cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17305632
title: Additional file 1 of The ecdysteroid receptor regulates salivary gland degeneration through apoptosis in Rhipicephalus haemaphysaloides

description: Additional file 1: Figure S1. Alignment of the deduced amino acid sequences of Rhipicephalus haemaphysaloides-EcR; Amblyomma americanum-EcR; Ixodes scapularis-EcR; Ornithodoros moubata-EcR; Bombyx mori-EcR; Drosophila melanogaster-EcR; Danio rerio-LXRα; Homo sapiens-LXRα; Mus musculus-LXRβ. All species had a DBD domain and an LBD domain, and the DBD domain had two conserved C4-type zinc finger motifs. Especially, the position of four cysteine residues in the ZF_C4 was highly conservative. In arthropods, the DBD and LBD domains were relatively conserved. Figure S2. Alignment of the deduced amino acid sequences of Rhipicephalus haemaphysaloides USP; Amblyomma americanum-USP; Ixodes scapularis-USP; Ornithodoros moubata-USP; Bombyx mori-USP; Drosophila melanogaster-USP; Danio rerio-USP; Homo sapiens-RXR; Mus musculus-RXR. Invertebrates and vertebrates both had a DBD domain and an LBD domain as EcR. Moreover, the DBD domain of USP was highly conserved not only in invertebrates but also in vertebrates, which was different from EcR. Figure S3. Phylogenetic tree constructed using amino acid sequences of the ecdysteroid receptor heterodimeric complex, EcR (a) and USP (b) of Rhipicephalus haemaphysaloides. Figure S4. Results of a BLAST search of RhEcR and RhUSP sequences against genomic sequences of six tick species. The query was RhEcR and RhUSP gene nucleotide sequences in a search against genomic sequences of six tick species (Ixodes persulcatus, Haemaphysalis longicornis, Dermacentor silvarum, Hyalomma asiaticum, Rhipicephalus sanguineus, Rhipicephalus microplus and Ixodes scapularisis). Figure S5. Temporal and spatial distribution of RhEcR and RhUSP in Rhipicephalus haemaphysaloides. Tissues were dissected from female ticks. Using qRT-PCR, relative RNA levels of RhEcR and RhUSP were measured at each time point. a In the period of blood-feeding, the expression of RhEcR2 was higher than RhEcR1 before E 24 h. After E 24 h, the expression of RhEcR1 was higher than RhEcR2. b Two isoforms of RhUSP were detected during all time points, but the level of RhUSP1 was high and RhUSP3 was very low. The data represent the mean ± SD of the experiments (10 ticks/time point) performed in triplicate and normalized to EF1α. c The translation of RhEcR isoforms was detected with anti-mouse RhEcR polyclonal antibody. After E 24 h, the expression of all isoforms of RhEcR gradually decreased. Table S1 Oligonucleotide sequences and names of the primers used for qRT-PCR, RNAi and cloning of Rhipicephalus haemaphysaloides genes. Table S2 Accession numbers for sequences of EcR/LXR and USP/RXR in vertebrates and invertebrates.
DOI: 10.6084/m9.figshare.17305632.v1
title: Additional file 1 of The ecdysteroid receptor regulates salivary gland degeneration through apoptosis in Rhipicephalus haemaphysaloides

