cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17219042.v4
title: Supplementary table 1

description: Table providing features of all B. tabaci plant-derived genes included in this study and references supporting involvement in plant-pathogen interactions.<br>
DOI: 10.6084/m9.figshare.19785883.v1
title: Best hit for the flanks of plant-derived genes

description: Table indicating the best hit of each protein corresponding to genes flanking plant-derived genes in MEAM1
DOI: 10.6084/m9.figshare.17218094
title: Supplementary table 3

description: Table listing all transcripts covering at least 75% of the B. tabaci MEAM1 plant-derived genes with at least 95% identity.<br>
DOI: 10.6084/m9.figshare.17218094.v2
title: Supplementary table 3

description: Table listing all transcripts covering at least 75% of the B. tabaci MEAM1 plant-derived genes with at least 95% identity.<br>
DOI: 10.6084/m9.figshare.17218094.v1
title: Transcripts_ParsedBlastnOutputALL.txt

description: Table listing all transcripts covering at least 75% of the B. tabaci MEAM1 plant-derived genes with at least 95% identity.<br>
DOI: 10.6084/m9.figshare.17278340
title: Supplementary dataset 4

description: Fasta file combining the plant-derived MEAM1 representative sequences.
DOI: 10.6084/m9.figshare.17278340.v2
title: Supplementary dataset 4

description: Fasta file combining the plant-derived MEAM1 representative sequences.
DOI: 10.6084/m9.figshare.17278340.v1
title: MEAM1 representative sequences

description: Fasta file combining the plant-derived MEAM1 representative sequences.
DOI: 10.6084/m9.figshare.19782688
title: Supplementary dataset 2

description: This archive contains, for each cluster with false-positive plant LCA prediction, the initial (.aln files) and trimmed (.trim files) protein alignments in fasta format, and the phylogenetic trees in Newick format (.annot files).
DOI: 10.6084/m9.figshare.19782688.v2
title: Supplementary dataset 2

description: This archive contains, for each cluster with false-positive plant LCA prediction, the initial (.aln files) and trimmed (.trim files) protein alignments in fasta format, and the phylogenetic trees in Newick format (.annot files).
DOI: 10.6084/m9.figshare.19782688.v1
title: Multiple sequence alignments and phylogenetic trees - False positives

description: This archive contains, for each cluster with false-positive plant LCA prediction, the initial (.aln files) and trimmed (.trim files) protein alignments in fasta format, and the phylogenetic trees in Newick format (.annot files).
DOI: 10.6084/m9.figshare.17278415
title: Supplementary dataset 3

description: This archive contains, for each cluster of plant-derived genes, the initial (.aln files) and trimmed (.trim files) protein alignments in fasta format, and the phylogenetic trees in Newick format (.annot files).
DOI: 10.6084/m9.figshare.17278415.v2
title: Supplementary dataset 3

description: This archive contains, for each cluster of plant-derived genes, the initial (.aln files) and trimmed (.trim files) protein alignments in fasta format, and the phylogenetic trees in Newick format (.annot files).
DOI: 10.6084/m9.figshare.17278415.v1
title: Multiple sequence alignments and phylogenetic trees

description: This archive contains, for each cluster of plant-derived genes, the initial (.aln files) and trimmed (.trim files) protein alignments in fasta format, and the phylogenetic trees in Newick format (.annot files).
DOI: 10.5281/zenodo.15548
title: MD simulation trajectory and related files for POPC bilayer (Chiu et al. Gromos version, Gromacs 4.5)

description: Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Chiu et al. force field (http://dx.doi.org/10.1021/jp807056c), 50ns, T=298K, 128 POPC molecules, 3552 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (http://dx.doi.org/10.1021/jp807056c).
description: {"references": ["nmrlipids.blogspot.fi", "An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers", "See-Wing Chiu, Sagar A. Pandit, H. L. Scott and Eric Jakobsson", "J. Phys. Chem. B, 2009, 113 (9), pp 2748\u20132763"]}
DOI: 10.22008/fk2/uvzjdq/npozhe
title: Atlantic_mapv_UU-P07.mov

description: Map view animation going down through the mantle from 20 km to 2840 km in 20 km increments.
DOI: 10.22008/fk2/uvzjdq/pqcl8d
title: Fig8.3_all_slices.mov

