cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8797886
title: Are farmed European seabass (<i>Dicentrarchus labrax</i>) prices in European Union markets affected by Turkish exports of farmed European seabass?

description: Often, increases in farmed seabass and seabream production surpluses from Turkey and Greece have been blamed to lead to price declines and aquaculture sector crises. In this study, we investigate whether Turkish exports of farmed European seabass affect prices of European Union (EU) farmed European seabass. This is done by examining the existence of market integration between the prices of Turkish exports of farmed European seabass into the EU and the prices of farmed European seabass commercialized in wholesale markets in Barcelona, Madrid and Paris. Market integration and competition studies in fisheries and aquaculture products have generally focused on analyzing substitutability between species and between wild and farmed conspecifics. Few studies have focused on analyzing market integration between different geographic areas. Market integration analyses between different geographic areas have proven useful in anti-dumping investigations. Results show the lack of market integration between EU imports of Turkish farmed European seabass and main EU wholesale markets; in other words, farmed European seabass prices in EU markets do not seem to be affected by export prices of Turkish farmed seabass.
DOI: 10.6084/m9.figshare.8798045.v2
title: Enzyme replacement therapy with recombinant pro-CTSD (cathepsin D) corrects defective proteolysis and autophagy in neuronal ceroid lipofuscinosis

description: CTSD (cathepsin D) is one of the major lysosomal proteases indispensable for the maintenance of cellular proteostasis by turning over substrates of endocytosis, phagocytosis and autophagy. Consequently, CTSD deficiency leads to a strong impairment of the lysosomal-autophagy machinery. In mice and humans CTSD dysfunction underlies the congenital variant (CLN10) of neuronal ceroid lipofuscinosis (NCL). NCLs are distinct lysosomal storage disorders (LSDs) sharing various hallmarks, namely accumulation of protein aggregates and ceroid lipofuscin leading to neurodegeneration and blindness. The most established and clinically approved approach to treat LSDs is enzyme replacement therapy (ERT) aiming to replace the defective hydrolase with an exogenously applied recombinant protein. Here we reveal that recombinant human pro-CTSD produced in a mammalian expression system can be efficiently taken up by a variety of cell models, is correctly targeted to lysosomes and processed to the active mature form of the protease. In proof-of-principle experiments we provide evidence that recombinant human CTSD (rhCTSD) can improve the biochemical phenotype of CTSD-deficient hippocampal slice cultures <i>in vitro</i> and retinal cells <i>in vivo</i>. Furthermore, we demonstrate that dosing of rhCTSD in the murine CLN10 model leads to a correction of lysosomal hypertrophy, storage accumulation and impaired autophagic flux in the viscera and central nervous system (CNS). We establish that direct delivery of the recombinant protease to the CNS is required for improvement of neuropathology and lifespan extension. Together these data support the continuation of the pre-clinical studies for the application of rhCTSD in the treatment of NCL. <b>Abbreviations:</b> AIF1/IBA1: allograft inflammatory factor 1; BBB: blood brain barrier; CNS: central nervous system; CTSB: cathepsin B; CTSD: cathepsin D; CTSL: cathepsin L; ERT: enzyme replacement therapy; GFAP: glial fibrillary acidic protein; INL: inner nuclear layer; LAMP1: lysosomal-associated membrane protein 1; LAMP2: lysosomal-associated membrane protein 2; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; LDL: low-density lipoprotein; LRP1: low density lipoprotein receptor-related protein 1; LSD: lysosomal storage disorder; MEFs: mouse embryonic fibroblasts; M6P: mannose 6-phosphate; mCTSD: mature CTSD; NCL: neuronal ceroid lipofuscinosis; ONL: outer nuclear layer; PB: phosphate buffer; proCTSD: pro-cathepsin D; LRPAP1: low density lipoprotein receptor-related protein associated protein 1; rhCTSD: human recombinant CTSD; SAPC: saposin C; SAPD: saposin D; ATP5G1: ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9); SQSTM1/p62: sequestosome 1; TPP1: tripeptidyl peptidase I.
DOI: 10.6084/m9.figshare.8797886.v1
title: Are farmed European seabass (<i>Dicentrarchus labrax</i>) prices in European Union markets affected by Turkish exports of farmed European seabass?

