cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5519/qd.62aatuuu
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (482579 records)
DOI: 10.21227/jxrd-fa23
title: 2018-2019 PV Generation of a Rooftop Plant in the University of Macau and Weather Report

description: Solar power geneartion from 2018 to 2019 at a 3kW rooftop pv plant in the university of macau, with a resolation of 30 s, and the public weather report of Macau with a resolution of 1 hour.
DOI: 10.6084/m9.figshare.5752761.v1
title: Pulmonary toxicity and global gene expression changes in response to sub-chronic inhalation exposure to crystalline silica in rats

description: Exposure to crystalline silica results in serious adverse health effects, most notably, silicosis. An understanding of the mechanism(s) underlying silica-induced pulmonary toxicity is critical for the intervention and/or prevention of its adverse health effects. Rats were exposed by inhalation to crystalline silica at a concentration of 15 mg/m<sup>3</sup>, 6 hr/day, 5 days/week for 3, 6 or 12 weeks. Pulmonary toxicity and global gene expression profiles were determined in lungs at the end of each exposure period. Crystalline silica was visible in lungs of rats especially in the 12-week group. Pulmonary toxicity, as evidenced by an increase in lactate dehydrogenase (LDH) activity and albumin content and accumulation of macrophages and neutrophils in the bronchoalveolar lavage (BAL), was seen in animals depending upon silica exposure duration. The most severe histological changes, noted in the 12-week exposure group, consisted of chronic active inflammation, type II pneumocyte hyperplasia, and fibrosis. Microarray analysis of lung gene expression profiles detected significant differential expression of 38, 77, and 99 genes in rats exposed to silica for 3-, 6-, or 12-weeks, respectively, compared to time-matched controls. Among the significantly differentially expressed genes (SDEG), 32 genes were common in all exposure groups. Bioinformatics analysis of the SDEG identified enrichment of functions, networks and canonical pathways related to inflammation, cancer, oxidative stress, fibrosis, and tissue remodeling in response to silica exposure. Collectively, these results provided insights into the molecular mechanisms underlying pulmonary toxicity following sub-chronic inhalation exposure to crystalline silica in rats.
DOI: 10.6084/m9.figshare.5752761
title: Pulmonary toxicity and global gene expression changes in response to sub-chronic inhalation exposure to crystalline silica in rats

description: Exposure to crystalline silica results in serious adverse health effects, most notably, silicosis. An understanding of the mechanism(s) underlying silica-induced pulmonary toxicity is critical for the intervention and/or prevention of its adverse health effects. Rats were exposed by inhalation to crystalline silica at a concentration of 15 mg/m<sup>3</sup>, 6 hr/day, 5 days/week for 3, 6 or 12 weeks. Pulmonary toxicity and global gene expression profiles were determined in lungs at the end of each exposure period. Crystalline silica was visible in lungs of rats especially in the 12-week group. Pulmonary toxicity, as evidenced by an increase in lactate dehydrogenase (LDH) activity and albumin content and accumulation of macrophages and neutrophils in the bronchoalveolar lavage (BAL), was seen in animals depending upon silica exposure duration. The most severe histological changes, noted in the 12-week exposure group, consisted of chronic active inflammation, type II pneumocyte hyperplasia, and fibrosis. Microarray analysis of lung gene expression profiles detected significant differential expression of 38, 77, and 99 genes in rats exposed to silica for 3-, 6-, or 12-weeks, respectively, compared to time-matched controls. Among the significantly differentially expressed genes (SDEG), 32 genes were common in all exposure groups. Bioinformatics analysis of the SDEG identified enrichment of functions, networks and canonical pathways related to inflammation, cancer, oxidative stress, fibrosis, and tissue remodeling in response to silica exposure. Collectively, these results provided insights into the molecular mechanisms underlying pulmonary toxicity following sub-chronic inhalation exposure to crystalline silica in rats.
DOI: 10.6084/m9.figshare.5752758
title: Citrinin induces apoptosis in human HCT116 colon cancer cells through endoplasmic reticulum stress