description: Animation of cross sections slices for different transects oriented perpendicular to the mid-Atlantic Ridge. Sections are shown in Figure 8.3 of the Atlas.
DOI: 10.22008/fk2/uvzjdq/sdil8x
title: Tomo_README.txt

description: Readme!
DOI: 10.22008/fk2/uvzjdq/pbxnsq
title: Tomo_NAGTEC.asc

description: :unav
DOI: 10.22008/fk2/uvzjdq/cmldyk
title: Atlantic_6mod_Atlas 2.mov

description: Map view animation going down through the mantle from 20 km to 2840 km in 20 km increments. This animation shows 6 different published models for comparison. See Chapter 10 of the Atlas for more details.
DOI: 10.22008/fk2/uvzjdq
title: Mantle Tomography Model UU-P07

description: Tomographic model of Earth's mantle developed for the project.
DOI: 10.5281/zenodo.6619767
title: JetClass: A Large-Scale Dataset for Deep Learning in Jet Physics

description: JetClass is a new large-scale dataset to facilitate deep learning research in jet physics. It consists of 100M jets for training, 5M for validation and 20M for testing. The dataset contains 10 classes of jets, simulated with MadGraph + Pythia + Delphes. <br> <br> A detailed description of the JetClass dataset is presented in the paper Particle Transformer for Jet Tagging. An interface to use the dataset is provided in https://github.com/jet-universe/particle_transformer.
DOI: 10.34740/kaggle/dsv/3818559
title: YouTube Daily
DOI: 10.21943/auas.20073767
title: Vrij reizen over de arbeidsmarkt: onderzoek naar het skillspaspoort

description: De data bestaat uit interviews met werkgevers en werknemers betrekking tot het skillspaspoort.
DOI: 10.5281/zenodo.6656031
title: MD simulation trajectory and related files for POPC bilayer (Chiu et al. Gromos version, Gromacs 4.5)

description: Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Chiu et al. force field (http://dx.doi.org/10.1021/jp807056c), 50ns, T=298K, 128 POPC molecules, 3552 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (http://dx.doi.org/10.1021/jp807056c).
description: {"references": ["nmrlipids.blogspot.fi", "An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers", "See-Wing Chiu, Sagar A. Pandit, H. L. Scott and Eric Jakobsson", "J. Phys. Chem. B, 2009, 113 (9), pp 2748\u20132763"]}
DOI: 10.5281/zenodo.608544
title: MD simulation trajectory and related files for POPC bilayer (Chiu et al. Gromos version, Gromacs 4.5)

description: Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Chiu et al. force field (http://dx.doi.org/10.1021/jp807056c), 50ns, T=298K, 128 POPC molecules, 3552 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (http://dx.doi.org/10.1021/jp807056c).
description: {"references": ["nmrlipids.blogspot.fi", "An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers", "See-Wing Chiu, Sagar A. Pandit, H. L. Scott and Eric Jakobsson", "J. Phys. Chem. B, 2009, 113 (9), pp 2748\u20132763"]}
DOI: 10.6084/m9.figshare.20088566
title: Table S3 MurA hits accession numbers.xlsx

description: <strong>Accession numbers of MurA hits in Bacteria and Firmicutes, related to Figure 7.</strong>
DOI: 10.6084/m9.figshare.20088566.v1
title: Table S3 MurA hits accession numbers.xlsx

description: <strong>Accession numbers of MurA hits in Bacteria and Firmicutes, related to Figure 7.</strong>
DOI: 10.5517/ccdc.csd.cc2bmzyx
title: CCDC 2164170: Experimental Crystal Structure Determination

description: Related Article: Lin-Lin Chen, Ying-Ying Wu, Wen-Wen Wu, Meng-Meng Wang, Hui-Jie Lun, Dong-Bin Dang, Yan Bai, Ya-Min Li|2022|Inorg.Chem.|61|8629|doi:10.1021/acs.inorgchem.2c01150
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.20088626
title: CRONOGRAMA EVENTO

description: Cronograma Organizativo del Evento
DOI: 10.6084/m9.figshare.20088626.v1
title: CRONOGRAMA EVENTO

description: Cronograma Organizativo del Evento
DOI: 10.5281/zenodo.6651589
title: Supporting Data for "Decarbonization pathways for the residential sector in the United States"

