cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14343302.v1
title: Transcriptome analysis D. stramonium and D. metel

description: We downloaded the whole genome and transcriptome of <i>D. stramonium </i>to extract the TPSs genes and gene prediction was performed using AUGUSTUS (Stanke et al., 2006).
DOI: 10.5281/zenodo.4767996
title: PTP1B in complex with TCS401 by Native S-SAD at Room Temperature

description: Intermediate processing results used to solve a structure of PTP1B in complex with TCS401 by native S-SAD at room temperature.
DOI: 10.5281/zenodo.4767995
title: PTP1B in complex with TCS401 by Native S-SAD at Room Temperature

description: Intermediate processing results used to solve a structure of PTP1B in complex with TCS401 by native S-SAD at room temperature.
DOI: 10.6084/m9.figshare.14343296
title: Transcriptome assembly D. metel

description: The assembly of the transcriptome was carried out with Trinity
DOI: 10.6084/m9.figshare.14343296.v2
title: Transcriptome assembly D. metel

description: The assembly of the transcriptome was carried out with Trinity
DOI: 10.6084/m9.figshare.14343296.v1
title: Transcriptome assembly D. metel

description: The assembly of the transcriptome was carried out with Trinity
DOI: 10.6084/m9.figshare.14343272
title: Tropinone reductase

description: We downloaded all orthologous sequences of TAa and TPSs of <i>D. stramonium</i>, <i>D. metel</i> and 11 species of Solanaceae to construct the orthogrpups. Downloades sequenceso of proteins and ORF were extracted using TransDecoder and corroborated with GenScan. TPS genes were translated with GenScan, are in the right direction and are the correct CDS; we corroborated this with the NCBI. The database used for BLAST was Uniprot; all available data for the analyzed plant species were downloaded. These amounts 847,544 3. BLAST was carried out with a filtering evalue of 1e-<sup>3</sup>, and only hits above 85 % were selected. Orthogroups was inferred using Orthofinser v 2.3.3. DIAMONS (Emms and Kelly 2015, 2019) while OrthoMCL was used to assess orthologs among species (Chen et al., 2006).
DOI: 10.6084/m9.figshare.14343272.v3
title: Tropinone reductase

description: We downloaded all orthologous sequences of TAa and TPSs of <i>D. stramonium</i>, <i>D. metel</i> and 11 species of Solanaceae to construct the orthogrpups. Downloades sequenceso of proteins and ORF were extracted using TransDecoder and corroborated with GenScan. TPS genes were translated with GenScan, are in the right direction and are the correct CDS; we corroborated this with the NCBI. The database used for BLAST was Uniprot; all available data for the analyzed plant species were downloaded. These amounts 847,544 3. BLAST was carried out with a filtering evalue of 1e-<sup>3</sup>, and only hits above 85 % were selected. Orthogroups was inferred using Orthofinser v 2.3.3. DIAMONS (Emms and Kelly 2015, 2019) while OrthoMCL was used to assess orthologs among species (Chen et al., 2006).
DOI: 10.6084/m9.figshare.14343272.v2
title: Tropinone reductase

description: We downloaded all orthologous sequences of TAa and TPSs of <i>D. stramonium</i>, <i>D. metel</i> and 11 species of Solanaceae to construct the orthogrpups. Downloades sequenceso of proteins and ORF were extracted using TransDecoder and corroborated with GenScan. TPS genes were translated with GenScan, are in the right direction and are the correct CDS; we corroborated this with the NCBI. The database used for BLAST was Uniprot; all available data for the analyzed plant species were downloaded. These amounts 847,544 3. BLAST was carried out with a filtering evalue of 1e-<sup>3</sup>, and only hits above 85 % were selected. Orthogroups was inferred using Orthofinser v 2.3.3. DIAMONS (Emms and Kelly 2015, 2019) while OrthoMCL was used to assess orthologs among species (Chen et al., 2006).
DOI: 10.6084/m9.figshare.14343263.v1
title: H6H Tropane alkaloid

description: We downloaded all orthologous sequences of TAa and TPSs of <i>D. stramonium</i>, <i>D. metel</i> and 11 species of Solanaceae (see Table XXXX) to construct the orthogrpups. Downloades sequenceso of proteins and ORF were extracted using TransDecoder and corroborated with GenScan. TPS genes were translated with GenScan, are in the right direction and are the correct CDS; we corroborated this with the NCBI. The database used for BLAST was Uniprot; all available data for the analyzed plant species were downloaded. These amounts 847,544 3. BLAST was carried out with a filtering evalue of 1e-<sup>3</sup>, and only hits above 85 % were selected.
DOI: 10.6084/m9.figshare.14605842
title: Effects of nitrate exposure on nitrate reduction processes in the wetland sediments from the Yellow River Estuary