description: The mycotoxin citrinin (CTN) is a natural contaminant of various human foods that may produce serious adverse health problems. Several studies demonstrated that citrinin exerts cytotoxic and genotoxic effects in both <i>in vivo</i> and <i>in vitro</i> systems. However, the precise mechanisms of action (MOA), particularly in intestinal cells remain unclear. The aim of the present study was to examine the precise MOA of citrinin <i>in vitro</i>. Data demonstrated that CTN significantly decreased the number of viable human intestinal HCT116 cells and induced apoptotic events including (1) decrease in ΔѰm indicative of mitochondrial membrane permeabilization, (2) activation of caspase 3, (3) elevated production of reactive oxygen species (ROS) and (4) relative persistence of plasma membrane integrity. Further, the genetic deficiency of the pro-apoptotic protein Bax protected cells against CTN-induced apoptosis, indicating that Bax is required for CTN-mediated toxicity. It was also found that CTN triggered endoplasmic reticulum (ER) stress and activated different arms of the unfolded protein response (UPR) as demonstrated by increase in expression of GRP78 (glucose-regulated protein-78), GRP94 (glucose-regulated protein-94), GADD34 (growth arrest and DNA damage-inducible protein-34), the protein disulfide isomerase associated 6 (PDIA6), CHOP (C/EBP-homologous protein) and the splicing of XBP1 (X-Box Binding Protein 1). Pretreatment of cells with the chemical chaperone 4-phenylbutyrate (PBA), known to alleviate ER stress, prevented significantly the apoptotic process triggered by CTN. Taken together, these results suggest that CTN exerts its cytotoxic effects in HCT116 cells by inducing apoptosis, at least in part, through induction of ER stress.
DOI: 10.6084/m9.figshare.5752758.v1
title: Citrinin induces apoptosis in human HCT116 colon cancer cells through endoplasmic reticulum stress

description: The mycotoxin citrinin (CTN) is a natural contaminant of various human foods that may produce serious adverse health problems. Several studies demonstrated that citrinin exerts cytotoxic and genotoxic effects in both <i>in vivo</i> and <i>in vitro</i> systems. However, the precise mechanisms of action (MOA), particularly in intestinal cells remain unclear. The aim of the present study was to examine the precise MOA of citrinin <i>in vitro</i>. Data demonstrated that CTN significantly decreased the number of viable human intestinal HCT116 cells and induced apoptotic events including (1) decrease in ΔѰm indicative of mitochondrial membrane permeabilization, (2) activation of caspase 3, (3) elevated production of reactive oxygen species (ROS) and (4) relative persistence of plasma membrane integrity. Further, the genetic deficiency of the pro-apoptotic protein Bax protected cells against CTN-induced apoptosis, indicating that Bax is required for CTN-mediated toxicity. It was also found that CTN triggered endoplasmic reticulum (ER) stress and activated different arms of the unfolded protein response (UPR) as demonstrated by increase in expression of GRP78 (glucose-regulated protein-78), GRP94 (glucose-regulated protein-94), GADD34 (growth arrest and DNA damage-inducible protein-34), the protein disulfide isomerase associated 6 (PDIA6), CHOP (C/EBP-homologous protein) and the splicing of XBP1 (X-Box Binding Protein 1). Pretreatment of cells with the chemical chaperone 4-phenylbutyrate (PBA), known to alleviate ER stress, prevented significantly the apoptotic process triggered by CTN. Taken together, these results suggest that CTN exerts its cytotoxic effects in HCT116 cells by inducing apoptosis, at least in part, through induction of ER stress.
DOI: 10.21227/nw22-mn43
title: Effect of Millet Rice vegetation on path-loss between CC2650 SoC based sensor nodes operating at 2.4 GHz Radio Frequency (RF)