description: This repository contains input and processed data for the analysis presented in "Decarbonization pathways for the residential sector in the United States" by Berrill et al. (2022), in Nature Climate Change. Description of the files can be found in the 'Data_Descriptors.docx' file. Please direct any enquiries relating to this dataset to peter.berrill@aya.yale.edu
DOI: 10.5281/zenodo.6651588
title: Supporting Data for "Decarbonization pathways for the residential sector in the United States"

description: This repository contains input and processed data for the analysis presented in "Decarbonization pathways for the residential sector in the United States" by Berrill et al. (2022), in Nature Climate Change. Description of the files can be found in the 'Data_Descriptors.docx' file. Please direct any enquiries relating to this dataset to peter.berrill@aya.yale.edu
DOI: 10.6084/m9.figshare.20088578
title: Baseflow trends for midsize Carpathian catchments in Poland and Slovakia in 1970-2019

description: Daily river discharge and basflow calculated with Eckhardt filter for 20 midsize carpathian catchments in 1970-2019.
DOI: 10.6084/m9.figshare.15149247
title: Viral biogeography of the mammalian gut and parenchymal organs

description: Little is known on how the gastrointestinal virome is structured along the longitudinal axis of the mammalian digestive system. In this study we report a comprehensive metagenomic analysis of the prokaryotic and eukaryotic virome occupying luminal and mucosa-associated habitats along the length of the gastrointestinal tract (GIT) in two representative mammalian species, the domestic pig and rhesus macaque (six animals of each species), chosen for their relevance to humans. The highest loads and diversity of bacteriophages (class <em>Caudoviricetes</em>, family <em>Microviridae</em> and others) were detected in the lumen of the large intestine in both mammals. Mucosal samples contained much lower viral loads but a higher proportion of eukaryotic viruses (families <em>Astroviridae</em>, <em>Caliciviridae</em>, <em>Parvoviridae</em>). Parenchymal organs (liver, lung and spleen) contained significant numbers of bacteriophages of gut origin, in addition to some eukaryotic viruses. GIT virome composition is both region- and species-specific and is distinct between upper and lower gut. Upper GIT and mucosa-specific viruses are greatly under-represented in distal colon samples, which is used as a proxy for faeces. Nonetheless, certain viral and phage species are found ubiquitously from the oral cavity to the distal colon. The dataset and its accompanying methodology may provide an important resource for future work investigating the biogeography of the mammalian gut virome.
DOI: 10.6084/m9.figshare.15149247.v1
title: Viral biogeography of the mammalian gut and parenchymal organs

description: Little is known on how the gastrointestinal virome is structured along the longitudinal axis of the mammalian digestive system. In this study we report a comprehensive metagenomic analysis of the prokaryotic and eukaryotic virome occupying luminal and mucosa-associated habitats along the length of the gastrointestinal tract (GIT) in two representative mammalian species, the domestic pig and rhesus macaque (six animals of each species), chosen for their relevance to humans. The highest loads and diversity of bacteriophages (class <em>Caudoviricetes</em>, family <em>Microviridae</em> and others) were detected in the lumen of the large intestine in both mammals. Mucosal samples contained much lower viral loads but a higher proportion of eukaryotic viruses (families <em>Astroviridae</em>, <em>Caliciviridae</em>, <em>Parvoviridae</em>). Parenchymal organs (liver, lung and spleen) contained significant numbers of bacteriophages of gut origin, in addition to some eukaryotic viruses. GIT virome composition is both region- and species-specific and is distinct between upper and lower gut. Upper GIT and mucosa-specific viruses are greatly under-represented in distal colon samples, which is used as a proxy for faeces. Nonetheless, certain viral and phage species are found ubiquitously from the oral cavity to the distal colon. The dataset and its accompanying methodology may provide an important resource for future work investigating the biogeography of the mammalian gut virome.
DOI: 10.6084/m9.figshare.13415913
title: Effect of ligand conjugation site on the micellization of Bio-Targeted PLGA-Based nanohybrids: A computational biology approach