description: <b>Nitrogen cycling, Yellow River estuary, High-throughput sequencing, raw sequences, </b>trimmed and filtered sequences<br>
DOI: 10.6084/m9.figshare.14605842.v1
title: Effects of nitrate exposure on nitrate reduction processes in the wetland sediments from the Yellow River Estuary

description: <b>Nitrogen cycling, Yellow River estuary, High-throughput sequencing, raw sequences, </b>trimmed and filtered sequences<br>
DOI: 10.6084/m9.figshare.14343284
title: TPS Genes and Tropane Alkaloids

description: The selected TPSs genes were blasted against the NCBI, UNIPROT databases and the nine genomes of Solanaceae, using a threshold value of 1E<sup>-5</sup>. All TPSs were downloaded from Viridiplantae followed by a protein-protein blast; hits above 80% of similarity and 70% of cover were saved for further analyses. Meta-alignments of protein sequences were performed using T-coffee (Wallace et al., 2006), MUSCLE v3.8 (Edgar, 2004) and MAFF v6. (Rowicki et al., 2019).
DOI: 10.6084/m9.figshare.14343284.v2
title: TPS Genes and Tropane Alkaloids

description: The selected TPSs genes were blasted against the NCBI, UNIPROT databases and the nine genomes of Solanaceae, using a threshold value of 1E<sup>-5</sup>. All TPSs were downloaded from Viridiplantae followed by a protein-protein blast; hits above 80% of similarity and 70% of cover were saved for further analyses. Meta-alignments of protein sequences were performed using T-coffee (Wallace et al., 2006), MUSCLE v3.8 (Edgar, 2004) and MAFF v6. (Rowicki et al., 2019).
DOI: 10.6084/m9.figshare.14343284.v1
title: TPS Genes and Tropanes Alkaloids

description: The selected TPSs genes were blasted against the NCBI, UNIPROT databases and the nine genomes of Solanaceae, using a threshold value of 1E<sup>-5</sup>. All TPSs were downloaded from Viridiplantae followed by a protein-protein blast; hits above 80% of similarity and 70% of cover were saved for further analyses. Meta-alignments of protein sequences were performed using T-coffee (Wallace et al., 2006), MUSCLE v3.8 (Edgar, 2004) and MAFF v6. (Rowicki et al., 2019).
DOI: 10.21227/8fmh-3d09
title: Data for the article "A New Efficient Algorithm Addressing the (d, c)-MC Problem"

description: Many real-world systems can be modeled by multistate flow networks (MFNs) and their reliability evaluation features in designing and control of these systems. Considering the cost constraint makes the problem of reliability evaluation of an MFN more realistic. For a given demand value $d$ and a given cost limit $c$, the reliability of an MFN at level $(d, c)$ is the probability of transmitting at least $d$ units from the source node to the sink node through the network within the cost of $c$. This article addresses this so-called $(d, c)$-MC problem in terms of minimal cuts. It presents new results on which a new algorithm is based. This algorithm finds all $(d, c)$-MC candidates without duplicates and verifies them more efficiently than existing ones. The complexity results for this algorithm and an example of its use are provided. Finally, numerical experiments with R implementations of the presented algorithm and other competitive algorithms are considered. Both, the time complexity analysis and numerical experiments demonstrate the presented algorithm to be more efficient than other existing ones in the majority of cases.
DOI: 10.5286/isis.e.rb1910473-2
title: Understanding the structure of linear alkylbenzene sulfonates in water.

