cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9577859
title: Supplementary Material for: Is Reaction Time Slowing an Early Sign of Alzheimer’s Disease? A Meta-Analysis

description: <b><i>Background:</i></b> Although simple reaction time (SRT) slowing is associated with dementia in Alzheimer’s disease (AD), its presence in individuals with mild cognitive impairment (MCI) is subject to debate. <b><i>Objective:</i></b> The aim of this study was to perform a systematic review and meta-analysis of the literature data on SRT slowing in MCI. <b><i>Methods:</i></b> Publications with data on SRT, age, and educational level in participants with MCI were included. After calculating the log SRT and its variance for each study, we took interstudy heterogeneity into account by conducting a random effects (restricted maximum likelihood estimation) meta-analysis. <b><i>Results:</i></b> The 7 selected studies featured a total of 327 participants with MCI and 468 healthy controls (HCs). The mean age was 68.2 years for participants with MCI and 72.3 years for HCs. The weighted mean Mini-Mental State Examination score was 26.4 in the MCI group, and 28.4 in the HC group. The mean SRT was significantly (<i>p</i> = 0.0217) longer in the MCI group (by 11%) than in the HC group. <b><i>Conclusion:</i></b> This meta-analysis showed that SRTs are longer in individuals with MCI. Further studies are needed to determine the mechanism of SRT slowing, its anatomical correlates, and a threshold value for diagnosing prodromal AD.
DOI: 10.6084/m9.figshare.9577745
title: Data Reduction

description: Instructions to download the SCUBA-2 and PACS data. Instructions to reduce the SCUBA-2 data and the reduced data products.
DOI: 10.6084/m9.figshare.9577859.v1
title: Supplementary Material for: Is Reaction Time Slowing an Early Sign of Alzheimer’s Disease? A Meta-Analysis

description: <b><i>Background:</i></b> Although simple reaction time (SRT) slowing is associated with dementia in Alzheimer’s disease (AD), its presence in individuals with mild cognitive impairment (MCI) is subject to debate. <b><i>Objective:</i></b> The aim of this study was to perform a systematic review and meta-analysis of the literature data on SRT slowing in MCI. <b><i>Methods:</i></b> Publications with data on SRT, age, and educational level in participants with MCI were included. After calculating the log SRT and its variance for each study, we took interstudy heterogeneity into account by conducting a random effects (restricted maximum likelihood estimation) meta-analysis. <b><i>Results:</i></b> The 7 selected studies featured a total of 327 participants with MCI and 468 healthy controls (HCs). The mean age was 68.2 years for participants with MCI and 72.3 years for HCs. The weighted mean Mini-Mental State Examination score was 26.4 in the MCI group, and 28.4 in the HC group. The mean SRT was significantly (<i>p</i> = 0.0217) longer in the MCI group (by 11%) than in the HC group. <b><i>Conclusion:</i></b> This meta-analysis showed that SRTs are longer in individuals with MCI. Further studies are needed to determine the mechanism of SRT slowing, its anatomical correlates, and a threshold value for diagnosing prodromal AD.
DOI: 10.6084/m9.figshare.9577745.v1
title: Data Reduction

description: Instructions to download the SCUBA-2 and PACS data. Instructions to reduce the SCUBA-2 data and the reduced data products.
DOI: 10.17045/sthlmuni.9577118
title: Target taxa and primers used for identification of genes involved in nodule development of the actinorhizal plant Datisca glomerata

description: The dataset (in Excel format) shows the target taxa used for phylogenetic reconstruction of genes from <i>Datisca glomerata </i>that have an orthologous in legumes plants committed with functions in nodule development. In addition, in a separated tab, the dataset lists the primers used for Reverse Transcriptase quantitative Polymerase Chain Reaction of the identified genes. <br><br><br>
DOI: 10.17045/sthlmuni.9577118.v1
title: Target taxa and primers used for identification of genes involved in nodule development of the actinorhizal plant Datisca glomerata