description: Additional file 1: Figure S1. Alignment of the deduced amino acid sequences of Rhipicephalus haemaphysaloides-EcR; Amblyomma americanum-EcR; Ixodes scapularis-EcR; Ornithodoros moubata-EcR; Bombyx mori-EcR; Drosophila melanogaster-EcR; Danio rerio-LXRα; Homo sapiens-LXRα; Mus musculus-LXRβ. All species had a DBD domain and an LBD domain, and the DBD domain had two conserved C4-type zinc finger motifs. Especially, the position of four cysteine residues in the ZF_C4 was highly conservative. In arthropods, the DBD and LBD domains were relatively conserved. Figure S2. Alignment of the deduced amino acid sequences of Rhipicephalus haemaphysaloides USP; Amblyomma americanum-USP; Ixodes scapularis-USP; Ornithodoros moubata-USP; Bombyx mori-USP; Drosophila melanogaster-USP; Danio rerio-USP; Homo sapiens-RXR; Mus musculus-RXR. Invertebrates and vertebrates both had a DBD domain and an LBD domain as EcR. Moreover, the DBD domain of USP was highly conserved not only in invertebrates but also in vertebrates, which was different from EcR. Figure S3. Phylogenetic tree constructed using amino acid sequences of the ecdysteroid receptor heterodimeric complex, EcR (a) and USP (b) of Rhipicephalus haemaphysaloides. Figure S4. Results of a BLAST search of RhEcR and RhUSP sequences against genomic sequences of six tick species. The query was RhEcR and RhUSP gene nucleotide sequences in a search against genomic sequences of six tick species (Ixodes persulcatus, Haemaphysalis longicornis, Dermacentor silvarum, Hyalomma asiaticum, Rhipicephalus sanguineus, Rhipicephalus microplus and Ixodes scapularisis). Figure S5. Temporal and spatial distribution of RhEcR and RhUSP in Rhipicephalus haemaphysaloides. Tissues were dissected from female ticks. Using qRT-PCR, relative RNA levels of RhEcR and RhUSP were measured at each time point. a In the period of blood-feeding, the expression of RhEcR2 was higher than RhEcR1 before E 24 h. After E 24 h, the expression of RhEcR1 was higher than RhEcR2. b Two isoforms of RhUSP were detected during all time points, but the level of RhUSP1 was high and RhUSP3 was very low. The data represent the mean ± SD of the experiments (10 ticks/time point) performed in triplicate and normalized to EF1α. c The translation of RhEcR isoforms was detected with anti-mouse RhEcR polyclonal antibody. After E 24 h, the expression of all isoforms of RhEcR gradually decreased. Table S1 Oligonucleotide sequences and names of the primers used for qRT-PCR, RNAi and cloning of Rhipicephalus haemaphysaloides genes. Table S2 Accession numbers for sequences of EcR/LXR and USP/RXR in vertebrates and invertebrates.
DOI: 10.6084/m9.figshare.17305635
title: Additional file 2 of The ecdysteroid receptor regulates salivary gland degeneration through apoptosis in Rhipicephalus haemaphysaloides

description: Additional file 2: Dataset S1. Contigs of the Rhipicephalus haemaphysaloides salivary gland for RhEcR cloning. Dataset S2. Contig of the Rhipicephalus haemaphysaloides salivary gland for RhUSP cloning.
DOI: 10.6084/m9.figshare.17305635.v1
title: Additional file 2 of The ecdysteroid receptor regulates salivary gland degeneration through apoptosis in Rhipicephalus haemaphysaloides

description: Additional file 2: Dataset S1. Contigs of the Rhipicephalus haemaphysaloides salivary gland for RhEcR cloning. Dataset S2. Contig of the Rhipicephalus haemaphysaloides salivary gland for RhUSP cloning.
DOI: 10.5281/zenodo.10611051
title: Exemplary ecodesign of a smartphone based on a parametric life cycle assessment - Database (Excel)

description: Obsolete, please refer to https://zenodo.org/doi/10.5281/zenodo.10617911
DOI: 10.5281/zenodo.10611052
title: Exemplary ecodesign of a smartphone based on a parametric life cycle assessment - Database (Excel)

description: This study presents the development of a novel ecodesign approach based on a parametric life cycle assessment (LCA). The developed method allows for the comparison of environmental impacts of a vast number of different product configurations, which are derived automatically by determining every possible combination of the given design options. The life cycle model features a stochastic failure and repair simulation to account for a wide range of use cases as well as a recycling simulation that can determine the environmentally optimal recycling route. The developed method is tested on an exemplary case study of a smartphone. Despite efficiency limitations of the accompanying software tool prototype that was developed and used for the case study, it could be shown that the method allows to identify the environmental influence of different design options as well as the product configuration with the least annual global warming potential.