description: The objective of this research is to understand the detailed structure of water-surfactant solutions as a function of concentration and chemical structure. This is important as these materials form the main components of cleaning detergents and personal care products and this fundamental understanding will provide the basis of new formulations.
DOI: 10.25921/1fzf-c836
title: EM2040 Water Column Sonar Data Collected During F00802
DOI: 10.6084/m9.figshare.14607432.v1
title: brainExtractionT1v1.h5

description: weights for antsxnet brain extraction<br>
DOI: 10.6084/m9.figshare.14607432
title: brainExtractionT1v1.h5

description: weights for antsxnet brain extraction<br>
DOI: 10.5281/zenodo.3941127
title: IODP Expedition 367, Hole U1499B - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 367: South China Sea Rifted Margin A
DOI: 10.5281/zenodo.3941126
title: IODP Expedition 367, Hole U1499B - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 367: South China Sea Rifted Margin A
DOI: 10.5281/zenodo.3941129
title: IODP Expedition 367, Hole U1500B - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 367: South China Sea Rifted Margin A
DOI: 10.5281/zenodo.3941128
title: IODP Expedition 367, Hole U1500B - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 367: South China Sea Rifted Margin A
DOI: 10.6084/m9.figshare.12851291
title: Mitophagy deficiency increases NLRP3 to induce brown fat dysfunction in mice

description: Although macroautophagy/autophagy deficiency causes degenerative diseases, the deletion of essential autophagy genes in adipocytes paradoxically reduces body weight. Brown adipose tissue (BAT) plays an important role in body weight regulation and metabolic control. However, the key cellular mechanisms that maintain BAT function remain poorly understood. in this study, we showed that global or brown adipocyte-specific deletion of <i>pink1</i>, a Parkinson disease-related gene involved in selective mitochondrial autophagy (mitophagy), induced BAT dysfunction, and obesity-prone type in mice. Defective mitochondrial function is among the upstream signals that activate the NLRP3 inflammasome. NLRP3 was induced in brown adipocyte precursors (BAPs) from <i>pink1</i> knockout (KO) mice. Unexpectedly, NLRP3 induction did not induce canonical inflammasome activity. Instead, NLRP3 induction led to the differentiation of <i>pink1</i> KO BAPs into white-like adipocytes by increasing the expression of white adipocyte-specific genes and repressing the expression of brown adipocyte-specific genes. <i>nlrp3</i> deletion in <i>pink1</i> knockout mice reversed BAT dysfunction. Conversely, adipose tissue-specific <i>atg7</i> KO mice showed significantly lower expression of <i>Nlrp3</i> in their BAT. Overall, our data suggest that the role of mitophagy is different from general autophagy in regulating adipose tissue and whole-body energy metabolism. Our results uncovered a new mitochondria-NLRP3 pathway that induces BAT dysfunction. The ability of the <i>nlrp3</i> knockouts to rescue BAT dysfunction suggests the transcriptional function of NLRP3 as an unexpected, but a quite specific therapeutic target for obesity-related metabolic diseases. <b>Abbreviations:</b> ACTB: actin, beta; BAPs: brown adipocyte precursors; BAT: brown adipose tissue; BMDMs: bone marrow-derived macrophages; CASP1: caspase 1; CEBPA: CCAAT/enhancer binding protein (C/EBP), alpha; ChIP: chromatin immunoprecipitation; EE: energy expenditure; HFD: high-fat diet; IL1B: interleukin 1 beta; ITT: insulin tolerance test; KO: knockout; LPS: lipopolysaccharide; NLRP3: NLR family, pyrin domain containing 3; PINK1: PTEN induced putative kinase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; RD: regular diet; ROS: reactive oxygen species; RT: room temperature; UCP1: uncoupling protein 1 (mitochondrial, proton carrier); WT: wild-type.
DOI: 10.6084/m9.figshare.12851291.v1
title: Mitophagy deficiency increases NLRP3 to induce brown fat dysfunction in mice

