cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9916436
title: Opposing roles of C/EBPα and eEF1A1 in Sp1-regulated miR-122 transcription

description: We previously showed that miR-122 was frequently downregulated in hepatocellular carcinoma (HCC) and C/EBPα transactivated miR-122 expression. In this study, we found that Sp1 bound to the miR-122 promoter at two different sites. Interestingly, either inhibition or overexpression of Sp1 could decrease the miR-122 promoter activity and the cellular miR-122 level in hepatoma cells. Further investigations disclosed that Sp1 cooperated with C/EBPα to induce miR-122 transcription by binding to the positive regulatory site D in the miR-122 promoter, whereas eEF1A1 interacted with Sp1 to bind to the negative regulatory site E and inhibit miR-122 transcription. Significantly, both Sp1 and eEF1A1 levels were enhanced, but C/EBPα and miR-122 expression were reduced in HCC tissues. Knockdown of eEF1A1 enhanced miR-122 level and inhibited cell growth, and these effects were abrogated when Sp1 was silenced. Consistently, the promoter activity enhanced by site E deletion was attenuated by silencing Sp1. Moreover, reduction of miR-122 resulted from Sp1 overexpression was rescued by coexpressing C/EBPα. These data suggest that C/EBPα and eEF1A1 may play opposing roles in Sp1-regulating miR-122 transcription, and the eEF1A1 upregulation accompanied by C/EBPα downregulation in HCC may switch the regulatory functions of Sp1 and led to reduced miR-122 transcription. These findings highlight the complex regulatory network of miR-122 expression and its significance in hepatocarcinogenesis. <b>Abbreviations:</b> MiRNA: microRNA; HCC, hepatocellular carcinoma; eEF1A1: eukaryote translation elongation factor 1A1; siRNA: small interfering RNA; qPCR: real-time quantitative RT-PCR; EMSA: electrophoretic mobility shift assay; ChIP: chromatin immunoprecipitation; TSS: transcription start site.
DOI: 10.6084/m9.figshare.9916436.v1
title: Opposing roles of C/EBPα and eEF1A1 in Sp1-regulated miR-122 transcription

description: We previously showed that miR-122 was frequently downregulated in hepatocellular carcinoma (HCC) and C/EBPα transactivated miR-122 expression. In this study, we found that Sp1 bound to the miR-122 promoter at two different sites. Interestingly, either inhibition or overexpression of Sp1 could decrease the miR-122 promoter activity and the cellular miR-122 level in hepatoma cells. Further investigations disclosed that Sp1 cooperated with C/EBPα to induce miR-122 transcription by binding to the positive regulatory site D in the miR-122 promoter, whereas eEF1A1 interacted with Sp1 to bind to the negative regulatory site E and inhibit miR-122 transcription. Significantly, both Sp1 and eEF1A1 levels were enhanced, but C/EBPα and miR-122 expression were reduced in HCC tissues. Knockdown of eEF1A1 enhanced miR-122 level and inhibited cell growth, and these effects were abrogated when Sp1 was silenced. Consistently, the promoter activity enhanced by site E deletion was attenuated by silencing Sp1. Moreover, reduction of miR-122 resulted from Sp1 overexpression was rescued by coexpressing C/EBPα. These data suggest that C/EBPα and eEF1A1 may play opposing roles in Sp1-regulating miR-122 transcription, and the eEF1A1 upregulation accompanied by C/EBPα downregulation in HCC may switch the regulatory functions of Sp1 and led to reduced miR-122 transcription. These findings highlight the complex regulatory network of miR-122 expression and its significance in hepatocarcinogenesis. <b>Abbreviations:</b> MiRNA: microRNA; HCC, hepatocellular carcinoma; eEF1A1: eukaryote translation elongation factor 1A1; siRNA: small interfering RNA; qPCR: real-time quantitative RT-PCR; EMSA: electrophoretic mobility shift assay; ChIP: chromatin immunoprecipitation; TSS: transcription start site.
DOI: 10.6084/m9.figshare.9916394
title: Li isotope fractionation

description: Chemical compositions and Li isotope compositions of whole-rock and minerals from the Xihuashan and Yaogangxian plutons, South China.
DOI: 10.6084/m9.figshare.9916328
title: Raw data for Fecchio et al 2019: An inverse latitudinal gradient in infection probability and phylogenetic diversity for Leucocytozoon blood parasites in New World birds