This file contains the database Excel file with data and calculations on failure and repair statistics, material compositions, and input tables for the software tool prototype developed in the study. It can be inspected as is to understand the underlying data and procedure presented in the study or used as an input for the Python source code to run the LCA model, which can be found here: 10.5281/zenodo.10611008

Note: References to licensed environmental datasets from the Sphera and ecoinvent databases have been deleted in the published version. In order to run the software tool, please add the respective values for the Global Warming Potential (or alternative impact categories) in the "processes_data" sheet and delete the suffix "_noLCIA" from the file name.
DOI: 10.5281/zenodo.10617932
title: Exemplary ecodesign of a smartphone based on a parametric life cycle assessment - Database (Excel)

description: Obsolete, please refer to https://zenodo.org/doi/10.5281/zenodo.10617911
DOI: 10.6084/m9.figshare.14160032
title: Insights into the mechanism regulating the differential expression of the P28-OMP outer membrane proteins in obligatory intracellular pathogen <i>Ehrlichia chaffeensis</i>

description: <i>Ehrlichia chaffeensis</i> causes human monocytic ehrlichiosis (HME), which is one of the most prevalent, life-threatening emerging infectious zoonoses. The life cycle of <i>E. chaffeensis</i> includes ticks and mammals, in which <i>E. chaffeensis</i> proteins are expressed differentially contributing to bacterial survival and infection. Among the <i>E. chaffeensis</i> P28-OMP outer membrane proteins, OMP-1B and P28 are predominantly expressed in tick cells and mammalian macrophages, respectively. The mechanisms regulating this differential expression have not been comprehensively studied. Here, we demonstrate that the transcriptional regulators EcxR and Tr1 regulate the differential expression of <i>omp-1B</i> and <i>p28</i> in <i>E. chaffeensis.</i> Recombinant <i>E. chaffeensis</i> Tr1 bound to the promoters of <i>omp-1B</i> and <i>p28,</i> and transactivated <i>omp-1B</i> and <i>p28</i> promoter-EGFP fusion constructs in <i>Escherichia coli</i>. The consensus sequence of Tr1 binding motifs was A<sup>C</sup>/<sub>T</sub>TATA as determined with DNase I footprint assay. Tr1 showed a higher affinity towards the <i>p28</i> promoter than the <i>omp-1B</i> promoter as determined with surface plasmon resonance. EcxR activated the <i>tr1</i> expression in response to a temperature decrease. At 37°C low level of Tr1 activated the <i>p28</i> expression. At 25°C high level of Tr1 activated the <i>omp-1B</i> expression, while repressing the <i>p28</i> expression by binding to an additional site upstream of the <i>p28</i> gene. Our data provide insights into a novel mechanism mediated by Tr1 regulating <i>E. chaffeensis</i> differential gene expression, which may aid in the development of new therapeutics for HME.
DOI: 10.6084/m9.figshare.14160032.v2
title: Insights into the mechanism regulating the differential expression of the P28-OMP outer membrane proteins in obligatory intracellular pathogen <i>Ehrlichia chaffeensis</i>

description: <i>Ehrlichia chaffeensis</i> causes human monocytic ehrlichiosis (HME), which is one of the most prevalent, life-threatening emerging infectious zoonoses. The life cycle of <i>E. chaffeensis</i> includes ticks and mammals, in which <i>E. chaffeensis</i> proteins are expressed differentially contributing to bacterial survival and infection. Among the <i>E. chaffeensis</i> P28-OMP outer membrane proteins, OMP-1B and P28 are predominantly expressed in tick cells and mammalian macrophages, respectively. The mechanisms regulating this differential expression have not been comprehensively studied. Here, we demonstrate that the transcriptional regulators EcxR and Tr1 regulate the differential expression of <i>omp-1B</i> and <i>p28</i> in <i>E. chaffeensis.</i> Recombinant <i>E. chaffeensis</i> Tr1 bound to the promoters of <i>omp-1B</i> and <i>p28,</i> and transactivated <i>omp-1B</i> and <i>p28</i> promoter-EGFP fusion constructs in <i>Escherichia coli</i>. The consensus sequence of Tr1 binding motifs was A<sup>C</sup>/<sub>T</sub>TATA as determined with DNase I footprint assay. Tr1 showed a higher affinity towards the <i>p28</i> promoter than the <i>omp-1B</i> promoter as determined with surface plasmon resonance. EcxR activated the <i>tr1</i> expression in response to a temperature decrease. At 37°C low level of Tr1 activated the <i>p28</i> expression. At 25°C high level of Tr1 activated the <i>omp-1B</i> expression, while repressing the <i>p28</i> expression by binding to an additional site upstream of the <i>p28</i> gene. Our data provide insights into a novel mechanism mediated by Tr1 regulating <i>E. chaffeensis</i> differential gene expression, which may aid in the development of new therapeutics for HME.
DOI: 10.18167/dvn1/p69nuk
title: Enquêtes de demande-consommation de produits maraîchers en Côte d'Ivoire, en 2021