description: In this study, the effect of ligand binding position on the polymeric nanoparticles (NPs) is based on poly(lactic-co-glycolic acid) (PLGA) with two different polymer chain length at the atomistic level was presented. We explored the conjugation of riboflavin (RF) ligand from the end of the ribityl chain (N-10) to the polymer strands as well as from the amine group on the isoalloxazine head (N-3). The energy interactions for all samples revealed that the NPs containing ligands from N-10 positions have higher total attraction energies and lower stability in comparison with their peers conjugated from N-3. As NPs containing RF conjugated from N-3 exhibit the lower energy level with 20% and 10% of RF-containing composition for lower and higher. The introduction of RF from the N-10 position in any composition has increased the energy level of nanocarriers. The results of Gibb's free energy confirm the interatomic interaction energies trend where the lowest Gibbs free energy level for N-3 NPs occurs at 20 and 10% of RF-containing polymer content for PLGA10- and PLGA11- based NPs. Furthermore, with N-10 samples based on both polymers, non-targeted models form the stablest particles in each category. These findings are further confirmed with molecular docking analysis which revealed affinity energy of RF toward polymer chain from N-3 and N-10 are −981.57 kJ/mole and −298.23 kJ/mole, respectively. This in-silico study paves the new way for molecular engineering of the bio-responsive PLGA-PEG-RF micelles and can be used to nanoscale tunning of smart carriers used in cancer treatment. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13369752.v1
title: Atomistic simulation on flavonoids derivatives as potential inhibitors of bacterial gyrase of <i>Staphylococcus aureus</i>

description: The bacterial DNA gyrase is an attractive target to identify the novel antibacterial agents. The flavonoid derivatives possess various biological activities such as antimicrobial, anti-inflammatory and anticancer activities. The aim of present study is to identify the potential molecule from flavonoid derivatives against <i>Staphylococcus aureus</i> using atomistic simulation namely Molecular Docking, Quantum Chemical and Molecular Dynamics. The molecules Cpd58, Cpd65 and Cpd70 are identified as potential molecules through molecular docking approaches by exploring through the N – H…O hydrogen bonding interactions with Asn31 and Glu35 of Gyrase B. To confirm the intramolecular charge transfer in the flavonoid derivatives, Frontier Molecular Orbital (FMO) calculation was performed at M06/6-31g(d) level in gas phase. The lowest HOMO-LUMO gap was calculated for Cpd58, Cpd65 and Cpd70 among the selected compounds used in this study. Molecular dynamics simulation were carried out for Cpd58 and Cpd70 for a time period of 50 ns and found to be stable throughout the analysis. Therefore, the identified compounds are found to be a potent inhibitor for GyrB of <i>S. aureus</i> that can be validated by experimental studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13415913.v1
title: Effect of ligand conjugation site on the micellization of Bio-Targeted PLGA-Based nanohybrids: A computational biology approach

description: In this study, the effect of ligand binding position on the polymeric nanoparticles (NPs) is based on poly(lactic-co-glycolic acid) (PLGA) with two different polymer chain length at the atomistic level was presented. We explored the conjugation of riboflavin (RF) ligand from the end of the ribityl chain (N-10) to the polymer strands as well as from the amine group on the isoalloxazine head (N-3). The energy interactions for all samples revealed that the NPs containing ligands from N-10 positions have higher total attraction energies and lower stability in comparison with their peers conjugated from N-3. As NPs containing RF conjugated from N-3 exhibit the lower energy level with 20% and 10% of RF-containing composition for lower and higher. The introduction of RF from the N-10 position in any composition has increased the energy level of nanocarriers. The results of Gibb's free energy confirm the interatomic interaction energies trend where the lowest Gibbs free energy level for N-3 NPs occurs at 20 and 10% of RF-containing polymer content for PLGA10- and PLGA11- based NPs. Furthermore, with N-10 samples based on both polymers, non-targeted models form the stablest particles in each category. These findings are further confirmed with molecular docking analysis which revealed affinity energy of RF toward polymer chain from N-3 and N-10 are −981.57 kJ/mole and −298.23 kJ/mole, respectively. This in-silico study paves the new way for molecular engineering of the bio-responsive PLGA-PEG-RF micelles and can be used to nanoscale tunning of smart carriers used in cancer treatment. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13369752
title: Atomistic simulation on flavonoids derivatives as potential inhibitors of bacterial gyrase of <i>Staphylococcus aureus</i>