description: Here we introduce so-far the largest subject-rated database of its kind, namely, "Effect of Milletvegetation on path-loss betweenCC2650 SoC 32-bit Arm Cortex-M3based sensor nodes operating at2.4 GHzRadio Frequency (RF)".This database contains received signal strengthmeasurementscollected through campaigns in theIEEE 802.15.4standard precision agricultural monitoring infrastructure developed for millet crop monitoring from period28/07/2019 to 29/10/2019.
DOI: 10.21227/42sm-se22
title: Effect of Millet Rice vegetation on path-loss between CC2650 SoC based sensor nodes operating at 2.4 GHz Radio Frequency (RF)

description: Here we introduce so-far the largest subject-rated database of its kind, namely, "Effect of Milletvegetation on path-loss betweenCC2650 SoC 32-bit Arm Cortex-M3based sensor nodes operating at2.4 GHzRadio Frequency (RF)".This database contains received signal strengthmeasurementscollected through campaigns in theIEEE 802.15.4standard precision agricultural monitoring infrastructure developed for millet crop monitoring from period28/07/2019 to 29/10/2019.
DOI: 10.6084/m9.figshare.13220921
title: Supplementary Material for: Prophylactic Fixation of the Gastric-Abdominal Cavity Wall Can Reduce Complications of Simultaneous Placement of Percutaneous Endoscopic Gastrostomy and Ventriculoperitoneal Shunt

description: Medicine
DOI: 10.6084/m9.figshare.13220921.v1
title: Supplementary Material for: Prophylactic Fixation of the Gastric-Abdominal Cavity Wall Can Reduce Complications of Simultaneous Placement of Percutaneous Endoscopic Gastrostomy and Ventriculoperitoneal Shunt

description: Medicine
DOI: 10.21227/99zg-rg18
title: xgboost_wuyh

description: The idea of our team is to use the data of the least missing December as the training set and the validation set, obtain the optimal parameters through grid search, and use the xgboost machine learning model to learn and predict the results of each month next year
DOI: 10.5519/qd.5isxzdt1
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (482579 records)
DOI: 10.15129/b3974689-3d7c-49d0-ab7a-c7fd7c1f1382
title: Data for: "Suspension and transfer printing of ZnCdMgSe membranes from an InP substrate"

description: This dataset corresponds to the work “Suspension and Transfer Printing of ZnCdMgSe Membranes from an InP Substrate”. The files “Episide AFM.csv” and “Etch side AFM.csv” correspond to the atomic force microscope measurements displayed in Figure 4a and b, respectively, of the paper. Both data sets have been shifted by a constant value in the height axis, z, to ensure a positive scale and in Figure 4 the colour scale has been carefully chosen to show the height range of the surface topography. “Membrane vs wafer PL at 3_6 MW_m-2.csv”, “Wafer IDPL.csv” and “Membrane IDPL.csv” correspond to the plots of the photoluminescence data shown in Figure 5a, b and c respectively.
DOI: 10.21227/j9jk-6466
title: xgboost_wuyuhan

description: The idea of our team is to use the data of the least missing December as the training set and the validation set, obtain the optimal parameters through grid search, and use the xgboost machine learning model to learn and predict the results of each month next year
DOI: 10.5519/qd.d2c4folm
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6084/m9.figshare.7594754
title: Extended_Data_Tables

description: <b>Extended data tables</b> <b><br></b><b></b><b>Extended Data Table S-R3A</b> - DyNet<sup>5</sup> rewiring scores of TF-TG 1-to-1 edges when all five species networks are compared. <b>Extended Data Table S-R3B </b>- List of candidate genes from previous molecular evolutionary and developmental studies<sup>2,6–8</sup> potentially associated with phenotypic novelty in cichlids that overlap the six tissues we studied. <b>Extended Data Table S-R3C</b> - DyNet<sup>5</sup> rewiring scores of candidate genes in TF-TG 1-to-1 edges when all five species networks are compared. <b>Extended Data Table S-R3D</b> - DyNet<sup>5</sup> rewiring scores of TF-TG all edges when all five species networks are compared. <b>Extended Data Table S-R3E</b> - DyNet<sup>5</sup> rewiring scores of candidate genes in TF-TG all edges when all five species networks are compared. <b>Extended Data Table S-R3F</b> – Rate of edge gain and loss in TF-TG all edges across the five cichlid phylogeny. Rates that are &gt;100 (and excluded from analyses) are rank shaded blue (gain) and green (loss) whereas likelihood scores are rank shaded orange.
DOI: 10.6084/m9.figshare.7599293
title: Motifs