description: The dataset (in Excel format) shows the target taxa used for phylogenetic reconstruction of genes from <i>Datisca glomerata </i>that have an orthologous in legumes plants committed with functions in nodule development. In addition, in a separated tab, the dataset lists the primers used for Reverse Transcriptase quantitative Polymerase Chain Reaction of the identified genes. <br><br><br>
DOI: 10.17637/rh.9573956
title: Kew Museum of Economic Botany: Object Dispersals to Schools, 1877-1982

description: This dataset is a record of object dispersals from the Kew Museum of Economic Botany to schools between 1877 and 1982. It is based on entries in the 'Specimens Distributed' books (or exit books) in the Museum archive, including date of dispersal; name of recipient; name of school; level, type and denomination of school; number of objects; and any other information given in the books. This is supplemented by information from schools archival correspondence from 'Schools Letter Books', consisting of correspondence to Kew. There are item-level links to original archive sources - both exit books and schools letter books (volume 1 only) - available on the Biodiversity Heritage Library website (https://biodiversitylibrary.org).<br>This dataset was created as part of research for the Mobile Museum research project, a collaboration between Royal Holloway, University of London, and the Royal Botanic Gardens, Kew. Links: <br>https://www.royalholloway.ac.uk/geography/research/mobile-museum/home.aspx <br>https://www.kew.org/science/collections/economic-botany-collection <br><br><br>
DOI: 10.6084/m9.figshare.9573566
title: Neuregulin-1 promote mitochondrial biogenesis, attenuates mitochondrial dysfunction and prevents hypoxia/reoxygenation injury in neonatal cardiomyocytes

description: Neuregulin-1 (NRG-1)/erythroblastic leukemia viral oncogene homologs (ErbB) pathway activation plays a crucial role in regulating the adaptation of the adult heart to physiological and pathological stress. In the present study, we investigate the effect of recombined human NRG-1 (rhNRG-1) on mitochondrial biogenesis, mitochondrial function and cell survival in neonatal rat cardiac myocytes (NRCMs) exposed to hypoxia/reoxygenation (H/R). The results of this study showed that, in the H/R-exposed NRCMs, mitochondrial biogenesis was impaired, as manifested by the decrease of the expression of Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) and mitochondrial membrane proteins, the inner membrane (Tim23), mitofusin 1 (Mfn1), and mitofusin 2 (Mfn2). RhNRG-1 pretreatment effectively restored the expression of PGC-1α and these membrane proteins, upregulated the expression of the anti-apoptosis proteins Bcl-2 and Bcl-xL, preserved the mitochondrial membrane potential, and attenuated H/R-induced cell apoptosis. Blocking PGC-1 expression with siRNA abolished the beneficial role of rhNRG-1 on mitochondrial function and cell survival. The results of the present study strongly suggest that NRG-1/ErbB activation enhances the adaption of cardiomyocytes to H/R injury via promoted mitochondrial biogenesis and improved mitochondrial homeostasis.
DOI: 10.6084/m9.figshare.9573566.v1
title: Neuregulin-1 promote mitochondrial biogenesis, attenuates mitochondrial dysfunction and prevents hypoxia/reoxygenation injury in neonatal cardiomyocytes

description: Neuregulin-1 (NRG-1)/erythroblastic leukemia viral oncogene homologs (ErbB) pathway activation plays a crucial role in regulating the adaptation of the adult heart to physiological and pathological stress. In the present study, we investigate the effect of recombined human NRG-1 (rhNRG-1) on mitochondrial biogenesis, mitochondrial function and cell survival in neonatal rat cardiac myocytes (NRCMs) exposed to hypoxia/reoxygenation (H/R). The results of this study showed that, in the H/R-exposed NRCMs, mitochondrial biogenesis was impaired, as manifested by the decrease of the expression of Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) and mitochondrial membrane proteins, the inner membrane (Tim23), mitofusin 1 (Mfn1), and mitofusin 2 (Mfn2). RhNRG-1 pretreatment effectively restored the expression of PGC-1α and these membrane proteins, upregulated the expression of the anti-apoptosis proteins Bcl-2 and Bcl-xL, preserved the mitochondrial membrane potential, and attenuated H/R-induced cell apoptosis. Blocking PGC-1 expression with siRNA abolished the beneficial role of rhNRG-1 on mitochondrial function and cell survival. The results of the present study strongly suggest that NRG-1/ErbB activation enhances the adaption of cardiomyocytes to H/R injury via promoted mitochondrial biogenesis and improved mitochondrial homeostasis.
DOI: 10.17637/rh.9573956.v1
title: Schools dispersals data with BHL links

