cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10001789.v2
title: The pathogenicity, structural and functional exploration of human HMGB1 single nucleotide polymorphisms using <i>in silico</i> study

description: The human HMGB1 gene mutations have a major impact on several immune-related diseases and cancer. The detrimental effect of non-synonymous mutations of HMGB1 has not been investigated yet, hence the present study aims to examine single nucleotide polymorphisms and their implications on the structure-function of human HMGB1. The multifaceted HMGB1 protein acts as pleiotropic cytokine and regulates essential genes for coordinated cellular functions. The mutational effect on HMGB1 was analyzed by sequence-based homology methods, supervised learning methods, and structure-based methods. The study identified 58 non-synonymous mutations in human HMGB1, out of which only 2 mutations; R10T (rs61742222) and F103C (rs61733675) were classified as the SNPs with highest deleterious and disease-causing mutants. The effect of these mutations in structure of HMGB1 was scrutinized and the R10T mutant found to have a distinct structural behaviour in the B-box domain. In addition, R10T mutant predicted that it affects the MoRF function of HMGB1 and it could disrupt the DNA binding or/and protein partner interaction activity by HMGB1. F103C mutation takes place at the TLR binding and cytokine inducing region of HMGB1, hence it could affect the protein binding activity which involves in many cellular signaling. The study identified potent mutations R10T (a cancer-causing somatic mutation) and F103C (a novel mutation) and these mutations either directly or indirectly hinder DNA binding activity and TLR and cytokine binding of HMGB1. These findings will help in understanding the molecular basis of these promising mutations and functional role of human HMGB1 in cancer and immunological diseases. AbbreviationsAGERAdvanced glycosylation end product-specific receptorCXCLChemokine (C-X-C motif) liganddbSNPThe single nucleotide polymorphism databaseHMGB1High mobility group box 1LINCSLINear Constraint SolverMDSMolecular dynamics simulationMoRFMolecular recognition featuresNPTNumber of particle, Pressure and TemperatureNVTNumber of particle, Volume and TemperaturensSNPNon-synonymous SNPPBCPartial boundary conditionPCAPrincipal component analysisPMEPartial mesh EwaldRMSDRoot mean square deviationRMSFRoot mean square fluctuationSNPSingle nucleotide polymorphismSPCSingle-point chargeTLRToll-like receptorUTRUn-translated Region Advanced glycosylation end product-specific receptor Chemokine (C-X-C motif) ligand The single nucleotide polymorphism database High mobility group box 1 LINear Constraint Solver Molecular dynamics simulation Molecular recognition features Number of particle, Pressure and Temperature Number of particle, Volume and Temperature Non-synonymous SNP Partial boundary condition Principal component analysis Partial mesh Ewald Root mean square deviation Root mean square fluctuation Single nucleotide polymorphism Single-point charge Toll-like receptor Un-translated Region Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9980720
title: Identification of therapeutic peptide scaffold from tritrpticin family for urinary tract infections using <i>in silico</i> techniques

description: Antimicrobial peptides (AMPs) like tritrpticins, exhibit non-specific membrane lysis of gram-negative bacteria and can replace antibiotics, combating multi-drug resistance observed in UTI patients. Tritrpticins designated – NT, T1, T2, T3, T5, T7 and T8, were computationally investigated by interaction with <i>Escherichia coli</i> membrane model, mammalian cell toxicity and structural stability to identify a potential drug scaffold for UTI. Initially T3 was eliminated due to low interaction with <i>Escherichia coli</i> membrane model, based on its computed solvation energy. Further, negative support vector machine (SVM) scores revealed non-toxicity of T1, T2, T5, T7 and T8. Finally, at 310 K and varying pH 4.5–9.0, T5 exhibited highest structural stability based on its highest consistency of hydrogen bonds (H-bonds), root mean square deviation (RMSD) and secondary structure profiles along with its lowest conformational free energy. Overall, T5 could be considered a promising peptide drug scaffold to combat UTI. ABBREVIATIONSAMPantimicrobial peptidePBEQPoisson Boltzmann equationH-bondshydrogen bondsMICminimum inhibitory concentrationLD50lethal dose, 50%RMSDroot mean square deviationSVMsupport vector machineUTIurinary tract infection antimicrobial peptide Poisson Boltzmann equation hydrogen bonds minimum inhibitory concentration lethal dose, 50% root mean square deviation support vector machine urinary tract infection Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9980720.v2
title: Identification of therapeutic peptide scaffold from tritrpticin family for urinary tract infections using <i>in silico</i> techniques