description: # These files are used for motif scanning of DNA using fimo in the MEME suite (see relevant documentation) <br><br># 1. Species-specific motif IDs, orthogrouping and cichlid gene IDs (Mz - M. zebra; Pn - p. nyererei; Ab - A. burtoni; Nb - N. brichardi; On - O. niloticus)<br><br>merged_mat_qual_pvals_ALL.out1.TF.* # e.g. merged_mat_qual_pvals_ALL.out1.TF.ab <br><br><br># 2. MEME files of all motifs for motif scanning according to:<br># A) those derived from i) human-based and ii) mouse-based predictions based on orthology (see Methods); and<br># B) different confidence levels: 2a - cichlid-specific (CS) matrices; 2b - cichlid-wide (CW) matrices; and 2c - JASPAR matrices<br><br><br># Ai) Derived from Human<br>HumanDerived/2a_CS_*.meme<br>HumanDerived/2b_CW_*.meme<br>HumanDerived/2c_JASPAR_*.meme<br># all meta data on above motifs, including motifID, genesymbol, EnsemblID, orthoGroup, cichlid_geneIDs, collated Optimal p-values for scanning<br>HumanDerived/cichlid_allHs_motifs_meta_info.txt<br><br># Aii) Derived from Mouse<br>MouseDerived/2a_CS_*.meme<br>MouseDerived/2b_CW_*.meme<br>MouseDerived/2c_JASPAR_*.meme<br># all meta data on above motifs, including motifID, genesymbol, EnsemblID, orthoGroup, cichlid_geneIDs, collated Optimal p-values for scanning<br>MouseDerived/cichlid_allMm_motifs_meta_info.txt
DOI: 10.6084/m9.figshare.7594754.v1
title: Extended_Data_Tables

description: <b>Extended data tables</b> <b><br></b><b></b><b>Extended Data Table S-R3A</b> - DyNet<sup>5</sup> rewiring scores of TF-TG 1-to-1 edges when all five species networks are compared. <b>Extended Data Table S-R3B </b>- List of candidate genes from previous molecular evolutionary and developmental studies<sup>2,6–8</sup> potentially associated with phenotypic novelty in cichlids that overlap the six tissues we studied. <b>Extended Data Table S-R3C</b> - DyNet<sup>5</sup> rewiring scores of candidate genes in TF-TG 1-to-1 edges when all five species networks are compared. <b>Extended Data Table S-R3D</b> - DyNet<sup>5</sup> rewiring scores of TF-TG all edges when all five species networks are compared. <b>Extended Data Table S-R3E</b> - DyNet<sup>5</sup> rewiring scores of candidate genes in TF-TG all edges when all five species networks are compared. <b>Extended Data Table S-R3F</b> – Rate of edge gain and loss in TF-TG all edges across the five cichlid phylogeny. Rates that are &gt;100 (and excluded from analyses) are rank shaded blue (gain) and green (loss) whereas likelihood scores are rank shaded orange.
DOI: 10.25345/c5pb52
title: MassIVE MSV000086434 - Collision energies on QTof and Orbitrap instruments: How to make proteomics measurements comparable?
title: Comparison of LeuEnk, enolase, and HeLa tryptic peptides MS/MS spectra obtained on a Bruker QTof CID and a Thermo Q-Exactive Focus Orbitrap HCD instrument as a function of collision energy using the similarity index.
DOI: 10.5281/zenodo.4267685
title: A Survey on Approaches for Coordination of Platoons - Paper Classification