description: This dataset is a record of object dispersals from the Kew Museum of Economic Botany to schools between 1877 and 1982. It is based on entries in the 'Specimens Distributed' books (or exit books) in the Museum archive, including date of dispersal; name of recipient; name of school; level, type and denomination of school; number of objects; and any other information given in the books. This is supplemented by information from schools archival correspondence from 'Schools Letter Books', consisting of correspondence to Kew. There are item-level links to original archive sources - both exit books and schools letter books (volume 1 only) - available on the Biodiversity Heritage Library website (https://biodiversitylibrary.org).<br>This dataset was created as part of research for the Mobile Museum research project, a collaboration between Royal Holloway, University of London, and the Royal Botanic Gardens, Kew. Links: <br>https://www.royalholloway.ac.uk/geography/research/mobile-museum/home.aspx <br>https://www.kew.org/science/collections/economic-botany-collection <br><br><br>
DOI: 10.6084/m9.figshare.9572501
title: Causal effects of genetically determined metabolites on risk of polycystic ovary syndrome: A Mendelian randomization study

description: genetically determined metabolites and PCOS<br>
DOI: 10.6084/m9.figshare.9572327
title: Flexible covariance dynamics, high-frequency data, and optimal futures hedging

description: This paper investigates the out-of-sample performance of hedged portfolios constructed using a novel rotated ARCH (RARCH) model class, which enables flexible covariance dynamics for spot and futures returns. The model’s empirical fit can be significantly improved when it incorporates rotated realized covariance matrix measures. The empirical results suggest that a highly risk-averse hedger implementing the restricted RARCH model would be willing to pay substantial switching fees to capture the incremental gains generated by the flexible and informative alternative; this thus supports the economic importance of incorporating high-frequency data into flexible RARCH modeling processes for the construction of optimal hedged portfolios.
DOI: 10.6084/m9.figshare.9572501.v3
title: Causal effects of genetically determined metabolites on risk of polycystic ovary syndrome: A Mendelian randomization study

description: genetically determined metabolites and PCOS<br>
DOI: 10.6084/m9.figshare.9568472
title: Chromosome instability caused by mutations in the genes involved in transcription and splicing

description: Mutations in molecules involved in transcription and splicing can cause chromosome instability such as sister chromatid exchanges. We isolated and characterized responsible genes from mammalian temperature-sensitive mutant cells showing chromosome instability. A mutation in the largest subunit of RNA polymerase II affected DNA synthesis in S phase-arrested cells, resulting in abnormal induction of sister chromatid exchanges. The yeast mutant harboring a homologous mutation showed very similar phenotype to that of the mammalian mutant. A mutation in Smu1, which is involved in splicing, also affected DNA synthesis in S and G2 phase-arrested cells, resulting in abnormal induction of sister chromatid exchanges and chromosomal aberrations. These cells showed a connection between defects of RNA metabolism and induction of chromosome instability. Genome instability appeared to be caused by links between RNA metabolism and replication resulting in genomic recombination. RNA metabolism can be regarded as one possible driver of genome modification triggering genome evolution
DOI: 10.6084/m9.figshare.9568472.v1
title: Chromosome instability caused by mutations in the genes involved in transcription and splicing