description: Often, increases in farmed seabass and seabream production surpluses from Turkey and Greece have been blamed to lead to price declines and aquaculture sector crises. In this study, we investigate whether Turkish exports of farmed European seabass affect prices of European Union (EU) farmed European seabass. This is done by examining the existence of market integration between the prices of Turkish exports of farmed European seabass into the EU and the prices of farmed European seabass commercialized in wholesale markets in Barcelona, Madrid and Paris. Market integration and competition studies in fisheries and aquaculture products have generally focused on analyzing substitutability between species and between wild and farmed conspecifics. Few studies have focused on analyzing market integration between different geographic areas. Market integration analyses between different geographic areas have proven useful in anti-dumping investigations. Results show the lack of market integration between EU imports of Turkish farmed European seabass and main EU wholesale markets; in other words, farmed European seabass prices in EU markets do not seem to be affected by export prices of Turkish farmed seabass.
DOI: 10.6084/m9.figshare.8797868
title: Reducing the Effort for Systematic Reviews in Software Engineering - Evaluation Data

description: All the data discussed in the paper<br>Osborne, F., Muccini, H., Lago, P. and Motta, E. (2019) Reducing the Effort for Systematic Reviews in Software Engineering. Data Science. <br>The paper presents an Expert-Driven Automatic Methodology (EDAM) for assisting researchers in performing systematic reviews. <br><br>
DOI: 10.6084/m9.figshare.8797868.v1
title: Reducing the Effort for Systematic Reviews in Software Engineering - Evaluation Data

description: All the data discussed in the paper<br>Osborne, F., Muccini, H., Lago, P. and Motta, E. (2019) Reducing the Effort for Systematic Reviews in Software Engineering. Data Science. <br>The paper presents an Expert-Driven Automatic Methodology (EDAM) for assisting researchers in performing systematic reviews. <br><br>
DOI: 10.6084/m9.figshare.8797748
title: Data for this study from Temperature- versus precipitation-limitation shape local temperature tolerance in a Holarctic freshwater crustacean

description: The excel table includes the geographic locations of all populations samples, the data generated during the study and the climate data for all locations.
DOI: 10.6084/m9.figshare.8797748.v1
title: Data for this study from Temperature- versus precipitation-limitation shape local temperature tolerance in a Holarctic freshwater crustacean

description: The excel table includes the geographic locations of all populations samples, the data generated during the study and the climate data for all locations.
DOI: 10.6084/m9.figshare.8797733
title: Annotation of full-length transcriptome of Lilium

description: The dataset contains functional annotations from non-redundant protein (NR), non-redundant nucleotide (NT), Gene Ontology (GO), Clusters of Orthologous Groups (KOG), Kyoto Encyclopaedia of Genes and Genomes (KEGG), SwissProt and Interpro database.
DOI: 10.6084/m9.figshare.8797733.v2
title: Annotation of full-length transcriptome of Lilium

description: The dataset contains functional annotations from non-redundant protein (NR), non-redundant nucleotide (NT), Gene Ontology (GO), Clusters of Orthologous Groups (KOG), Kyoto Encyclopaedia of Genes and Genomes (KEGG), SwissProt and Interpro database.
DOI: 10.6084/m9.figshare.8797733.v1
title: Untitled Item

description: The dataset contains functional annotations from non-redundant protein (NR), non-redundant nucleotide (NT), Gene Ontology (GO), Clusters of Orthologous Groups (KOG), Kyoto Encyclopaedia of Genes and Genomes (KEGG), SwissProt and Interpro database.
DOI: 10.6084/m9.figshare.8797718
title: Electron microprobe settings. Geochemical and Petrographic Variations in Pseudotachylyte along the Outer Hebrides Fault Zone, Scotland

description: Electron microprobe settings
DOI: 10.6084/m9.figshare.8797682
title: Sample locations. Geochemical and Petrographic Variations in Pseudotachylyte along the Outer Hebrides Fault Zone, Scotland

description: Sample locations
DOI: 10.6084/m9.figshare.8797688
title: Two Neoarchean tectonothermal events on the western edge of the North Atlantic Craton, as revealed by SIMS dating of the Saglek Block, Nain Province, Labrador

description: LABR Geochemistry
DOI: 10.6084/m9.figshare.8797718.v1
title: Electron microprobe settings. Geochemical and Petrographic Variations in Pseudotachylyte along the Outer Hebrides Fault Zone, Scotland

description: Electron microprobe settings
DOI: 10.6084/m9.figshare.8797688.v1
title: Two Neoarchean tectonothermal events on the western edge of the North Atlantic Craton, as revealed by SIMS dating of the Saglek Block, Nain Province, Labrador

