cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1452913.v7
title: Export-deficient monoubiquitinated PEX5 triggers peroxisome removal in SV40 large T antigen-transformed mouse embryonic fibroblasts

description: Peroxisomes are ubiquitous cell organelles essential for human health. To maintain a healthy cellular environment, dysfunctional and superfluous peroxisomes need to be selectively removed. Although emerging evidence suggests that peroxisomes are mainly degraded by pexophagy, little is known about the triggers and molecular mechanisms underlying this process in mammalian cells. In this study, we show that PEX5 proteins fused to a bulky C-terminal tag trigger peroxisome degradation in SV40 large T antigen-transformed mouse embryonic fibroblasts. In addition, we provide evidence that this process is autophagy-dependent and requires monoubiquitination of the N-terminal cysteine residue that marks PEX5 for recycling. As our findings also demonstrate that the addition of a bulky tag to the C terminus of PEX5 does not interfere with PEX5 monoubiquitination but strongly inhibits its export from the peroxisomal membrane, we hypothesize that such a tag mimics a cargo protein that cannot be released from PEX5, thus keeping monoubiquitinated PEX5 at the membrane for a sufficiently long time to be recognized by the autophagic machinery. This in turn suggests that monoubiquitination of the N-terminal cysteine of peroxisome-associated PEX5 not only functions to recycle the peroxin back to the cytosol, but also serves as a quality control mechanism to eliminate peroxisomes with a defective protein import machinery.
DOI: 10.6084/m9.figshare.1452862.v1
title: RADseq library

description: .zip file containing a .vcf file with all individuals and all loci used in analyses
DOI: 10.6084/m9.figshare.1451681
title: Fileset: A Network Perspective on Soil Surveys

description: Poster presented at NetSci 2015, 1-5June, Zaragoza, Spain.
DOI: 10.6084/m9.figshare.1451427
title: netflix.part01.rar

description: This dataset was constructed to support participants in the Netflix Prize.
DOI: 10.6084/m9.figshare.1451681.v1
title: Fileset: A Network Perspective on Soil Surveys

description: Poster presented at NetSci 2015, 1-5June, Zaragoza, Spain.
DOI: 10.6084/m9.figshare.1451426
title: netflix.part02.rar

description: This dataset was constructed to support participants in the Netflix Prize.
DOI: 10.6084/m9.figshare.1451417
title: Characterization of Bacterial Genomic Reference Materials

description: Poster presented at ASM 2015 General Meeting
DOI: 10.6084/m9.figshare.1451417.v1
title: Characterization of Bacterial Genomic Reference Materials

description: Poster presented at ASM 2015 General Meeting
DOI: 10.6084/m9.figshare.1451406
title: Example BOLD brainmask

description: Example brainmask for a BOLD image
DOI: 10.6084/m9.figshare.1451407
title: Example BOLD segmentation.

description: Example segmentation for a BOLD image. 6 tissue types are labeled.
DOI: 10.6084/m9.figshare.1451408
title: lastfm.part02.rar

description: This dataset contains tuples collected from Last.fm API ( http://www.last.fm/api )
DOI: 10.6084/m9.figshare.1451409
title: lastfm.part01.rar

description: CF
DOI: 10.6084/m9.figshare.1451406.v1
title: Example BOLD brainmask

description: Example brainmask for a BOLD image
DOI: 10.6084/m9.figshare.1451409.v1
title: lastfm.part01.rar

description: CF
DOI: 10.6084/m9.figshare.1451405
title: Example resting BOLD data

description: Raw resting BOLD fMRI timeseries
DOI: 10.6084/m9.figshare.1451407.v1
title: Example BOLD segmentation.

description: Example segmentation for a BOLD image. 6 tissue types are labeled.
DOI: 10.6084/m9.figshare.1451402
title: AMF in old growth cedar age classes

description: We analysed root and soil DNA (LSU) from ancient cedars in the BC interior (N and S location). Young, intermediate and old trees were sampled.
DOI: 10.6084/m9.figshare.1451405.v1
title: Example resting BOLD data

description: Raw resting BOLD fMRI timeseries
DOI: 10.6084/m9.figshare.1451402.v1
title: AMF in old growth cedar age classes

description: We analysed root and soil DNA (LSU) from ancient cedars in the BC interior (N and S location). Young, intermediate and old trees were sampled.
DOI: 10.6084/m9.figshare.1451408.v1
title: Last.fm dataset