description: Although macroautophagy/autophagy deficiency causes degenerative diseases, the deletion of essential autophagy genes in adipocytes paradoxically reduces body weight. Brown adipose tissue (BAT) plays an important role in body weight regulation and metabolic control. However, the key cellular mechanisms that maintain BAT function remain poorly understood. in this study, we showed that global or brown adipocyte-specific deletion of <i>pink1</i>, a Parkinson disease-related gene involved in selective mitochondrial autophagy (mitophagy), induced BAT dysfunction, and obesity-prone type in mice. Defective mitochondrial function is among the upstream signals that activate the NLRP3 inflammasome. NLRP3 was induced in brown adipocyte precursors (BAPs) from <i>pink1</i> knockout (KO) mice. Unexpectedly, NLRP3 induction did not induce canonical inflammasome activity. Instead, NLRP3 induction led to the differentiation of <i>pink1</i> KO BAPs into white-like adipocytes by increasing the expression of white adipocyte-specific genes and repressing the expression of brown adipocyte-specific genes. <i>nlrp3</i> deletion in <i>pink1</i> knockout mice reversed BAT dysfunction. Conversely, adipose tissue-specific <i>atg7</i> KO mice showed significantly lower expression of <i>Nlrp3</i> in their BAT. Overall, our data suggest that the role of mitophagy is different from general autophagy in regulating adipose tissue and whole-body energy metabolism. Our results uncovered a new mitochondria-NLRP3 pathway that induces BAT dysfunction. The ability of the <i>nlrp3</i> knockouts to rescue BAT dysfunction suggests the transcriptional function of NLRP3 as an unexpected, but a quite specific therapeutic target for obesity-related metabolic diseases. <b>Abbreviations:</b> ACTB: actin, beta; BAPs: brown adipocyte precursors; BAT: brown adipose tissue; BMDMs: bone marrow-derived macrophages; CASP1: caspase 1; CEBPA: CCAAT/enhancer binding protein (C/EBP), alpha; ChIP: chromatin immunoprecipitation; EE: energy expenditure; HFD: high-fat diet; IL1B: interleukin 1 beta; ITT: insulin tolerance test; KO: knockout; LPS: lipopolysaccharide; NLRP3: NLR family, pyrin domain containing 3; PINK1: PTEN induced putative kinase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; RD: regular diet; ROS: reactive oxygen species; RT: room temperature; UCP1: uncoupling protein 1 (mitochondrial, proton carrier); WT: wild-type.
DOI: 10.6084/m9.figshare.12124323
title: Dimerization of mitophagy receptor BNIP3L/NIX is essential for recruitment of autophagic machinery

description: Mitophagy is a conserved intracellular catabolic process responsible for the selective removal of dysfunctional or superfluous mitochondria to maintain mitochondrial quality and need in cells. Here, we examine the mechanisms of receptor-mediated mitophagy activation, with the focus on BNIP3L/NIX mitophagy receptor, proven to be indispensable for selective removal of mitochondria during the terminal differentiation of reticulocytes. The molecular mechanisms of selecting damaged mitochondria from healthy ones are still very obscure. We investigated BNIP3L dimerization as a potentially novel molecular mechanism underlying BNIP3L-dependent mitophagy. Forming stable homodimers, BNIP3L recruits autophagosomes more robustly than its monomeric form. Amino acid substitutions of key transmembrane residues of BNIP3L, BNIP3L<sup>G204A</sup> or BNIP3L<sup>G208V</sup>, led to the abolishment of dimer formation, resulting in the lower LC3A-BNIP3L recognition and subsequently lower mitophagy induction. Moreover, we identified the serine 212 as the main amino acid residue at the C-terminal of BNIP3L, which extends to the intermembrane space, responsible for dimerization. In accordance, the phosphomimetic mutation BNIP3L<sup>S212E</sup> leads to a complete loss of BNIP3L dimerization. Thus, the interplay between BNIP3L phosphorylation and dimerization indicates that the combined mechanism of LIR phosphorylation and receptor dimerization is needed for proper BNIP3L-dependent mitophagy initiation and progression. <b>Abbreviations:</b> AMBRA1: autophagy and beclin 1 regulator 1; Baf A1: bafilomycin A<sub>1</sub>; BH3: BCL2 homology 3; BNIP3: BCL2 interacting protein 3; BNIP3L/NIX: BCL2 interacting protein 3 like; CCCP: carbonyl cyanide 3-chlorophenylhydrazone; CoCl<sub>2</sub>: cobalt (II) chloride; FKBP8: FKBP prolyl isomerase 8; FUNDC1: FUN14 domain containing 1; GABARAP: GABA type A receptor-associated protein; GST: glutathione S-transferase; IMM: inner mitochondrial membrane; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; OMM: outer mitochondrial membrane; PHB2: prohibitin 2; PI: propidium iodide; PINK1: PTEN induced kinase 1; TM: transmembrane domain; TOMM20: translocase of outer mitochondrial membrane 20
DOI: 10.6084/m9.figshare.12124323.v1
title: Dimerization of mitophagy receptor BNIP3L/NIX is essential for recruitment of autophagic machinery