description: LABR Geochemistry
DOI: 10.6084/m9.figshare.8797592
title: Postoperative Pain after Single versus Multiple Visits Endodontic Treatment of Necrotic Teeth with Apical Periodontitis with Triple Antibiotic Paste: A Randomized Clinical Trial

description: The data describes the age, gender, preoperative pain, postoperative pain, incidence and analgesic intake of the two groups of the study.
DOI: 10.6084/m9.figshare.8797655
title: NA

description: Nyssa<br>
DOI: 10.6084/m9.figshare.8797682.v1
title: Sample locations. Geochemical and Petrographic Variations in Pseudotachylyte along the Outer Hebrides Fault Zone, Scotland

description: Sample locations
DOI: 10.6084/m9.figshare.8797592.v1
title: Postoperative Pain after Single versus Multiple Visits Endodontic Treatment of Necrotic Teeth with Apical Periodontitis with Triple Antibiotic Paste: A Randomized Clinical Trial

description: The data describes the age, gender, preoperative pain, postoperative pain, incidence and analgesic intake of the two groups of the study.
DOI: 10.6084/m9.figshare.8797655.v2
title: Nyssa

description: Nyssa<br>
DOI: 10.6084/m9.figshare.8797682.v3
title: Sample locations. Geochemical and Petrographic Variations in Pseudotachylyte along the Outer Hebrides Fault Zone, Scotland

description: Sample locations
DOI: 10.6084/m9.figshare.8797682.v2
title: Sample locations. Geochemical and Petrographic Variations in Pseudotachylyte along the Outer Hebrides Fault Zone, Scotland

description: Sample locations
DOI: 10.6084/m9.figshare.8797580
title: Dataset for: Structural insights into repression of <i>Pneumococcal</i> fatty acid synthesis pathway via repressor FabT and co-repressor acyl-ACP

description: <i>Streptococcus pneumoniae</i> fatty acid synthesis pathway is globally controlled at the transcriptional level by repressor FabT and co-repressor acyl-ACP, the intermediate of phospholipid synthesis. Here we report the crystal structure of FabT complexed with a 23-bp dsDNA, indicating that FabT is a weak repressor of low DNA-binding affinity in the absence of acyl-ACP. Modification of ACP with a long-chain fatty acid is necessary for the formation of a stable complex with FabT, mimicking <i>in vitro</i> by cross-linking, which would significantly elevate the DNA-binding affinity of FabT. Altogether, we propose a putative working model of gene repression under the double controls of FabT and acyl-ACP, elucidating a distinct repression network for <i>Pneumococcus</i> to precisely coordinate fatty acid synthesis.
DOI: 10.6084/m9.figshare.8797655.v1
title: Nyssa sinensis genome gene prediction

description: The gff3 of the gene prediction in Nyssa sinensis<br>
DOI: 10.6084/m9.figshare.8797574
title: Plastic ingestion by marine fish in the wild

description: Marine plastic pollution has become a prominent environmental issue in the recent years. Plastic ingestion is of special concern, as its magnitude and consequences for marine organisms and potentially humans are still largely unknown. We reviewed 93 papers on plastic ingestion by wild marine fish published since 1972. Plastic ingestion was detected in 323 (65%) of 494 examined fish species, and in 262 (67%) of 391 examined commercial fish species. These proportions are likely greater, as a detailed analysis of the sampling effort and analytical methods used in the reviewed studies suggests an underestimation of plastic ingestion in some assessments. A significant positive relationship (<i>R</i> = + 0.845, <i>p</i> = 0.004) was found between the sample size up to <i>N</i> = 10 and the detection of plastic ingestion. We also found significant differences in detection and frequency of occurrence (FO, %) of plastic ingestion among the three main types of analytical methods: naked-eye, microscopic analysis and chemical digestion. The chemical digestion method, which is also the most robust laboratory method, had the greatest detection (86%) and the highest FO (37.6 ± 0.6%). To avoid the underestimation of plastic ingestion in future work, we provided recommendations for sample sizes and laboratory analysis.
DOI: 10.6084/m9.figshare.8797496
title: New approach to evaluating the effects of a drug on protein complexes with quantitative proteomics, using the SILAC method and bioinformatic approach