description: This dataset contains tuples collected from Last.fm API ( http://www.last.fm/api )
DOI: 10.6084/m9.figshare.1451397
title: Biometric iris, database ILEA

description: Biometric iris, database ILEA format RAW
DOI: 10.6084/m9.figshare.1451408.v3
title: lastfm.part02.rar

description: This dataset contains tuples collected from Last.fm API ( http://www.last.fm/api )
DOI: 10.6084/m9.figshare.1451408.v2
title: lastfm.part02

description: This dataset contains tuples collected from Last.fm API ( http://www.last.fm/api )
DOI: 10.6084/m9.figshare.1451389
title: Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt

description: The Delta Smelt <i>Hypomesus transpacificus</i>, listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive population's overall genetic diversity and to minimize inbreeding. We created a panel of single-nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site-associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single-pair crosses at 2,317 newly discovered loci with RAD-seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) greater than 0.20, neutrality (Hardy–Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a Fluidigm Integrated Fluidic Circuit 96.96 and were tested for marker accuracy and the ability to correctly assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs (mean MAF = 0.47) successfully assigned 100% of tested offspring if all of the samples were genotyped at a minimum of 18 loci. Given its capacity to streamline the screening of broodstock candidates, we foresee that the new SNP parentage panel will assume an integral role in genetic management of the Delta Smelt conservation hatchery. Furthermore, genomic resources created for this study have the potential to propel further advances in studying this imperiled species.Received November 29, 2014; accepted March 30, 2015
DOI: 10.6084/m9.figshare.1451392
title: Oligocene plotopterid skulls from western North America and their bearing on the phylogenetic affinities of these penguin-like seabirds

description: ABSTRACTPlotopterids are penguin-like, wing-propelled birds with controversial phylogenetic affinities. They are usually regarded as closely related to Suloidea (gannets, cormorants, and allies), with the penguin-like features considered to be of convergent origin. However, it has also been proposed that the similarities shared by plotopterids and penguins are due to common ancestry. An in-depth assessment of plotopterid affinities has been hampered by the fact that very little data about the skull of these birds were available. New fossils of <i>Tonsala</i> from the Oligocene Pysht Formation in Washington State (U.S.A.) include the first well-preserved cranial remains of this taxon. They show that although plotopterids share derived cranial features with members of Suloidea that are absent in species of Sphenisciformes (penguins), they lack diagnostic derived features of the representatives of crown group Suloidea. To assess the affinities of plotopterids, we performed a phylogenetic analysis that included, for the first time, early stem group representatives of Sphenisciformes, resulting in a sister-group relationship between Plotopteridae and Suloidea. Intriguingly, however, our reanalysis of the emended data of a more comprehensive recent analysis that supported a position of Plotopteridae within Suloidea recovered a sister-group relationship between Plotopteridae and Sphenisciformes. Although cranial morphology challenges the hypothesis of close affinities between plotopterids and penguins, more data on early stem lineage representatives of penguins are needed for a robust placement of Plotopteridae relative to Sphenisciformes. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1451392.v2
title: Oligocene plotopterid skulls from western North America and their bearing on the phylogenetic affinities of these penguin-like seabirds

description: ABSTRACTPlotopterids are penguin-like, wing-propelled birds with controversial phylogenetic affinities. They are usually regarded as closely related to Suloidea (gannets, cormorants, and allies), with the penguin-like features considered to be of convergent origin. However, it has also been proposed that the similarities shared by plotopterids and penguins are due to common ancestry. An in-depth assessment of plotopterid affinities has been hampered by the fact that very little data about the skull of these birds were available. New fossils of <i>Tonsala</i> from the Oligocene Pysht Formation in Washington State (U.S.A.) include the first well-preserved cranial remains of this taxon. They show that although plotopterids share derived cranial features with members of Suloidea that are absent in species of Sphenisciformes (penguins), they lack diagnostic derived features of the representatives of crown group Suloidea. To assess the affinities of plotopterids, we performed a phylogenetic analysis that included, for the first time, early stem group representatives of Sphenisciformes, resulting in a sister-group relationship between Plotopteridae and Suloidea. Intriguingly, however, our reanalysis of the emended data of a more comprehensive recent analysis that supported a position of Plotopteridae within Suloidea recovered a sister-group relationship between Plotopteridae and Sphenisciformes. Although cranial morphology challenges the hypothesis of close affinities between plotopterids and penguins, more data on early stem lineage representatives of penguins are needed for a robust placement of Plotopteridae relative to Sphenisciformes. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1451389.v2
title: Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt

description: The Delta Smelt <i>Hypomesus transpacificus</i>, listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive population's overall genetic diversity and to minimize inbreeding. We created a panel of single-nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site-associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single-pair crosses at 2,317 newly discovered loci with RAD-seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) greater than 0.20, neutrality (Hardy–Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a Fluidigm Integrated Fluidic Circuit 96.96 and were tested for marker accuracy and the ability to correctly assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs (mean MAF = 0.47) successfully assigned 100% of tested offspring if all of the samples were genotyped at a minimum of 18 loci. Given its capacity to streamline the screening of broodstock candidates, we foresee that the new SNP parentage panel will assume an integral role in genetic management of the Delta Smelt conservation hatchery. Furthermore, genomic resources created for this study have the potential to propel further advances in studying this imperiled species.Received November 29, 2014; accepted March 30, 2015
DOI: 10.6084/m9.figshare.1451389.v1
title: Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt

description: The Delta Smelt <i>Hypomesus transpacificus</i>, listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive population's overall genetic diversity and to minimize inbreeding. We created a panel of single-nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site-associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single-pair crosses at 2,317 newly discovered loci with RAD-seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) greater than 0.20, neutrality (Hardy–Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a Fluidigm Integrated Fluidic Circuit 96.96 and were tested for marker accuracy and the ability to correctly assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs (mean MAF = 0.47) successfully assigned 100% of tested offspring if all of the samples were genotyped at a minimum of 18 loci. Given its capacity to streamline the screening of broodstock candidates, we foresee that the new SNP parentage panel will assume an integral role in genetic management of the Delta Smelt conservation hatchery. Furthermore, genomic resources created for this study have the potential to propel further advances in studying this imperiled species.Received November 29, 2014; accepted March 30, 2015
DOI: 10.6084/m9.figshare.1451392.v1
title: Oligocene plotopterid skulls from western North America and their bearing on the phylogenetic affinities of these penguin-like seabirds

description: ABSTRACTPlotopterids are penguin-like, wing-propelled birds with controversial phylogenetic affinities. They are usually regarded as closely related to Suloidea (gannets, cormorants, and allies), with the penguin-like features considered to be of convergent origin. However, it has also been proposed that the similarities shared by plotopterids and penguins are due to common ancestry. An in-depth assessment of plotopterid affinities has been hampered by the fact that very little data about the skull of these birds were available. New fossils of <i>Tonsala</i> from the Oligocene Pysht Formation in Washington State (U.S.A.) include the first well-preserved cranial remains of this taxon. They show that although plotopterids share derived cranial features with members of Suloidea that are absent in species of Sphenisciformes (penguins), they lack diagnostic derived features of the representatives of crown group Suloidea. To assess the affinities of plotopterids, we performed a phylogenetic analysis that included, for the first time, early stem group representatives of Sphenisciformes, resulting in a sister-group relationship between Plotopteridae and Suloidea. Intriguingly, however, our reanalysis of the emended data of a more comprehensive recent analysis that supported a position of Plotopteridae within Suloidea recovered a sister-group relationship between Plotopteridae and Sphenisciformes. Although cranial morphology challenges the hypothesis of close affinities between plotopterids and penguins, more data on early stem lineage representatives of penguins are needed for a robust placement of Plotopteridae relative to Sphenisciformes. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1451387
title: Dataset 1

description: Dataset 1 for article 'Compendium of natural hyperbolic metamaterials'.
DOI: 10.6084/m9.figshare.1451386
title: Prevalence and characteristics of overweight and obesity in indigenous Australian children: A systematic review

description: Evidence-based profiling of obesity and overweight in Indigenous Australian children has been poor. This study systematically reviewed evidence of the prevalence and patterns of obesity/overweight, with respect to gender, age, remoteness, and birth weight, in Indigenous Australian children, 0–18 years (PROSPERO CRD42014007626). Study quality and risk of bias were assessed. Twenty-five publications (21 studies) met inclusion criteria, with large variations in prevalence for obesity or overweight (11 to 54%) reported. A high degree of heterogeneity in study design was observed, few studies (6/21) were representative of the target population, and few appropriately recruited Indigenous children (8/21). Variability in study design, conduct, and small sample sizes mean that it is not possible to derive a single estimate for prevalence although two high-quality studies indicate at least one in four Indigenous Australian children are overweight or obese. Four of six studies reporting on gender, found overweight/obesity higher in girls and eight studies reporting on overweight/obesity by age suggest prevalence increases with age with one high quality large national study reporting total overweight/obesity as 22.4% of children aged 2–4 years, 27.5% of those aged 5–9, 38.5% aged 10–14, and 36.3% aged 15–17. Three of four studies, reporting obesity/overweight by region, found lower rates for children living in more remote areas than urban areas.
DOI: 10.6084/m9.figshare.1451388.v1
title: Sumoylation regulates EXO1 stability and processing of DNA damage