description: Antimicrobial peptides (AMPs) like tritrpticins, exhibit non-specific membrane lysis of gram-negative bacteria and can replace antibiotics, combating multi-drug resistance observed in UTI patients. Tritrpticins designated – NT, T1, T2, T3, T5, T7 and T8, were computationally investigated by interaction with <i>Escherichia coli</i> membrane model, mammalian cell toxicity and structural stability to identify a potential drug scaffold for UTI. Initially T3 was eliminated due to low interaction with <i>Escherichia coli</i> membrane model, based on its computed solvation energy. Further, negative support vector machine (SVM) scores revealed non-toxicity of T1, T2, T5, T7 and T8. Finally, at 310 K and varying pH 4.5–9.0, T5 exhibited highest structural stability based on its highest consistency of hydrogen bonds (H-bonds), root mean square deviation (RMSD) and secondary structure profiles along with its lowest conformational free energy. Overall, T5 could be considered a promising peptide drug scaffold to combat UTI. ABBREVIATIONSAMPantimicrobial peptidePBEQPoisson Boltzmann equationH-bondshydrogen bondsMICminimum inhibitory concentrationLD50lethal dose, 50%RMSDroot mean square deviationSVMsupport vector machineUTIurinary tract infection antimicrobial peptide Poisson Boltzmann equation hydrogen bonds minimum inhibitory concentration lethal dose, 50% root mean square deviation support vector machine urinary tract infection Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.10008026
title: Uncovering the structure and function of <i>Pseudomonas aeruginosa</i> periplasmic proteins by an <i>in silico</i> approach

description: <i>Pseudomonas aeruginosa</i> is an opportunistic human pathogen highly relevant from a biomedical viewpoint. It is one of the main causes of infection in hospitalized patients and a major cause of mortality of cystic fibrosis patients. This is also due to its ability to develop resistance to antibiotics by various mechanisms. Therefore, it is urgent and desirable to identify novel targets for the development of new antibacterial drugs against <i>Pseudomonas aeruginosa</i>. In this work this problem was tackled by an <i>in silico</i> approach aimed at providing a reliable structural model and functional annotation for the <i>Pseudomonas aeruginosa</i> periplasmic proteins for which these data are not available yet. A total of 83 protein sequences were analyzed, and the corresponding structural models were built, leading to the identification of 32 periplasmic ‘substrate-binding proteins’, 14 enzymes and 4 proteins with different functions, including lipids and metals binding. The most interesting cases were found within the ‘enzymes’ group with the identification of a lipase, which can be regarded as a virulence factor, a protease involved in the assembly of β-barrel membrane proteins and a l,d-transpeptidase, which could contribute to confer resistance to β-lactam antibiotics to the bacterium. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.10272863.v1
title: The structural basis of acid resistance in <i>Mycobacterium tuberculosis</i>: insights from multiple pH regime molecular dynamics simulations

description: The dormant <i>Mycobacterium tuberculosis</i> is evolved to develop the tolerance against the acidification of phagolysosome by the action of gamma interferon. The molecular mechanism responsible for the development of the resistance towards the acidic conditions in <i>M. tuberculosis</i> is not fully understood. Therefore, the current analysis was performed which studies the mechanism of acid tolerance by correlating the alteration in the protonation state of conserved residues in virulent proteins with changes in their folding states. The pH dependencies of proteins were studied using an efficient computational scheme which enables the understanding of their conformational behavior by molecular dynamics (MD) simulations. The adopted methodology involves cyclically updating of the ionization states of titrable residues in the studied proteins with conventional MD steps, which were applied to the newly generated ionization configuration. Significant pH-dependent protein structural stability parameters consistent with the changes of the protonation states of conserved residues were observed. Among the studied proteins, the peptidoglycan binding protein ompATB, carboxylesterase LipF and two-component systems' transcriptional regulator PhoP showed highest structural conservation in the observed acidic pH range throughout the course of MD simulations. The current study provides a better understanding of acid tolerance mechanisms present in <i>M. tuberculosis</i> and can facilitate the drug development strategies against the dormant protein targets. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.10272863
title: The structural basis of acid resistance in <i>Mycobacterium tuberculosis</i>: insights from multiple pH regime molecular dynamics simulations