description: Mitophagy is a conserved intracellular catabolic process responsible for the selective removal of dysfunctional or superfluous mitochondria to maintain mitochondrial quality and need in cells. Here, we examine the mechanisms of receptor-mediated mitophagy activation, with the focus on BNIP3L/NIX mitophagy receptor, proven to be indispensable for selective removal of mitochondria during the terminal differentiation of reticulocytes. The molecular mechanisms of selecting damaged mitochondria from healthy ones are still very obscure. We investigated BNIP3L dimerization as a potentially novel molecular mechanism underlying BNIP3L-dependent mitophagy. Forming stable homodimers, BNIP3L recruits autophagosomes more robustly than its monomeric form. Amino acid substitutions of key transmembrane residues of BNIP3L, BNIP3L<sup>G204A</sup> or BNIP3L<sup>G208V</sup>, led to the abolishment of dimer formation, resulting in the lower LC3A-BNIP3L recognition and subsequently lower mitophagy induction. Moreover, we identified the serine 212 as the main amino acid residue at the C-terminal of BNIP3L, which extends to the intermembrane space, responsible for dimerization. In accordance, the phosphomimetic mutation BNIP3L<sup>S212E</sup> leads to a complete loss of BNIP3L dimerization. Thus, the interplay between BNIP3L phosphorylation and dimerization indicates that the combined mechanism of LIR phosphorylation and receptor dimerization is needed for proper BNIP3L-dependent mitophagy initiation and progression. <b>Abbreviations:</b> AMBRA1: autophagy and beclin 1 regulator 1; Baf A1: bafilomycin A<sub>1</sub>; BH3: BCL2 homology 3; BNIP3: BCL2 interacting protein 3; BNIP3L/NIX: BCL2 interacting protein 3 like; CCCP: carbonyl cyanide 3-chlorophenylhydrazone; CoCl<sub>2</sub>: cobalt (II) chloride; FKBP8: FKBP prolyl isomerase 8; FUNDC1: FUN14 domain containing 1; GABARAP: GABA type A receptor-associated protein; GST: glutathione S-transferase; IMM: inner mitochondrial membrane; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; OMM: outer mitochondrial membrane; PHB2: prohibitin 2; PI: propidium iodide; PINK1: PTEN induced kinase 1; TM: transmembrane domain; TOMM20: translocase of outer mitochondrial membrane 20
DOI: 10.6084/m9.figshare.14607444
title: Colliding Solitons

description: This is the data file for the measurements of the colliding solitons. you can run the .m file after downloading both files
DOI: 10.6084/m9.figshare.14607444.v1
title: Colliding Solitons

description: This is the data file for the measurements of the colliding solitons. you can run the .m file after downloading both files
DOI: 10.5066/p91kraad
title: Orthoimagery, digital elevation, digital terrain, final surface, and vegetation classification models for four stream catchments in western Colorado 2016

description: Unmanned Aerial System (UAS) flights were conducted over four stream catchments in Rio Blanco County, Colorado, during the summer of 2016. Two sties had active oil and gas operations within the basin whereas the other two sites did not. Structure from motion (SfM) was used to align raw images and create a dense point cloud, georectified orthoimage, and Digital Elevation Model (DEM) for each basin. A Digital Terrain Model (DTM), or bare earth model, for each basin was created by reclassifying the dense point cloud as either bare ground or other (vegetation, oil and gas infrastructure, etc.) and interpolating the land surface between bare ground points. Ideally, the DTM would always be equal or lower than the DEM; however, the interpolated surface can sometimes be higher than the DEM if bare ground points surround depressions with vegetation or in thick vegetation strands with an undulating surface. Therefore, a final surface model, created by merging the DTM with the DEM for all areas where the DTM was greater than the DEM, was produced for each basin. Lastly, a random forest classification approach was used to classify the orthoimagery on a pixel level into five vegetation/land cover classifications - bare ground, grass, litter, shrub/woody vegetation, and shadow.
DOI: 10.5281/zenodo.4768075
title: ANANSE: trained model based on enhancers created using REMAP peaks.

description: This contains all trained models to predict TF binding using ANANSE in a set of putative enhancers (human genome version hg38; https://doi.org/10.5281/zenodo.4066424).
DOI: 10.5281/zenodo.4768074
title: ANANSE: trained model based on enhancers created using REMAP peaks.

description: This contains all trained models to predict TF binding using ANANSE in a set of putative enhancers (human genome version hg38; https://doi.org/10.5281/zenodo.4066424).
DOI: 10.5281/zenodo.3941182
title: IODP Expedition 375, Hole U1520C - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 375: Hikurangi Subduction Margin