S1. Genotypes of RILs. Table S2. Additional markers using genotypes of RILs. Table S3Â Days to heading of CSSLs and parents. (XLSX 212 kb)
DOI: 10.6084/m9.figshare.7097006
title: Additional file 8: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Number private GWAS SNPs by genetic subgroup. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7097006.v1
title: Additional file 8: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Number private GWAS SNPs by genetic subgroup. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7097000
title: Additional file 4: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Protein sequences of identified CAZy genes in A. vulgare transcriptome. (FA 861Â kb)
DOI: 10.6084/m9.figshare.7097000.v1
title: Additional file 4: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Protein sequences of identified CAZy genes in A. vulgare transcriptome. (FA 861Â kb)
DOI: 10.6084/m9.figshare.7096994
title: Additional file 7: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Average SNP allele effects for each GWAS peak by trait and treatment. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.7096994.v1
title: Additional file 7: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Average SNP allele effects for each GWAS peak by trait and treatment. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.7096991
title: Additional file 3: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Protein sequences of identified CAZy genes in metagenome assemblies. (FA 596Â kb)
DOI: 10.6084/m9.figshare.7096991.v1
title: Additional file 3: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Protein sequences of identified CAZy genes in metagenome assemblies. (FA 596Â kb)
DOI: 10.6084/m9.figshare.7096976
title: MOESM2 of Complex delay dynamics on railway networks from universal laws to realistic modelling

description: Supplementary interactive simulation files (ZIP 78.5 MB)
DOI: 10.6084/m9.figshare.7096979
title: Additional file 6: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Summary of percent variance explained across 460 GWAS runs. (XLSX 131 kb)
DOI: 10.6084/m9.figshare.7096976.v1
title: MOESM2 of Complex delay dynamics on railway networks from universal laws to realistic modelling

description: Supplementary interactive simulation files (ZIP 78.5 MB)
DOI: 10.6084/m9.figshare.7096979.v1
title: Additional file 6: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Summary of percent variance explained across 460 GWAS runs. (XLSX 131 kb)
DOI: 10.6084/m9.figshare.7096973
title: Additional file 5: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Summary of GWAS peaks identified using deviations between control and treatment data. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.7096973.v1
title: Additional file 5: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Summary of GWAS peaks identified using deviations between control and treatment data. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.7096970
title: Additional file 2: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Table S2. List of CAZymes identified in metagenome assemblies and in the transcriptome of A. vulgare. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.7096964
title: Additional file 4: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Summary of GWAS peaks identified using original trait data. (XLSX 137 kb)
DOI: 10.6084/m9.figshare.7096964.v1
title: Additional file 4: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Summary of GWAS peaks identified using original trait data. (XLSX 137 kb)
DOI: 10.6084/m9.figshare.7096970.v1
title: Additional file 2: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Table S2. List of CAZymes identified in metagenome assemblies and in the transcriptome of A. vulgare. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.7096952
title: Additional file 3: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Summary of pairwise LD across the ten chromosomes of S. bicolor in our GWAS diversity panel. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7096955
title: Additional file 1: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Table S1. List of primers used in RT-qPCR. (XLSX 10Â kb)