description: The excel file contains individual-level observations of <i>Leucocytozoon</i> parasite infection status for birds sampled in the New World. The data was used to generate analyses presented in Fecchio et al (2019) <i>An inverse latitudinal gradient in infection probability and phylogenetic diversity for Leucocytozoon blood parasites in New World birds</i>, published in Journal of Animal Ecology. The included pdf files show the R code that was used to process the dataset, extract climate predictors and carry out analyses. Note that several functions are required to replicate analyses. These are all included in the zipped <b>Functions</b> folder.
DOI: 10.6084/m9.figshare.9916394.v2
title: Li isotope fractionation

description: Chemical compositions and Li isotope compositions of whole-rock and minerals from the Xihuashan and Yaogangxian plutons, South China.
DOI: 10.6084/m9.figshare.9916268
title: data for "Delamination drives Pangea breakup：a data-driven discovery"

description: data for "Delamination drives Pangea breakup：a data-driven discovery"
DOI: 10.6084/m9.figshare.9916394.v1
title: Li isotope fractionation

description: Chemical compositions and Li isotope compositions of whole-rock and minerals from the Xihuashan and Yaogangxian plutons, South China.
DOI: 10.5281/zenodo.4002074
title: Dataset_Brazilian_Elderly_COVID

description: This is the dataset used to analyse data.
DOI: 10.6084/m9.figshare.9916268.v1
title: data for "Delamination drives Pangea breakup：a data-driven discovery"

description: data for "Delamination drives Pangea breakup：a data-driven discovery"
DOI: 10.5281/zenodo.4002073
title: Dataset_Brazilian_Elderly_COVID

description: This is the dataset used to analyse data.
DOI: 10.25380/iastate.9916226
title: Phakopsora pachyrhizi transcriptome from PacBio Isoform Sequencing

description: <i>Phakopsora pachyrhizi </i>is an obligate biotrophic fungal pathogen of soybean that causes Asian soybean rust (ASR), a devastating disease that can cause yield losses of 80% or greater. <i>P. pachyrhizi</i> secretes an arsenal of effector proteins to manipulate host immunity and promote disease. Current knowledge of the<i> P. pachyrhizi</i> genome is limited and only a small number of the total <i>P. pachyrhizi</i> effectors have been identified. We therefore sequenced the transcriptome of <i>P. pachyrhizi </i>during infection to identify <i>P. pachyrhizi </i>Candidate Secreted Effector Proteins (CSEPs). Total RNA was extracted from <i>P. pachyrhizi</i>-infected soybean leaf tissue collected at 7, and 10 days after inoculation (dai). cDNA libraries were prepared according to the Iso-Seq protocol using Clontech SMARTer PCR cDNA synthesis kit with no size selection. Sequencing was performed on a PacBio RS II (https://www.pacb.com). For each time point, final libraries composed of transcripts with no size selection were sequenced on six SMRT cells. The subreads generated from six SMRT cells were pooled together for each time point and processed following the RS_IsoSeq protocol (https://www.pacb.com/support/software-downloads) available in SMRT analysis package v2.3.0. Each time point contains two fasta files: (1) The error-corrected transcripts of <i>P. pachyrhizi</i>, and<i> </i>(2) High quality and low quality consensus transcripts before error correction. The error-corrected transcripts were used for CSEP prediction.<br><b>Citation:</b>M.G.Elmore, S.Banerjee, K.F.Pedley, A.Ruck, S.A.Whitham. <i>De novo</i> transcriptome of <i>Phakopsora</i> <i>pachyrhizi</i> uncovers putative effector repertoire during infection. Physiological and Molecular Plant Pathology, 110 (2020),101464, 10.1016/j.pmpp.2020.101464<br>
DOI: 10.6084/m9.figshare.9916220
title: Stothart et al. 2019 R Script - Proc B

description: R script used to generate analyses and figures presented in Stothart et al. 2019 Proceedings of the Royal Society B primary research article (10.1098/rspb.2019.2111).
DOI: 10.6084/m9.figshare.9916238
title: Data Collection 1

description: Day 1 of collecting data at various all way stop intersections on York University campus
DOI: 10.25380/iastate.9916217
title: De novo transcriptome of Phakopsora pachyrhizi by Illumina short-read sequencing