description: Additional material upload for the Journal paper "A Survey on Approaches for Coordination of Platoons" in the Taylor & Francis Transport Reviews Journal. This csv file contains all relevant papers included in our survey with their classification regarding our proposed taxonomy.
DOI: 10.5281/zenodo.4267684
title: A Survey on Approaches for Coordination of Platoons - Paper Classification

description: Additional material upload for the Journal paper "A Survey on Approaches for Coordination of Platoons" in the Taylor & Francis Transport Reviews Journal. This csv file contains all relevant papers included in our survey with their classification regarding our proposed taxonomy.
DOI: 10.6084/m9.figshare.7707437
title: 1b.Network_Reconstruction_files

description: In Network_Reconstruction_files.tgz are the major files required to run network reconstruction and some output files:<br>- geneNamesTree # gene orthology of cichlid IDs, Ensembl IDs and gene descriptions<br>- Hs-Mm_EnsemblOrthology.txt # Ensembl orthology of Human and Mouse gene IDs<br>- full_orthologs_map3c.txt # contains the published orthologs gene IDs for mapping used previously<br>- list_k10 # list of k10 module numbers<br>- list_species # list of species<br>- OGIDS.txt # orthogroups<br>- OGIDS.txt5 # processed orthogroups file<br>- *_07.extrap.annotations.blast_out # extrapolation of motifs in cichlid gene promoters using human and mouse orthology <br>- mz-speciesspecnames_clusterassign.txt # Arboretum module assignment of M. zebra genes<br>- pn-speciesspecnames_clusterassign.txt # Arboretum module assignment of P. nyererei genes<br>- ab-speciesspecnames_clusterassign.txt # Arboretum module assignment of A. burtoni genes<br>- nb-speciesspecnames_clusterassign.txt # Arboretum module assignment of N. brichardi genes<br>- on-speciesspecnames_clusterassign.txt # Arboretum module assignment of O. niloticus genes<br>- geneNamesMapping.txt # gene orthology of cichlid IDs, Ensembl IDs and gene descriptions<br>- MzPnAbNbOnGenome-BLAST_PresentNULLOGIDS-noCand-noTF.txt2 # 4209 orthogroups with NULL orthogroup IDs for one or species are actually present in the genome (mis-annotations etc.) and not lost/absent<br>- motifenr_merged-TFBSs_map2d.txt # output of processing files in TFBSs - Motif Discovery in gene promoter regions<br>- tftgco_merged.txt # output of processing TF-TG co-expression files
DOI: 10.6084/m9.figshare.7707455
title: 1c.Edge_attribute_file_RewiringAnalysis_file

description: Based on the NetworkReconstruction_v1.0_2019.sh script and subsequent formation of a matrix for each edge (1 for present and 0 for absent), the file in the below zip file was used for 1.enrichment analysis and 2.Regulatory network rewiring analysis of gene sets <br>- Edge_Attributes_Collated4c.coexpr_promONLY.NEWsimplified.matrix3.filteredPresentNULLOGIDS.txt.zip <br>
DOI: 10.6084/m9.figshare.7712423
title: 1a.TF_motif_scanning_outputs

description: This contains output files from the TF motif scanning scripts:<br># Motif Scanning scripts are shared in the '2a.TF_motif_scanning' folder<br># Summary of motif scanning<br># Species-specific promoter sequences used as 0-order markov backgrounds<br># FIMO ran with default p-value (1e-4)<br># Files will be of Mouse and Human Extrapolations, Cichlid-specific (CS) and Cichlid-wide (CW) and Vertebrate JASPAR motifs - NOTE: with the exception of extrapolation files (*_07.extrap.annotations.blast_out), all other raw output files (CS and CW) are available upon requests<br># Otherwise, the final file prepared from these outputs - 'motifenr_merged-TFBSs_map2d.txt' is found with all the other files in '1.Network_Reconstruction_files'<br>
DOI: 10.5517/ccdc.csd.cc24wd0g
title: CCDC 1992525: Experimental Crystal Structure Determination