description: Mutations in molecules involved in transcription and splicing can cause chromosome instability such as sister chromatid exchanges. We isolated and characterized responsible genes from mammalian temperature-sensitive mutant cells showing chromosome instability. A mutation in the largest subunit of RNA polymerase II affected DNA synthesis in S phase-arrested cells, resulting in abnormal induction of sister chromatid exchanges. The yeast mutant harboring a homologous mutation showed very similar phenotype to that of the mammalian mutant. A mutation in Smu1, which is involved in splicing, also affected DNA synthesis in S and G2 phase-arrested cells, resulting in abnormal induction of sister chromatid exchanges and chromosomal aberrations. These cells showed a connection between defects of RNA metabolism and induction of chromosome instability. Genome instability appeared to be caused by links between RNA metabolism and replication resulting in genomic recombination. RNA metabolism can be regarded as one possible driver of genome modification triggering genome evolution
DOI: 10.6084/m9.figshare.9567008
title: landslide data.xlsx

description: Average slope and curvature of landslides triggered by Hokkaido Eastern Iburi earthquake in 2019. Landslides were identified by Kita (2018): https://github.com/koukita/2018_09_06_atumathou. Slope angle and curvature were calculated with a 10 m DEM using ArcGIS software, made available to the public by Geospatial Information Authority of Japan (https://www.gsi.go.jp/kiban/index.html; index number: 6341-77, 6441-07, 6441-17, 6442-00, 6442-10). With the averaged curvature, each landslide was classified into four types: Cc, concave for profile and planform curvature, Ccpr, concave for profile and convex for planform curvature; Ccpl, concave for planform and convex for profile curvature, and Cv, convex for both curvatures. 'Planer' surface was not considered because of the data uncertainty. <br>
DOI: 10.6084/m9.figshare.9565937
title: Additional file 9 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis for the 301 global Pst isolates, 55 Ethiopian Pst-infected field samples and Pst isolates representative of several major genetic groups. Data for the Ethiopian Pst isolates and representative genetic group isolates were generated on the MinION platform. Newick format. (NEWICK 20 kb)
DOI: 10.6084/m9.figshare.9565937.v1
title: Additional file 9 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis for the 301 global Pst isolates, 55 Ethiopian Pst-infected field samples and Pst isolates representative of several major genetic groups. Data for the Ethiopian Pst isolates and representative genetic group isolates were generated on the MinION platform. Newick format. (NEWICK 20 kb)
DOI: 10.6084/m9.figshare.9565925
title: Additional file 7 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates using sequences for the 242 selected genes, with bootstrap values. Newick format. (NEWICK 17 kb)
DOI: 10.6084/m9.figshare.9565925.v1
title: Additional file 7 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates using sequences for the 242 selected genes, with bootstrap values. Newick format. (NEWICK 17 kb)
DOI: 10.6084/m9.figshare.9565919
title: Additional file 6 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates using sequences for the 242 selected genes. Newick format. (NEWICK 16 kb)
DOI: 10.6084/m9.figshare.9565919.v1
title: Additional file 6 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates using sequences for the 242 selected genes. Newick format. (NEWICK 16 kb)
DOI: 10.6084/m9.figshare.9565898
title: Additional file 3 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates with bootstrap values. Newick format. (NEWICK 16 kb)
DOI: 10.6084/m9.figshare.9565898.v1
title: Additional file 3 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates with bootstrap values. Newick format. (NEWICK 16 kb)
DOI: 10.6084/m9.figshare.9565886
title: Additional file 2 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates. Newick format. (NEWICK 16 kb)
DOI: 10.6084/m9.figshare.9565880