description: ABSTRACTDNA double-strand break repair by the error-free pathway of homologous recombination (HR) requires the concerted action of several factors. Among these, EXO1 and DNA2/BLM are responsible for the extensive resection of DNA ends to produce 3′-overhangs, which are essential intermediates for downstream steps of HR. Here we show that EXO1 is a SUMO target and that sumoylation affects EXO1 ubiquitylation and protein stability. We identify an UBC9-PIAS1/PIAS4-dependent mechanism controlling human EXO1 sumoylation <i>in vivo</i> and demonstrate conservation of this mechanism in yeast by the Ubc9-Siz1/Siz2 using an <i>in vitro</i> reconstituted system. Furthermore, we show physical interaction between EXO1 and the de-sumoylating enzyme SENP6 both <i>in vitro</i> and <i>in vivo</i>, promoting EXO1 stability. Finally, we identify the major sites of sumoylation in EXO1 and show that ectopic expression of a sumoylation-deficient form of EXO1 rescues the DNA damage-induced chromosomal aberrations observed upon wt-EXO1 expression. Thus, our study identifies a novel layer of regulation of EXO1, making the pathways that regulate its function an ideal target for therapeutic intervention.
DOI: 10.6084/m9.figshare.1451386.v2
title: Prevalence and characteristics of overweight and obesity in indigenous Australian children: A systematic review

description: Evidence-based profiling of obesity and overweight in Indigenous Australian children has been poor. This study systematically reviewed evidence of the prevalence and patterns of obesity/overweight, with respect to gender, age, remoteness, and birth weight, in Indigenous Australian children, 0–18 years (PROSPERO CRD42014007626). Study quality and risk of bias were assessed. Twenty-five publications (21 studies) met inclusion criteria, with large variations in prevalence for obesity or overweight (11 to 54%) reported. A high degree of heterogeneity in study design was observed, few studies (6/21) were representative of the target population, and few appropriately recruited Indigenous children (8/21). Variability in study design, conduct, and small sample sizes mean that it is not possible to derive a single estimate for prevalence although two high-quality studies indicate at least one in four Indigenous Australian children are overweight or obese. Four of six studies reporting on gender, found overweight/obesity higher in girls and eight studies reporting on overweight/obesity by age suggest prevalence increases with age with one high quality large national study reporting total overweight/obesity as 22.4% of children aged 2–4 years, 27.5% of those aged 5–9, 38.5% aged 10–14, and 36.3% aged 15–17. Three of four studies, reporting obesity/overweight by region, found lower rates for children living in more remote areas than urban areas.
DOI: 10.6084/m9.figshare.1451383
title: MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors

description: MicroRNAs (miRNAs) are small non-coding RNAs that have important regulatory functions in plant growth, development, and response to abiotic stress. Increasing evidence also supports that plant miRNAs contribute to immune responses to pathogens. Here, we used deep sequencing of small RNA libraries for global identification of rice miRNAs that are regulated by fungal elicitors. We also describe 9 previously uncharacterized miRNAs in rice. Combined small RNA and degradome analyses revealed regulatory networks enriched in elicitor-regulated miRNAs supported by the identification of their corresponding target genes. Specifically, we identified an important number of miRNA/target gene pairs involved in small RNA pathways, including miRNA, heterochromatic and trans-acting siRNA pathways. We present evidence for miRNA/target gene pairs implicated in hormone signaling and cross-talk among hormone pathways having great potential in regulating rice immunity. Furthermore, we describe miRNA-mediated regulation of Conserved-Peptide upstream Open Reading Frame (CPuORF)-containing genes in rice, which suggests the existence of a novel regulatory network that integrates miRNA and CPuORF functions in plants. The knowledge gained in this study will help in understanding the underlying regulatory mechanisms of miRNAs in rice immunity and develop appropriate strategies for rice protection.