description: Related Article: Yuka Kobayashi, Kazuto Hirata, Samantha N. Hood, Hui Yang, Aron Walsh, Yoshitaka Matsushita, Kunie Ishioka|2020|Chemical Science|11|11699|doi:10.1039/D0SC03521A
DOI: 10.5517/ccdc.csd.cc25g53y
title: CCDC 2009609: Experimental Crystal Structure Determination

description: Related Article: Lucy M. C. Luong, Christopher D. Lowe, Alexandria V. Adams, Venoos Moshayedi, Marilyn M. Olmstead, Alan L. Balch|2020|Chemical Science|11|11705|doi:10.1039/D0SC03299A
DOI: 10.5517/ccdc.csd.cc25yb4m
title: CCDC 2024180: Experimental Crystal Structure Determination

description: Related Article: Erika Amemiya, Aaron Loo, Daniel G. Shlian, Gerard Parkin|2020|Chemical Science|11|11763|doi:10.1039/D0SC04596A
DOI: 10.5517/ccdc.csd.cc25yb5n
title: CCDC 2024181: Experimental Crystal Structure Determination

description: Related Article: Erika Amemiya, Aaron Loo, Daniel G. Shlian, Gerard Parkin|2020|Chemical Science|11|11763|doi:10.1039/D0SC04596A
DOI: 10.5286/isis.e.rb2010346
title: Probing the sensing performance of metal-organic frameworks via inelastic neutron scattering at TOSCA

description: We aim to perform inelastic neutron scattering measurements at the TOSCA spectrometer to study the vibrational behaviour of novel Guest@MOF composite systems (namely: ZnQ@OX-1 and Ag/Zn@OX-2) subject to a gas or vapour analyte. The results will enable rational design of Guest@MOF sensors with high sensitivity for detection of volatile organic compound (VOCs) and flammable gases. The objectives are: (i) To pinpoint the precise nature of the vibrational dynamics of the Guest@OX composites compared to the vacant pristine framework. (ii) To understand how the vibrational dynamics of the composite system can be altered when the material is exposed to a VOC (such as acetone) or a gas analyte (such as methane). (iii) To determine the precise modification to the THz modes of the Guest@OX composite systems during the adsorption and subsequent desorption of a VOC or gas analyte.
DOI: 10.5286/isis.e.rb2010346-1
title: Probing the sensing performance of metal-organic frameworks via inelastic neutron scattering at TOSCA

description: We aim to perform inelastic neutron scattering measurements at the TOSCA spectrometer to study the vibrational behaviour of novel Guest@MOF composite systems (namely: ZnQ@OX-1 and Ag/Zn@OX-2) subject to a gas or vapour analyte. The results will enable rational design of Guest@MOF sensors with high sensitivity for detection of volatile organic compound (VOCs) and flammable gases. The objectives are: (i) To pinpoint the precise nature of the vibrational dynamics of the Guest@OX composites compared to the vacant pristine framework. (ii) To understand how the vibrational dynamics of the composite system can be altered when the material is exposed to a VOC (such as acetone) or a gas analyte (such as methane). (iii) To determine the precise modification to the THz modes of the Guest@OX composite systems during the adsorption and subsequent desorption of a VOC or gas analyte.
DOI: 10.5286/isis.e.rb2010373-1
title: Chain arrangement of hydrophobically modified thermo-responsive block-polymers in interaction with oil-in-water microemulsion droplets

description: Materials with controlled response on external stimuli are very attractive for research and applications. Accordingly, hydrophobically modified (HM) thermo-responsive (TR) block-polymers are of special interest. Previously, HM telechelic multiarm polymers were investigated in mixtures with oil-in-water (O/W) microemulsions (MEs) in respect to the network formation and rheologic properties. The hydrophobic domains interact with the hydrophobic core of the MEs and form interconnected networks where the ME droplets act as knots and the polymer as interconnections. With an added TR block, the interaction between ME and HMTR block-polymer should change according to the mesoscopic phase separation of the polymer. The aim of this proposal is to investigate the arrangement of the hydrophobic end-caps of polymer chains interacting with ME droplets, thereby yielding TR polymer modified MEs.