description: Données issus d'enquêtes administrées à 5514 ménages répartis dans les quartiers d’Abidjan, de Yamoussoukro, de Bouaké et de Korhogo, à domicile, entre juillet et septembre 2021. Les enquêtes incluent des questions visant à faire une caractérisation socio-économique des ménages. Les données ont été obtenus pour informer le choix de produits maraîchers à étudier dans le projet MARIGO.
DOI: 10.5281/zenodo.10617910
title: Exemplary ecodesign of a smartphone based on a parametric life cycle assessment - Database (Excel)

description: This study presents the development of a novel ecodesign approach based on a parametric life cycle assessment (LCA). The developed method allows for the comparison of environmental impacts of a vast number of different product configurations, which are derived automatically by determining every possible combination of the given design options. The life cycle model features a stochastic failure and repair simulation to account for a wide range of use cases as well as a recycling simulation that can determine the environmentally optimal recycling route. The developed method is tested on an exemplary case study of a smartphone. Despite efficiency limitations of the accompanying software tool prototype that was developed and used for the case study, it could be shown that the method allows to identify the environmental influence of different design options as well as the product configuration with the least annual global warming potential.

This file contains the database Excel file with data and calculations on failure and repair statistics, material compositions, and input tables for the software tool prototype developed in the study. It can be inspected as is to understand the underlying data and procedure presented in the study or used as an input for the Python source code to run the LCA model, which can be found here: https://zenodo.org/doi/10.5281/zenodo.10617863 

Note: References to licensed environmental datasets from the Sphera and ecoinvent databases have been deleted in the published version. In order to run the software tool, please add the respective values for the Global Warming Potential (or alternative impact categories) in the "processes_data" sheet and delete the suffix "_noLCIA" from the file name.
DOI: 10.5281/zenodo.10617911
title: Exemplary ecodesign of a smartphone based on a parametric life cycle assessment - Database (Excel)

description: This study presents the development of a novel ecodesign approach based on a parametric life cycle assessment (LCA). The developed method allows for the comparison of environmental impacts of a vast number of different product configurations, which are derived automatically by determining every possible combination of the given design options. The life cycle model features a stochastic failure and repair simulation to account for a wide range of use cases as well as a recycling simulation that can determine the environmentally optimal recycling route. The developed method is tested on an exemplary case study of a smartphone. Despite efficiency limitations of the accompanying software tool prototype that was developed and used for the case study, it could be shown that the method allows to identify the environmental influence of different design options as well as the product configuration with the least annual global warming potential.

This file contains the database Excel file with data and calculations on failure and repair statistics, material compositions, and input tables for the software tool prototype developed in the study. It can be inspected as is to understand the underlying data and procedure presented in the study or used as an input for the Python source code to run the LCA model, which can be found here: https://zenodo.org/doi/10.5281/zenodo.10617863 

Note: References to licensed environmental datasets from the Sphera and ecoinvent databases have been deleted in the published version. In order to run the software tool, please add the respective values for the Global Warming Potential (or alternative impact categories) in the "processes_data" sheet and delete the suffix "_noLCIA" from the file name.
DOI: 10.6084/m9.figshare.23597289
title: Additional file 2 of ST6GALNAC4 promotes hepatocellular carcinogenesis by inducing abnormal glycosylation

description: Additional file 2. Code.
DOI: 10.6084/m9.figshare.23597289.v1
title: Additional file 2 of ST6GALNAC4 promotes hepatocellular carcinogenesis by inducing abnormal glycosylation

description: Additional file 2. Code.
DOI: 10.15468/dl.xfk8df
title: Occurrence Download