description: <i>Phakopsora pachyrhizi</i> is an obligate biotrophic fungal pathogen of soybean that causes Asian soybean rust (ASR), a devastating disease that can cause yield losses of 80% or greater. <i>P. pachyrhizi</i> secretes an arsenal of effector proteins to manipulate host immunity and promote disease. Current knowledge of the <i>P. pachyrhizi </i>genome is limited and only a small number of the total <i>P. pachyrhizi </i>effectors have been identified. We therefore sequenced the transcriptome of <i>P. pachyrhizi</i> during infection to identify <i>P. pachyrhizi </i>Candidate Secreted Effector Proteins (CSEPs). Total RNA was extracted from <i>P. pachyrhizi</i>-infected soybean leaf tissue collected at 3, 7, 10, and 14 days after inoculation (dai). Strand-specific cDNA libraries were prepared from ribosomal depleted RNA using NEBNext Ultra II RNA library prep kit according to the manufacturer's instructions. Paired-end short-read Illumina sequencing was performed on dual-indexed cDNA libraries using HiSeq3000 (150bp from each end; https://www.illumina.com/) and MiSeq (300bp from each end; https://www.illumina.com/). The raw reads obtained from Illumina short-read sequencing were quality assessed using FastQC v.0.11.2. Paired-end read trimming was conducted by Trimmomatic 0.36 using sliding window 4:15 and excluding read below a minimal length of 36. Trimmed paired-end RNA-Seq reads from 3, 7, 10, and 14 dai were mapped against the soybean genome v2.1 (https://plants.ensembl.org/Glycine_max) using STAR 2.5.3a aligner to remove soybean reads. The non-soybean short-reads were <i>de novo</i> assembled using Trinity v2.6.6. BLASTN (Basic Local Alignment Search Tool) search was performed on non-soybean transcripts using Blastplus v2.6.0 (NCBI: National Center for Biotechnology Information) to remove any plant transcripts with a query coverage greater than 80% and identity greater than 95%. The final <i>de novo </i>transcriptome containing non-plant, non-soybean transcripts for each time point was used for prediction of candidate effectors.<br><b>Citation:</b>M.G.Elmore, S.Banerjee, K.F.Pedley, A.Ruck, S.A.Whitham. <i>De novo</i> transcriptome of <i>Phakopsora</i> <i>pachyrhizi</i> uncovers putative effector repertoire during infection. Physiological and Molecular Plant Pathology.,<br>110 (2020),101464, 10.1016/j.pmpp.2020.101464
DOI: 10.25380/iastate.9916226.v1
title: Phakopsora pachyrhizi transcriptome from PacBio Isoform Sequencing

description: <i>Phakopsora pachyrhizi </i>is an obligate biotrophic fungal pathogen of soybean that causes Asian soybean rust (ASR), a devastating disease that can cause yield losses of 80% or greater. <i>P. pachyrhizi</i> secretes an arsenal of effector proteins to manipulate host immunity and promote disease. Current knowledge of the<i> P. pachyrhizi</i> genome is limited and only a small number of the total <i>P. pachyrhizi</i> effectors have been identified. We therefore sequenced the transcriptome of <i>P. pachyrhizi </i>during infection to identify <i>P. pachyrhizi </i>Candidate Secreted Effector Proteins (CSEPs). Total RNA was extracted from <i>P. pachyrhizi</i>-infected soybean leaf tissue collected at 7, and 10 days after inoculation (dai). cDNA libraries were prepared according to the Iso-Seq protocol using Clontech SMARTer PCR cDNA synthesis kit with no size selection. Sequencing was performed on a PacBio RS II (https://www.pacb.com). For each time point, final libraries composed of transcripts with no size selection were sequenced on six SMRT cells. The subreads generated from six SMRT cells were pooled together for each time point and processed following the RS_IsoSeq protocol (https://www.pacb.com/support/software-downloads) available in SMRT analysis package v2.3.0. Each time point contains two fasta files: (1) The error-corrected transcripts of <i>P. pachyrhizi</i>, and<i> </i>(2) High quality and low quality consensus transcripts before error correction. The error-corrected transcripts were used for CSEP prediction.<br><b>Citation:</b>M.G.Elmore, S.Banerjee, K.F.Pedley, A.Ruck, S.A.Whitham. <i>De novo</i> transcriptome of <i>Phakopsora</i> <i>pachyrhizi</i> uncovers putative effector repertoire during infection. Physiological and Molecular Plant Pathology, 110 (2020),101464, 10.1016/j.pmpp.2020.101464<br>
DOI: 10.6084/m9.figshare.9916220.v1
title: Stothart et al. 2019 R Script - Proc B