description: The dormant <i>Mycobacterium tuberculosis</i> is evolved to develop the tolerance against the acidification of phagolysosome by the action of gamma interferon. The molecular mechanism responsible for the development of the resistance towards the acidic conditions in <i>M. tuberculosis</i> is not fully understood. Therefore, the current analysis was performed which studies the mechanism of acid tolerance by correlating the alteration in the protonation state of conserved residues in virulent proteins with changes in their folding states. The pH dependencies of proteins were studied using an efficient computational scheme which enables the understanding of their conformational behavior by molecular dynamics (MD) simulations. The adopted methodology involves cyclically updating of the ionization states of titrable residues in the studied proteins with conventional MD steps, which were applied to the newly generated ionization configuration. Significant pH-dependent protein structural stability parameters consistent with the changes of the protonation states of conserved residues were observed. Among the studied proteins, the peptidoglycan binding protein ompATB, carboxylesterase LipF and two-component systems' transcriptional regulator PhoP showed highest structural conservation in the observed acidic pH range throughout the course of MD simulations. The current study provides a better understanding of acid tolerance mechanisms present in <i>M. tuberculosis</i> and can facilitate the drug development strategies against the dormant protein targets. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12924551
title: 18 microhaplotype loci genotyped from Han and Yi in Sichuan, China.

description: We genotyped 200 unrelated individuals and 83 parent–child pairs from Sichuan using our panel of 18 multi-Indel markers (microhaplotypes) containing 54 Indel loci multiplex systems.
DOI: 10.6084/m9.figshare.12924551.v2
title: 18 microhaplotype loci genotyped from Han and Yi in Sichuan, China.

description: We genotyped 200 unrelated individuals and 83 parent–child pairs from Sichuan using our panel of 18 multi-Indel markers (microhaplotypes) containing 54 Indel loci multiplex systems.
DOI: 10.6084/m9.figshare.12924551.v1
title: 18 microhaplotype loci genotyped from Han and Yi in Sichuan, China.

description: We genotyped 200 unrelated individuals and 83 parent–child pairs from Sichuan using our panel of 18 multi-Indel markers (microhaplotypes) containing 54 Indel loci multiplex systems.
DOI: 10.5281/zenodo.4018772
title: Delft3D input and output files

description: Supplementary data for: Hepkema et al., Oblique sand ridges in confined tidal channels due to Coriolis and frictional torques (submitted to Ocean Dynamics, 2020) Two .mat (matlab) files with the bathymetric output of the D3D runs. One where the Coriolis effect is taken into account and one where it is not. The zip file contains all the necessary inputfiles to rerun the Delft3D model.
DOI: 10.5281/zenodo.4018771
title: Delft3D input and output files

description: Supplementary data for: Hepkema et al., Oblique sand ridges in confined tidal channels due to Coriolis and frictional torques (submitted to Ocean Dynamics, 2020) Two .mat (matlab) files with the bathymetric output of the D3D runs. One where the Coriolis effect is taken into account and one where it is not. The zip file contains all the necessary inputfiles to rerun the Delft3D model.
DOI: 10.6084/m9.figshare.12925772
title: R0195_20171022a_videos

description: Rat 0195, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12925772.v1
title: R0195_20171022a_videos

description: Rat 0195, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.5517/ccdc.csd.cc1mlhvk
title: CCDC 1507339: Experimental Crystal Structure Determination

description: Related Article: Ming Jia, Yabo Li, Mengmeng Huang, Jung Keun Kim, Yingliang Liu, Yangjie Wu, Shaokui Cao|2020|Tetrahedron|76|131471|doi:10.1016/j.tet.2020.131471
DOI: 10.5517/ccdc.csd.cc1q1jlw
title: CCDC 1580398: Experimental Crystal Structure Determination

description: Related Article: Ming Jia, Yabo Li, Mengmeng Huang, Jung Keun Kim, Yingliang Liu, Yangjie Wu, Shaokui Cao|2020|Tetrahedron|76|131471|doi:10.1016/j.tet.2020.131471
DOI: 10.6084/m9.figshare.12927890
title: Database from Antimary State Forest