description: The bacterial DNA gyrase is an attractive target to identify the novel antibacterial agents. The flavonoid derivatives possess various biological activities such as antimicrobial, anti-inflammatory and anticancer activities. The aim of present study is to identify the potential molecule from flavonoid derivatives against <i>Staphylococcus aureus</i> using atomistic simulation namely Molecular Docking, Quantum Chemical and Molecular Dynamics. The molecules Cpd58, Cpd65 and Cpd70 are identified as potential molecules through molecular docking approaches by exploring through the N – H…O hydrogen bonding interactions with Asn31 and Glu35 of Gyrase B. To confirm the intramolecular charge transfer in the flavonoid derivatives, Frontier Molecular Orbital (FMO) calculation was performed at M06/6-31g(d) level in gas phase. The lowest HOMO-LUMO gap was calculated for Cpd58, Cpd65 and Cpd70 among the selected compounds used in this study. Molecular dynamics simulation were carried out for Cpd58 and Cpd70 for a time period of 50 ns and found to be stable throughout the analysis. Therefore, the identified compounds are found to be a potent inhibitor for GyrB of <i>S. aureus</i> that can be validated by experimental studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13359708.v1
title: Cytotoxicity, <i>in silico</i> predictions and molecular studies for androstane heterocycle compounds revealed potential antitumor agent against lung cancer cells

description: The IL6/JAK2/STAT3 axis dysregulation and the related downstream pathways are a major contributor to the progression of non-small-cell lung carcinoma (NSCLC) and mainly affect apoptosis. Furthermore, tubulin inhibitors are potential chemotherapeutic agents against NSCLC. In this study, we have provided new molecular insights into the antiproliferative activity of six 3β-acetoxy-5α-androstane heterocycle compounds against NSCLC. The cell line A549, which represents a good model of NSCLC, was used to evaluate the antitumour activity of tested androstane derivatives, and non-cancerous gingival mesenchymal stem cell line (GMSC) were used to assess the specificity and toxicity of the tested compounds. Further on, molecular docking predictions were used to determine the molecular targets for the most promising cytotoxic compound. To assess apoptosis and cell cycle progression in treated A549 cells, flow cytometry was used. RT-qPCR and ELISA analyses were used to gain deep insights into cellular and molecular mechanisms. Results revealed that compound <b>4</b> has potential cytotoxicity on A549 cells, with lower IC<sub>50</sub> value (27.36 μM). Moreover, <i>in silico</i>, compound <b>4</b> showed a good binding affinity to JAK2 and tubulin-colchicine soblidotin molecular targets. This was further confirmed on the molecular level. Compound <b>4</b> has also led to apoptosis and increased fragmentation of DNA, and mitochondrial dysfunction. Our findings have provided good evidence that compound <b>4</b> may be a dual inhibitor of IL6/JAK2/STAT3 and tubulin formation in lung cancer. These findings support further molecular exploration of this androstane derivative as promising anti-lung cancer agent. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13359708
title: Cytotoxicity, <i>in silico</i> predictions and molecular studies for androstane heterocycle compounds revealed potential antitumor agent against lung cancer cells

description: The IL6/JAK2/STAT3 axis dysregulation and the related downstream pathways are a major contributor to the progression of non-small-cell lung carcinoma (NSCLC) and mainly affect apoptosis. Furthermore, tubulin inhibitors are potential chemotherapeutic agents against NSCLC. In this study, we have provided new molecular insights into the antiproliferative activity of six 3β-acetoxy-5α-androstane heterocycle compounds against NSCLC. The cell line A549, which represents a good model of NSCLC, was used to evaluate the antitumour activity of tested androstane derivatives, and non-cancerous gingival mesenchymal stem cell line (GMSC) were used to assess the specificity and toxicity of the tested compounds. Further on, molecular docking predictions were used to determine the molecular targets for the most promising cytotoxic compound. To assess apoptosis and cell cycle progression in treated A549 cells, flow cytometry was used. RT-qPCR and ELISA analyses were used to gain deep insights into cellular and molecular mechanisms. Results revealed that compound <b>4</b> has potential cytotoxicity on A549 cells, with lower IC<sub>50</sub> value (27.36 μM). Moreover, <i>in silico</i>, compound <b>4</b> showed a good binding affinity to JAK2 and tubulin-colchicine soblidotin molecular targets. This was further confirmed on the molecular level. Compound <b>4</b> has also led to apoptosis and increased fragmentation of DNA, and mitochondrial dysfunction. Our findings have provided good evidence that compound <b>4</b> may be a dual inhibitor of IL6/JAK2/STAT3 and tubulin formation in lung cancer. These findings support further molecular exploration of this androstane derivative as promising anti-lung cancer agent. Communicated by Ramaswamy H. Sarma