title: Additional file 1 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Tables S1-S15. Microsoft Excel Workbook containing 15 worksheets. Table S1: Description of Pst isolates. Table S2: Number of reads aligned to the PST-130 reference genome for the 100 RNA-seq datasets. Table S3: Number of reads aligned to the PST-130 reference genome for the 25 genomic datasets utilised herein. Table S4: Oligonucleotide (primer) sequences and pooling strategy for the 242 Pst genes selected. Table S5: Genomic location and functional annotation of the 242 Pst genes selected. Table S6: Number of reads aligned to the PST-130 reference genome for the 4 MiSeq amplicon datasets. Table S7: Number of reads generated on the MinION platform that aligned to the 242 Pst genes selected. Table S8: Time taken to generate a given number of MinION reads for the four Ethiopian Pst-infected wheat samples. Table S9: Details of SNP positions per gene detected in MinION and Illumina datasets generated from four Pst isolates. Table S10: Details of homokaryotic and heterokaryotic positions in consensus sequences obtained from Illumina MiSeq and MinION platforms. Table S11: Number of reads aligned to the PST-130 reference genome for the Ethiopian Pst RNA-seq datasets. Table S12: Additional Pst reference isolates representing diverse virulence phenotypes and key genetic groups of a worldwide phylogeny of Pst. Table S13: Components used in the MARPLE pipeline. Table S14: Details of Illumina library preparation of 4 Pst-infected samples. Table S15: Details of libraries made for MinION sequencing of Pst-infected wheat leaf samples. (XLSX 4138 kb)
DOI: 10.6084/m9.figshare.9565886.v1
title: Additional file 2 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates. Newick format. (NEWICK 16 kb)
DOI: 10.6084/m9.figshare.9565871
title: Additional file 12 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates using sequences for the 242 genes selected and data for these genes generated on the HiSeq platform for the 51 Ethiopian Pst isolates with bootstrap values. Newick format. (NEWICK 20 kb)
DOI: 10.6084/m9.figshare.9565880.v1
title: Additional file 1 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Tables S1-S15. Microsoft Excel Workbook containing 15 worksheets. Table S1: Description of Pst isolates. Table S2: Number of reads aligned to the PST-130 reference genome for the 100 RNA-seq datasets. Table S3: Number of reads aligned to the PST-130 reference genome for the 25 genomic datasets utilised herein. Table S4: Oligonucleotide (primer) sequences and pooling strategy for the 242 Pst genes selected. Table S5: Genomic location and functional annotation of the 242 Pst genes selected. Table S6: Number of reads aligned to the PST-130 reference genome for the 4 MiSeq amplicon datasets. Table S7: Number of reads generated on the MinION platform that aligned to the 242 Pst genes selected. Table S8: Time taken to generate a given number of MinION reads for the four Ethiopian Pst-infected wheat samples. Table S9: Details of SNP positions per gene detected in MinION and Illumina datasets generated from four Pst isolates. Table S10: Details of homokaryotic and heterokaryotic positions in consensus sequences obtained from Illumina MiSeq and MinION platforms. Table S11: Number of reads aligned to the PST-130 reference genome for the Ethiopian Pst RNA-seq datasets. Table S12: Additional Pst reference isolates representing diverse virulence phenotypes and key genetic groups of a worldwide phylogeny of Pst. Table S13: Components used in the MARPLE pipeline. Table S14: Details of Illumina library preparation of 4 Pst-infected samples. Table S15: Details of libraries made for MinION sequencing of Pst-infected wheat leaf samples. (XLSX 4138 kb)
DOI: 10.6084/m9.figshare.9565862
title: Additional file 11 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates using sequences for the 242 genes selected and data for these genes generated on the HiSeq platform for the 51 Ethiopian Pst isolates. Newick format. (NEWICK 19 kb)
DOI: 10.6084/m9.figshare.9565862.v1
title: Additional file 11 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates using sequences for the 242 genes selected and data for these genes generated on the HiSeq platform for the 51 Ethiopian Pst isolates. Newick format. (NEWICK 19 kb)
DOI: 10.6084/m9.figshare.9565871.v1
title: Additional file 12 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

description: Phylogenetic analysis of the 301 global Pst isolates using sequences for the 242 genes selected and data for these genes generated on the HiSeq platform for the 51 Ethiopian Pst isolates with bootstrap values. Newick format. (NEWICK 20 kb)