description: The database used in this study was collected in the the Antimary State Forest (FEA), located in the municipalities of Sena Madureira and Bujari, Acre State, in the southwest region of the western Brazilian Amazon (68° 23′ W; 9° 13′; 9° 31′ S). It was measure the variables: total heights, diameter at breast height taken at 1.3 m above ground or above tree buttresses and the commercial height. <br> <br>
DOI: 10.6084/m9.figshare.12927890.v2
title: Database from Antimary State Forest

description: The database used in this study was collected in the the Antimary State Forest (FEA), located in the municipalities of Sena Madureira and Bujari, Acre State, in the southwest region of the western Brazilian Amazon (68° 23′ W; 9° 13′; 9° 31′ S). It was measure the variables: total heights, diameter at breast height taken at 1.3 m above ground or above tree buttresses and the commercial height. <br> <br>
DOI: 10.6084/m9.figshare.12927890.v1
title: Database from Antimary State Forest

description: The database used in this study was collected in the the Antimary State Forest (FEA), located in the municipalities of Sena Madureira and Bujari, Acre State, in the southwest region of the western Brazilian Amazon (68° 23′ W; 9° 13′; 9° 31′ S). It was measure the variables: total heights, diameter at breast height taken at 1.3 m above ground or above tree buttresses and the commercial height. <br> <br>
DOI: 10.6084/m9.figshare.12927860
title: Soil Microbial Communities Profiles with Next Generation Sequencing

description: Soil Microbial Communities Profiles obtained by Next Generation Sequencing and QIIME2 Processing.
DOI: 10.6084/m9.figshare.12927860.v1
title: Soil Microbial Communities Profiles with Next Generation Sequencing

description: Soil Microbial Communities Profiles obtained by Next Generation Sequencing and QIIME2 Processing.
DOI: 10.5519/qd.9mz9baos
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6084/m9.figshare.8956697
title: Restrictive lung disease in TNF-transgenic mice: correlation of pulmonary function testing and micro-CT imaging

description: <b>Purpose:</b> Micro-computed tomography (µCT) is increasingly being used on animal models as a minimally-invasive longitudinal outcome measure of pulmonary disease progression. However, while imaging can elucidate macroscopic structural changes over the whole lung, µCT is unable to describe the mechanical changes and functional impairments imposed by progressive disease, which can only be measured via pulmonary function tests (PFTs). The tumor necrosis factor-transgenic (TNF-Tg) mouse model of rheumatoid arthritis (RA) develops pulmonary pathology that mimics many aspects of the inflammatory interstitial lung disease (ILD) seen in a subset of patients with RA. Prior studies using µCT imaging of these mice found increased pulmonary density, characteristic of restrictive disease; however, there have been conflicting reports in the literature regarding the obstructive versus restrictive phenotype of this model. Our study looks to 1) define the functional impairments and 2) characterize the restrictive/obstructive nature of the disease found in this model. <b>Materials and Methods:</b> In this study, we performed PFTs at end-stage ILD, and paired these findings with µCT results, correlating radiology to functional parameters. TNF-Tg and WT littermates of both sexes underwent µCT imaging and PFT testing at 5.5 months-old. Spearman’s correlation analyses were performed comparing lung tissue volume (LTV) to PFT parameters of gas exchange and tissue stiffness. <b>Results:</b> Compared to WT, TNF-Tg mice had impaired gas exchange capacity, increased respiratory resistance, and reduced lung compliance, elastance, and inspiratory capacity, indicating increased tissue stiffness and compromised pulmonary function. LTV was also consistently higher in TNF-Tg lungs. <b>Conclusions:</b> These findings demonstrate that: 1) TNF-Tg mice display a restrictive pathology, and 2) in vivo µCT is a valid outcome measure to infer changes in pulmonary mechanical and functional parameters.
DOI: 10.6084/m9.figshare.8956697.v2
title: Restrictive lung disease in TNF-transgenic mice: correlation of pulmonary function testing and micro-CT imaging