description: R script used to generate analyses and figures presented in Stothart et al. 2019 Proceedings of the Royal Society B primary research article (10.1098/rspb.2019.2111).
DOI: 10.25380/iastate.9916217.v1
title: De novo transcriptome of Phakopsora pachyrhizi by Illumina short-read sequencing

description: <i>Phakopsora pachyrhizi</i> is an obligate biotrophic fungal pathogen of soybean that causes Asian soybean rust (ASR), a devastating disease that can cause yield losses of 80% or greater. <i>P. pachyrhizi</i> secretes an arsenal of effector proteins to manipulate host immunity and promote disease. Current knowledge of the <i>P. pachyrhizi </i>genome is limited and only a small number of the total <i>P. pachyrhizi </i>effectors have been identified. We therefore sequenced the transcriptome of <i>P. pachyrhizi</i> during infection to identify <i>P. pachyrhizi </i>Candidate Secreted Effector Proteins (CSEPs). Total RNA was extracted from <i>P. pachyrhizi</i>-infected soybean leaf tissue collected at 3, 7, 10, and 14 days after inoculation (dai). Strand-specific cDNA libraries were prepared from ribosomal depleted RNA using NEBNext Ultra II RNA library prep kit according to the manufacturer's instructions. Paired-end short-read Illumina sequencing was performed on dual-indexed cDNA libraries using HiSeq3000 (150bp from each end; https://www.illumina.com/) and MiSeq (300bp from each end; https://www.illumina.com/). The raw reads obtained from Illumina short-read sequencing were quality assessed using FastQC v.0.11.2. Paired-end read trimming was conducted by Trimmomatic 0.36 using sliding window 4:15 and excluding read below a minimal length of 36. Trimmed paired-end RNA-Seq reads from 3, 7, 10, and 14 dai were mapped against the soybean genome v2.1 (https://plants.ensembl.org/Glycine_max) using STAR 2.5.3a aligner to remove soybean reads. The non-soybean short-reads were <i>de novo</i> assembled using Trinity v2.6.6. BLASTN (Basic Local Alignment Search Tool) search was performed on non-soybean transcripts using Blastplus v2.6.0 (NCBI: National Center for Biotechnology Information) to remove any plant transcripts with a query coverage greater than 80% and identity greater than 95%. The final <i>de novo </i>transcriptome containing non-plant, non-soybean transcripts for each time point was used for prediction of candidate effectors.<br><b>Citation:</b>M.G.Elmore, S.Banerjee, K.F.Pedley, A.Ruck, S.A.Whitham. <i>De novo</i> transcriptome of <i>Phakopsora</i> <i>pachyrhizi</i> uncovers putative effector repertoire during infection. Physiological and Molecular Plant Pathology.,<br>110 (2020),101464, 10.1016/j.pmpp.2020.101464
DOI: 10.6084/m9.figshare.9916238.v1
title: Data Collection 1

description: Day 1 of collecting data at various all way stop intersections on York University campus
DOI: 10.6084/m9.figshare.9916160
title: Dataset for: Bayesian Finite Population Modeling for Spatial Process Settings

description: We develop a Bayesian model-based approach to finite population estimation accounting for spatial dependence. Our innovation here is a framework that achieves inference for finite population quantities in spatial process settings. A key distinction from the small area estimation setting is that we analyze finite populations referenced by their geographic coordinates (point-referenced data). Specifically, we consider a two-stage sampling design in which the primary units are geographic regions, the secondary units are point-referenced locations, and the measured values are assumed to be a partial realization of a spatial process. Traditional geostatistical models do not account for variation attributable to finite population sampling designs, which can impair inferential performance. On the other hand, design-based estimates will ignore the spatial dependence in the finite population. This motivates the introduction of geostatistical processes that will enable inference at arbitrary locations in our domain of interest.We demonstrate using simulation experiments that process-based finite population sampling models considerably improve model fit and inference over models that fail to account for spatial correlation. Furthermore, the process based models offer richer inference with spatially interpolated maps over the entire region. We reinforce these improvements and demonstrate scalable inference for groundwater Nitrate levels in the population of California Central Valley wells by offering estimates of mean Nitrate levels and their spatially interpolated maps.
DOI: 10.6084/m9.figshare.9916127
title: Thyroptera contact calling rates

description: We provide data regarding calling rates for two types of contact calls recorded in Spix's disc-winged bats. Each data sheet presents results for each call type, inquiry and response.<br>
DOI: 10.6084/m9.figshare.9915992
title: Buffelgrass invasion Sonoran desert