description: A dataset containing 1842387 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-4.05879 36.72896,-2.9182 36.72896,-2.9182 37.44386,-4.05879 37.44386,-4.05879 36.72896))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1842387 records from 435 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021306-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15454/eobum0/ypcrns
title: oak8-4-ec.xyz

description: :unav
DOI: 10.15454/eobum0/ypzwnz
title: oak0-46-pi.xyz

description: :unav
DOI: 10.15454/eobum0/yssvl4
title: oak613-1000-ec.xyz

description: :unav
DOI: 10.15454/eobum0/ytt8nw
title: oak2-6-pi.xyz

description: :unav
DOI: 10.15454/eobum0/yuxqcp
title: oak613-1016-ec.xyz

description: :unav
DOI: 10.15454/eobum0/yvxkii
title: beech1-13-un.xyz

description: :unav
DOI: 10.15454/eobum0/z1qpur
title: oak613-5-br.xyz

description: :unav
DOI: 10.15454/eobum0/zbi7l9
title: oak5-5-br3.xyz

description: :unav
DOI: 10.15454/eobum0/zbjuhw
title: beech7-10011-sp.xyz

description: :unav
DOI: 10.15454/eobum0/zcjmxg
title: oak613-171-pi.xyz

description: :unav
DOI: 10.15454/eobum0/zgjjbi
title: oak2-1012-ec.xyz

description: :unav
DOI: 10.15454/eobum0/zgkq2p
title: fir3-7-ci.xyz

description: :unav
DOI: 10.15454/eobum0/zibmyx
title: beech2-8-br.xyz

description: :unav
DOI: 10.15454/eobum0/zjfrj4
title: beech7-1-ci.xyz

description: :unav
DOI: 10.15454/eobum0/zkignv
title: beech2-107-unk.xyz

description: :unav
DOI: 10.15454/eobum0/zkxwmk
title: oak4-18-br.xyz

description: :unav
DOI: 10.15454/eobum0/zrbpku
title: beech103-23-ci.xyz

description: :unav
DOI: 10.15454/eobum0/zrm039
title: oak613-1015-ec.xyz

description: :unav
DOI: 10.15454/eobum0/zrsml0
title: oak613-12-pi.xyz

description: :unav
DOI: 10.15454/eobum0/zsiiro
title: oak2-1028-ec.xyz

description: :unav
DOI: 10.15454/eobum0/ztcqie
title: oak1-1004-ec.xyz

description: :unav
DOI: 10.15454/eobum0/zutug9
title: beech9-1-gm.xyz

description: :unav
DOI: 10.15454/eobum0/zvv0iw
title: oak0-69-unk.xyz

description: :unav
DOI: 10.15454/eobum0/zxux0n
title: oak0-96-unk.xyz

description: :unav
DOI: 10.15454/eorhl8/ilzyk5
title: Supp_DataSetS2F.xlsx
DOI: 10.15454/eoudkq/mdbsqf
title: 6-Analyses_physico-chimiques.tab
DOI: 10.15454/eptdos/0sgosu
title: ambigous_annotations.bed

description: :unav
DOI: 10.15454/eptdos/4a0mim
title: draftAnnot.genomic_regions_covered_by_TE.bed

description: :unav
DOI: 10.15454/eptdos/4wq8li
title: REPETpostAnal-V1.0.5.py

description: In-house python (&gt;= 3) script. Used to parse REPET draft annotation (repeatome) and isolate canonical TE annotations.Requires as input i) REPET draft TE-annotation output (.gff3), ii) the TE-consensus library used for the annotation, iii) the genome fasta file. Default parameters are set for stringent filtering post-processing (e.g canonical TE-annotations). External Dependencies: bedtools (&gt;= 2), blast+, bash. Required python libraries: subprocess, os, sys, re, pandas, argparse, numpy, Bio (SeqIO).
DOI: 10.15454/eptdos/5fpy9y
title: logs_REPETpostAnal-V1.0.5_minc_v3.TEannotation.19-07-19.txt

description: Logs from M. incognita TE annotation post-processing. Summarize annotations statistics for each post-processing steps.
DOI: 10.15454/eptdos/84yh08
title: draftAnnot.perCopyStats.txt