description: Protein–protein interactions (PPIs) lead the formation of protein complexes that perform biochemical reactions that maintain the living state of the living cell. Although therapeutic drugs should influence the formation of protein complexes in addition to PPI network, the methodology analyzing such influences remain to be developed. Here, we demonstrate that a new approach combining HPLC (high performance liquid chromatography) for separating protein complexes, and the SILAC (stable isotope labeling using amino acids in cell culture) method for relative protein quantification, enable us to identify the protein complexes influenced by a drug. We applied this approach to the analysis of thalidomide action on HepG2 cells, assessed the identified proteins by clustering data analyses, and assigned 135 novel protein complexes affected by the drug. We propose that this approach is applicable to elucidating the mechanisms of actions of other therapeutic drugs on the PPI network, and the formation of protein complexes. We developed a new approach detecting protein complexes affected with a drug by analysis of protein-protein interaction using a combination of IEC and SILAC LC-MS/MS.
DOI: 10.6084/m9.figshare.8797502
title: seismic data

description: the seismic waveform is a vertical component of velocity at depth of 3465 inch on a 15Hz geophone installed deep underground pilot hole. The seismic signal was observed by San Andreas Fault Observatory at Depth (SAFOD). The sampling frequency is 8000Hz.
DOI: 10.6084/m9.figshare.8797580.v1
title: Dataset for: Structural insights into repression of <i>Pneumococcal</i> fatty acid synthesis pathway via repressor FabT and co-repressor acyl-ACP

description: <i>Streptococcus pneumoniae</i> fatty acid synthesis pathway is globally controlled at the transcriptional level by repressor FabT and co-repressor acyl-ACP, the intermediate of phospholipid synthesis. Here we report the crystal structure of FabT complexed with a 23-bp dsDNA, indicating that FabT is a weak repressor of low DNA-binding affinity in the absence of acyl-ACP. Modification of ACP with a long-chain fatty acid is necessary for the formation of a stable complex with FabT, mimicking <i>in vitro</i> by cross-linking, which would significantly elevate the DNA-binding affinity of FabT. Altogether, we propose a putative working model of gene repression under the double controls of FabT and acyl-ACP, elucidating a distinct repression network for <i>Pneumococcus</i> to precisely coordinate fatty acid synthesis.
DOI: 10.6084/m9.figshare.8797574.v1
title: Plastic ingestion by marine fish in the wild

description: Marine plastic pollution has become a prominent environmental issue in the recent years. Plastic ingestion is of special concern, as its magnitude and consequences for marine organisms and potentially humans are still largely unknown. We reviewed 93 papers on plastic ingestion by wild marine fish published since 1972. Plastic ingestion was detected in 323 (65%) of 494 examined fish species, and in 262 (67%) of 391 examined commercial fish species. These proportions are likely greater, as a detailed analysis of the sampling effort and analytical methods used in the reviewed studies suggests an underestimation of plastic ingestion in some assessments. A significant positive relationship (<i>R</i> = + 0.845, <i>p</i> = 0.004) was found between the sample size up to <i>N</i> = 10 and the detection of plastic ingestion. We also found significant differences in detection and frequency of occurrence (FO, %) of plastic ingestion among the three main types of analytical methods: naked-eye, microscopic analysis and chemical digestion. The chemical digestion method, which is also the most robust laboratory method, had the greatest detection (86%) and the highest FO (37.6 ± 0.6%). To avoid the underestimation of plastic ingestion in future work, we provided recommendations for sample sizes and laboratory analysis.
DOI: 10.6084/m9.figshare.8797496.v1
title: New approach to evaluating the effects of a drug on protein complexes with quantitative proteomics, using the SILAC method and bioinformatic approach

description: Protein–protein interactions (PPIs) lead the formation of protein complexes that perform biochemical reactions that maintain the living state of the living cell. Although therapeutic drugs should influence the formation of protein complexes in addition to PPI network, the methodology analyzing such influences remain to be developed. Here, we demonstrate that a new approach combining HPLC (high performance liquid chromatography) for separating protein complexes, and the SILAC (stable isotope labeling using amino acids in cell culture) method for relative protein quantification, enable us to identify the protein complexes influenced by a drug. We applied this approach to the analysis of thalidomide action on HepG2 cells, assessed the identified proteins by clustering data analyses, and assigned 135 novel protein complexes affected by the drug. We propose that this approach is applicable to elucidating the mechanisms of actions of other therapeutic drugs on the PPI network, and the formation of protein complexes. We developed a new approach detecting protein complexes affected with a drug by analysis of protein-protein interaction using a combination of IEC and SILAC LC-MS/MS.
DOI: 10.6084/m9.figshare.8797190
title: Dataset 4

description: The qRT-PCR validation data of <i>M. oryzae</i> and <i>O. sativa </i>transcriptome
DOI: 10.6084/m9.figshare.8797184
title: Transcriptome assembly of Richtersius coronifer with annotated BLAST result against Ramazzottius varieornatus.