description: <b>Purpose:</b> Micro-computed tomography (µCT) is increasingly being used on animal models as a minimally-invasive longitudinal outcome measure of pulmonary disease progression. However, while imaging can elucidate macroscopic structural changes over the whole lung, µCT is unable to describe the mechanical changes and functional impairments imposed by progressive disease, which can only be measured via pulmonary function tests (PFTs). The tumor necrosis factor-transgenic (TNF-Tg) mouse model of rheumatoid arthritis (RA) develops pulmonary pathology that mimics many aspects of the inflammatory interstitial lung disease (ILD) seen in a subset of patients with RA. Prior studies using µCT imaging of these mice found increased pulmonary density, characteristic of restrictive disease; however, there have been conflicting reports in the literature regarding the obstructive versus restrictive phenotype of this model. Our study looks to 1) define the functional impairments and 2) characterize the restrictive/obstructive nature of the disease found in this model. <b>Materials and Methods:</b> In this study, we performed PFTs at end-stage ILD, and paired these findings with µCT results, correlating radiology to functional parameters. TNF-Tg and WT littermates of both sexes underwent µCT imaging and PFT testing at 5.5 months-old. Spearman’s correlation analyses were performed comparing lung tissue volume (LTV) to PFT parameters of gas exchange and tissue stiffness. <b>Results:</b> Compared to WT, TNF-Tg mice had impaired gas exchange capacity, increased respiratory resistance, and reduced lung compliance, elastance, and inspiratory capacity, indicating increased tissue stiffness and compromised pulmonary function. LTV was also consistently higher in TNF-Tg lungs. <b>Conclusions:</b> These findings demonstrate that: 1) TNF-Tg mice display a restrictive pathology, and 2) in vivo µCT is a valid outcome measure to infer changes in pulmonary mechanical and functional parameters.
DOI: 10.6084/m9.figshare.8956697.v1
title: Restrictive lung disease in TNF-transgenic mice: correlation of pulmonary function testing and micro-CT imaging

description: <b>Purpose:</b> Micro-computed tomography (µCT) is increasingly being used on animal models as a minimally-invasive longitudinal outcome measure of pulmonary disease progression. However, while imaging can elucidate macroscopic structural changes over the whole lung, µCT is unable to describe the mechanical changes and functional impairments imposed by progressive disease, which can only be measured via pulmonary function tests (PFTs). The tumor necrosis factor-transgenic (TNF-Tg) mouse model of rheumatoid arthritis (RA) develops pulmonary pathology that mimics many aspects of the inflammatory interstitial lung disease (ILD) seen in a subset of patients with RA. Prior studies using µCT imaging of these mice found increased pulmonary density, characteristic of restrictive disease; however, there have been conflicting reports in the literature regarding the obstructive versus restrictive phenotype of this model. Our study looks to 1) define the functional impairments and 2) characterize the restrictive/obstructive nature of the disease found in this model. <b>Materials and Methods:</b> In this study, we performed PFTs at end-stage ILD, and paired these findings with µCT results, correlating radiology to functional parameters. TNF-Tg and WT littermates of both sexes underwent µCT imaging and PFT testing at 5.5 months-old. Spearman’s correlation analyses were performed comparing lung tissue volume (LTV) to PFT parameters of gas exchange and tissue stiffness. <b>Results:</b> Compared to WT, TNF-Tg mice had impaired gas exchange capacity, increased respiratory resistance, and reduced lung compliance, elastance, and inspiratory capacity, indicating increased tissue stiffness and compromised pulmonary function. LTV was also consistently higher in TNF-Tg lungs. <b>Conclusions:</b> These findings demonstrate that: 1) TNF-Tg mice display a restrictive pathology, and 2) in vivo µCT is a valid outcome measure to infer changes in pulmonary mechanical and functional parameters.
DOI: 10.5281/zenodo.3518037
title: Copernicus Global Land Service: Land Cover 100m: collection 3: epoch 2018: Globe

description: Consolidated epoch 2018 from the Collection 3 of annual, global 100m land cover maps. Other available epochs: 2015 2016 2017 2019 Produced by the global component of the Copernicus Land Service, derived from PROBA-V satellite observations and ancillary datasets. The maps include a main discrete classification with 23 classes aligned with UN-FAO's Land Cover Classification System, a set of versatile cover fractions: percentage (%) of ground cover for the 10 main classes a forest type layer quality layers on input data density and on the confidence of the detected land cover change Click here to view the maps More information about the land cover maps Product User Manual
DOI: 10.6084/m9.figshare.12925322
title: R0197_20171118a_videos

description: Rat 0197, skilled reaching data collected in Leventhal laboratory by Alexandra Bova