cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25442/hku.22828064.v1
title: Data for the manuscript " Experimental Investigation on Scouring v.s. Mass Failure of Unsaturated Soil Bed: Implications for Debris Flow Initiation and Erosion"

description: The data uploaded supports the content in the manuscript "Experimental Investigation on Scouring v.s. Mass Failure of Unsaturated Soil Bed: Implications for Debris Flow Initiation and Erosion". <br> The data uploaded are generated in the laborotory and includes the measurement of flow depth, erosion depth, erosion duration, etc. in 30 flume experiments. <br> The experiments carried out investigate the erosion of unsaturated soil bed by hydrodynamic shear stresses. During the experiments, an ultrasonic sensor, a high speed camera and a laser sensor are eqquipped with the flume. The ultrasonic sensor measured the evolution of flow depth during the experiment. The high speed camera is installed at the side of the flume, and captured the kinematics of the flow and the erosion process. The duration of the erosion process was deduced from the images captured by the high speed camera. The laser sensor is used to measure the depth of erosion, which is deduced by the difference in the height of the soil surface before and after the experiment.
DOI: 10.5281/zenodo.4310972
title: BiasCorrector: fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies

description: The dataset includes the data of the experiments used for the manuscript "BiasCorrector: fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies".
DOI: 10.5281/zenodo.4310973
title: BiasCorrector: fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies

description: The dataset includes the data of the experiments used for the manuscript "BiasCorrector: fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies".
DOI: 10.5281/zenodo.4626905
title: BiasCorrector: fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies

description: The dataset includes the data of the experiments used for the manuscript "BiasCorrector: fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies".
DOI: 10.5281/zenodo.3677642
title: Regional Atmospheric Climate Model 2 (RACMO2), version 2.3p2

description: In the 1990s the KNMI developed in cooperation with the Danish Meteorological Institute the research model RACMO based on the High Resolution Limited Area Model (HIRLAM) numerical weather prediction model. In 1993 UU/IMAU started to modify the model such that it better represented the extreme conditions over glacier surfaces. This first version of RACMO, RACMO1, combined the dynamical core of the HIRLAM model with ECHAM4 physics. The polar modified version of RACMO1 was mainly applied to the Antarctic Ice Sheet. The second version, RACMO2, combines the dynamical core of the HIRLAM model with the European Centre for Medium-range Weather Forecasts (ECMWF) Integrated Forecast System (ISF) physics. RACMO versions 2.0 and 2.1 included HIRLAM version 5.0.6 and ISF cycle CY23r4, while version 2.3 includes HIRLAM version 6.3.7 and cycle CY33r1. Due to the rapid increase in computer capacity over the years, these versions of RACMO have not only been applied to the Greenland and Antarctic Ice Sheets, but also at higher resolution to smaller areas such as Dronning Maud Land and Patagonia. For the RACMO model in general the grids are defined over the equator and then rotated to the area of interest. Grid distance is defined in fraction of degrees, which results in near equidistant grid points as long as the domain is small enough. Note that the domain is thus not on a (polar) stereographic projection plane. In the vertical, the model adopts a system of hybrid sigma levels, which evolve from terrain-following sigma levels close to the surface to pure pressure levels at higher elevation. The actual number of horizontal grid points varies per model run; in most simulations, 40 vertical layers were used. Since RACMO is a regional model, it needs external information at the lateral boundaries and sea surface. At the lateral boundary zone of the model, the temperature, specific humidity, zonal and meridional wind components, and the surface pressure are relaxed towards the fields of a global model every 6 model hours, as are the sea surface temperature and sea ice concentration. RACMO is not forced at the model top. The interior of the model is not nudged towards observations and allowed to evolve freely.
DOI: 10.6084/m9.figshare.22829048
title: Data S7-Raw read count matrix for technology optimizations

description: Data S7-Raw read count matrix for technology optimizations
DOI: 10.6084/m9.figshare.22829048.v1
title: Data S7-Raw read count matrix for technology optimizations

description: Data S7-Raw read count matrix for technology optimizations
DOI: 10.5281/zenodo.7907473
title: PNSDs and trajectory history datasets (Khadir et al., 2023)