description: :unav
DOI: 10.15454/eptdos/9f2plb
title: draftAnnot.StatsTE.stats

description: :unav
DOI: 10.15454/eptdos/ajinwa
title: finalAnnot.genomic_regions_covered_by_TE.bed

description: :unav
DOI: 10.15454/eptdos/bhj2v7
title: REPETpostAnal-V1.0.5.py

description: In-house python (&gt;= 3) script. Used to parse REPET draft annotation (repeatome) and isolate canonical TE annotations. Requires as input i) REPET draft TE-annotation output (.gff3), ii) the TE-consensus library used for the annotation, iii) the genome fasta file. Default parameters are set for stringent filtering post-processing (e.g canonical TE-annotations). External Dependencies: bedtools (&gt;= 2), blast+, bash. Required python libraries: subprocess, os, sys, re, pandas, argparse, numpy, Bio (SeqIO).
DOI: 10.15454/eptdos/brsfhv
title: TE_prediction_and_annotation_Minc_v3_19-07-19.lastVersion.Rmd

description: M. incognita TE prediction and annotation workflow (Rmarkdown file). Contains the executed command lines used to perform the analysis.
DOI: 10.15454/eptdos/gyeeni
title: logs_REPETpostAnal-V1.0.5_minc_v3.TEannotation.19-07-19.txt

description: :unav
DOI: 10.15454/eptdos/hhsujj
title: TEdenovo.cfg

description: TE denovo pipeline configuration file with parameters values. Mandatory for TEdenovo pipeline execution. For more information, see : https://urgi.versailles.inra.fr/Tools/REPET https://urgi.versailles.inra.fr/Tools/REPET/TEdenovo-tuto
DOI: 10.15454/eptdos/hrvkiq
title: finalAnnot.StatsTE.stats

description: :unav
DOI: 10.15454/eptdos/ippqmx
title: minc_v3_cleanedTEConsensusLibrary.19-07-19.fa

description: TE-consensus sequences library (REPET analysis : TEannot + automated cleaning with 1 loose round of TEannot)
DOI: 10.15454/eptdos/j7lpwe
title: finalAnnot.perCopyStats.txt

description: Per-TE-copy statistics e.g linked TE-consenus, copies length/identity statistics, etc
DOI: 10.15454/eptdos/kmjiqe
title: TE_prediction_and_annotation_Minc_v3_19-07-19.lastVersion.Rmd

description: M. incognita TE prediction and annotation workflow (Rmarkdown file). Contains the executed command lines used to perform the analysis.
DOI: 10.15454/eptdos/m6abnq
title: finalAnnot.perCopyStats.txt

description: Per-TE-copy statistics e.g linked TE-consenus, copies length/identity statistics, etc
DOI: 10.15454/eptdos/n2i3is
title: mincV3XA2_draftAnnot.19-07-19.sorted.gff3

description: draft TE annotation (REPET output; gff3 format)
DOI: 10.15454/eptdos/n63nss
title: minc_v3_cleanedTEConsensusLibrary.19-07-19.fa

description: TE-consensus sequences library (REPET analysis : TEannot + automated cleaning with 1 loose round of TEannot)
DOI: 10.15454/eptdos/nwek1z
title: readme.txt

description: :unav
DOI: 10.15454/eptdos/olgpob
title: draftAnnot.perConsensusStats.txt

description: :unav
DOI: 10.15454/eptdos/oslf7a
title: give_genome_Nxx_and_Lxx.py

description: :unav
DOI: 10.15454/eptdos/re5dah
title: launch_that.txt

description: :unav
DOI: 10.15454/eptdos/rrf9ys
title: TEannot.cfg

description: TE annot pipeline configuration file with parameters values. Mandatory for TEdenovo pipeline execution. For more information, see : https://urgi.versailles.inra.fr/Tools/REPET https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto
DOI: 10.15454/eptdos/sctxgm
title: readme.txt

description: :unav
DOI: 10.15454/eptdos/snq1xy
title: draftAnnot.bed

description: :unav
DOI: 10.15454/eptdos/sxn369
title: setEnv.sh

description: :unav