description: For transcriptome sequencing and assembly, total RNA was extracted from a single specimen of tardigrade using Direct-zol RNA kit (Zymo Research) and was amplified using SMARTer Ultra Low Input RNA Kit for Sequencing v.3 (Clonetech). Illumina libraries were prepared using KAPA HyperPlus Kit (KAPA BIosystems), and the library was sequenced using a NextSeq 500 High Output Mode 75 cycles kit (Illumina) as single-end 75bp layout. Protocols are detailed in Arakawa et al. (2016)andYoshida et al. (2018). Sequences were filtered for adapters and demultiplexed using the bcl2fastq v.2 software (Illumina), and were assembled <i>de novo</i>using Bridger software with default parameters (Chang et al. 2015). Completeness of the assembly was assessed using BUSCO v.2/3 transcriptome mode with Eukaryote reference through gVolante server (Nishimura et al. 2017). Gene content was compared with <i>Ramazzottius varieornatus</i>and <i>Hypsibius exemplaris </i>genomes (Yoshida et al. 2017), as well as <i>Drosophila melanogaster</i>and <i>Caenorhabditis elegans</i>reference proteomes obtained from Flybase and Wormbase, respectively. Annotated BLAST result to <i>R. varieornatus </i>reference proteome with BLASTX (-e 1e-5) is also provided with the transcriptome assembly.
DOI: 10.6084/m9.figshare.8797190.v1
title: Data Citation3

description: Data Citation3 including information of the qRT-PCR validation data.
DOI: 10.6084/m9.figshare.8797166
title: Data Citation Old

description: This work was supported by grants from National Research Foundation of Korea (NRF-2017R1A2A1A17069504, NRF-2015M3A9B8028679, and NRF-2018R1A5A1023599) and Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry through Agricultural Microbiome Program (918017-04-1-CG000).
DOI: 10.6084/m9.figshare.8797067
title: Exonisation_GB

description: Scripts and datafiles required to identify and quantify novel exonisation overlapping repeat elements
DOI: 10.6084/m9.figshare.8797100
title: MS-275 Chemical Analogues Promote Hemoglobin Production and Erythroid Differentiation of K562 Cells

description: β-Thalassemia (β-thal) is a hemoglobinopathy characterized by reduced or absent β-globin production. Pharmacological reactivation of the γ-globin gene for the production of fetal hemoglobin (Hb F) presents an attractive treatment strategy. In an effort to identify promising therapeutic agents, we evaluated 80 analogues of the histone deacetylase inhibitor MS-275, a known Hb F inducer. The chemical analogues were identified <i>via</i> molecular modeling and targeted chemical modifications. Nine novel agents exhibited significant hemoglobin (Hb)-inducing and erythroid differentiation activities in the human K562 erythroleukemia cell line. Five of them appeared to be stronger inducers than the lead compound, MS-275, demonstrating the effectiveness of our method.
DOI: 10.6084/m9.figshare.8797067.v1
title: Exonisation_GB

description: Scripts and datafiles required to identify and quantify novel exonisation overlapping repeat elements
DOI: 10.6084/m9.figshare.8797166.v1
title: Untitled Item

description: This work was supported by grants from National Research Foundation of Korea (NRF-2017R1A2A1A17069504, NRF-2015M3A9B8028679, and NRF-2018R1A5A1023599) and Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry through Agricultural Microbiome Program (918017-04-1-CG000).
DOI: 10.6084/m9.figshare.8797190.v2
title: Dataset 4

description: Dataset 4 including information of the qRT-PCR validation data.
DOI: 10.6084/m9.figshare.8796980
title: SIRI_WHU Dataset

description: The SIRI-WHU dataset comprises of 2400 images organized into 12 categories. Dataset is uploaded in parts. Complete dataset can be obtained by combining SIRI_WHU1 and SIRI_WHU2 respectively.<br>Zhao B, Zhong Y, Xia GS, Zhang L. Dirichlet-derived multiple topic sceneclassification model for high spatial resolution remote sensing imagery. IEEETransactions on Geoscience and Remote Sensing. 2016;54(4):2108{2123.
DOI: 10.6084/m9.figshare.8796953
title: Assessment of tonsil grade classification by measuring actual tonsil size during surgery

description: Adenotonsillar enlargement is a common cause of substantial pediatric illnesses, including obstructive respiratory disease and recurrent airway infection. The current tonsil grading systems in use allows clinicians to evaluate tonsil size, but the correlation with actual tonsillar size in a clinical setting has not been established.