description: Sample information, phylotypes abundance tables, and taxonomic information of soil microbial communities associated with buffelgrass invasion in the Sonoran desert
DOI: 10.6084/m9.figshare.9916160.v1
title: Dataset for: Bayesian Finite Population Modeling for Spatial Process Settings

description: We develop a Bayesian model-based approach to finite population estimation accounting for spatial dependence. Our innovation here is a framework that achieves inference for finite population quantities in spatial process settings. A key distinction from the small area estimation setting is that we analyze finite populations referenced by their geographic coordinates (point-referenced data). Specifically, we consider a two-stage sampling design in which the primary units are geographic regions, the secondary units are point-referenced locations, and the measured values are assumed to be a partial realization of a spatial process. Traditional geostatistical models do not account for variation attributable to finite population sampling designs, which can impair inferential performance. On the other hand, design-based estimates will ignore the spatial dependence in the finite population. This motivates the introduction of geostatistical processes that will enable inference at arbitrary locations in our domain of interest.We demonstrate using simulation experiments that process-based finite population sampling models considerably improve model fit and inference over models that fail to account for spatial correlation. Furthermore, the process based models offer richer inference with spatially interpolated maps over the entire region. We reinforce these improvements and demonstrate scalable inference for groundwater Nitrate levels in the population of California Central Valley wells by offering estimates of mean Nitrate levels and their spatially interpolated maps.
DOI: 10.6084/m9.figshare.9915911
title: Three novel Ambrosia <i>Fusarium</i> Clade species producing clavate macroconidia known (<i>F. floridanum</i> and <i>F. obliquiseptatum</i>) or predicted (<i>F. tuaranense</i>) to be farmed by <i>Euwallacea</i> spp. (Coleoptera: Scolytinae) on woody hosts

description: The Ambrosia <i>Fusarium</i> Clade (AFC) comprises at least 16 genealogically exclusive species-level lineages within clade 3 of the <i>Fusarium solani</i> species complex (FSSC). These fungi are either known or predicted to be farmed by Asian <i>Euwallacea</i> ambrosia beetles (Coleoptera: Curculionidae: Scolytinae) in the tribe Xyleborini as a source of nutrition. To date, only 4 of the 16 AFC lineages have been described formally. In the absence of Latin binomials, an ad hoc nomenclature was developed to distinguish the 16 species lineages as AF-1 to AF-16. Herein, <i>Fusarium</i> species AF-3, AF-5, and AF-7 were formally described as <i>F. floridanum, F. tuaranense</i>, and <i>F. obliquiseptatum</i>, respectively. <i>Fusarium floridanum</i> farmed by <i>E. interjectus</i> on box elder (<i>Acer negundo</i>) in Gainesville, Florida, was distinguished morphologically by the production of sporodochial conidia that were highly variable in size and shape together with greenish-pigmented chlamydospores. <i>Fusarium tuaranense</i> was isolated from a beetle-damaged Paŕa rubber tree (<i>Hevea brasiliense</i>) in North Borneo, Malaysia, and was diagnosed by production of the smallest sporodochial conidia of any species within the AFC. Lastly, <i>F. obliquiseptatum</i> was farmed by an unnamed ambrosia beetle designated <i>Euwallacea</i> sp. 3 (<i>E. fornicatus</i> species complex) on avocado (<i>Persea americana</i>) in Queensland, Australia. It uniquely produces some clavate sporodochial conidia with oblique septa. Maximum likelihood analysis of a multilocus data set resolved these three novel AFC taxa as phylogenetically distinct species based on genealogical concordance. Particularly where introduced into exotic environments, these exotic mutualists pose a serious threat to the avocado industry, native forests, and urban landscapes in diverse regions throughout the world.
DOI: 10.6084/m9.figshare.9916127.v2
title: Thyroptera contact calling rates

description: We provide data regarding calling rates for two types of contact calls recorded in Spix's disc-winged bats. Each data sheet presents results for each call type, inquiry and response.<br>
DOI: 10.6084/m9.figshare.9915902
title: Table S1.xlsx

description: geochronological data of 100 A-type granites
DOI: 10.6084/m9.figshare.9916127.v1
title: Thyroptera contact calling rates

description: We provide data regarding calling rates for two types of contact calls recorded in Spix's disc-winged bats. Each data sheet presents results for each call type, inquiry and response.<br>
DOI: 10.6084/m9.figshare.9915902.v1
title: Table S1.xlsx

description: geochronological data of 100 A-type granites