description: Three datasets (for ATTO Tower, Hyytiälä and Zeppelin stations): Contain hourly Particle Number Size Distributions and air mass history (96 hours) calculated using Hysplit - Hybrid Single Particle Lagrangian Integrated Trajectory model. Precipitation rates along trajectories are collocated using TRMM for the Atto dataset, and other meteorological conditions are given from GDAS1 reanalysis (output from Hysplit).
DOI: 10.6084/m9.figshare.22829045
title: Data S8-Raw read count matrix for all de-identified clinical samples

description: Data S8-Raw read count matrix for all de-identified clinical samples
DOI: 10.6084/m9.figshare.22829045.v1
title: Data S8-Raw read count matrix for all de-identified clinical samples

description: Data S8-Raw read count matrix for all de-identified clinical samples
DOI: 10.6084/m9.figshare.17067718
title: EhSir2c, a Sir2 homolog from the human pathogen <i>Entamoeba histolytica</i> interacts with a DNA repair protein, EhRAD23: Protein-protein interaction, docking and functional study

description: Chromosome segregation is a crucial phenomenon in the cell cycle and defects in genome segregation result in an abnormality in various cellular events. Unlike higher eukaryotes, chromosome segregation and a number of cell cycle events are unusual in the protozoan parasite <i>Entamoeba histolytica</i> (<i>E. histolytica</i>). Characterization of Sir2 proteins from <i>E. histolytica</i> may reveal its unique cellular events as they play role in diverse cellular processes including chromosome segregation. <i>E. histolytica</i> has four homologs of Sir2 proteins. EhSir2a and EhSir2b show sequence similarity towards eukaryotic Sir2 homologs, whereas EhSir2c and EhSir2d are more like prokaryotic sirtuins. Using both computational and experimental methods, EhSir2c has been characterized in this study. The three-dimensional structure of EhSir2c is predicted by homology modelling. The protein interactors of EhSir2c have been identified by yeast-two-hybrid screening against the cDNA library of <i>E. histolytica</i>. We have identified a novel interactor, EhRAD23 which is a homolog of UV excision repair protein RAD23. The interaction of EhSir2c and EhRAD23 was validated by pull-down assay. UV-C irradiation up-regulates the relative expression of EhSir2c, suggesting the necessity of EhSir2c in UV-induced stress in this parasite. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17067718.v1
title: EhSir2c, a Sir2 homolog from the human pathogen <i>Entamoeba histolytica</i> interacts with a DNA repair protein, EhRAD23: Protein-protein interaction, docking and functional study

description: Chromosome segregation is a crucial phenomenon in the cell cycle and defects in genome segregation result in an abnormality in various cellular events. Unlike higher eukaryotes, chromosome segregation and a number of cell cycle events are unusual in the protozoan parasite <i>Entamoeba histolytica</i> (<i>E. histolytica</i>). Characterization of Sir2 proteins from <i>E. histolytica</i> may reveal its unique cellular events as they play role in diverse cellular processes including chromosome segregation. <i>E. histolytica</i> has four homologs of Sir2 proteins. EhSir2a and EhSir2b show sequence similarity towards eukaryotic Sir2 homologs, whereas EhSir2c and EhSir2d are more like prokaryotic sirtuins. Using both computational and experimental methods, EhSir2c has been characterized in this study. The three-dimensional structure of EhSir2c is predicted by homology modelling. The protein interactors of EhSir2c have been identified by yeast-two-hybrid screening against the cDNA library of <i>E. histolytica</i>. We have identified a novel interactor, EhRAD23 which is a homolog of UV excision repair protein RAD23. The interaction of EhSir2c and EhRAD23 was validated by pull-down assay. UV-C irradiation up-regulates the relative expression of EhSir2c, suggesting the necessity of EhSir2c in UV-induced stress in this parasite. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17111909
title: Jatamansinol from <i>Nardostachys jatamansi</i>: a multi-targeted neuroprotective agent for Alzheimer’s disease

description: Alzheimer’s disease (AD) is a multifactorial progressive and irreversible neurodegenerative disorder characterized by severe memory impairment and cognitive disability in the middle and old-aged human population. There are no proven drugs for AD treatment and prevention. In Ayurveda, medhya plants are used to prepare Rasayana, and its consumption improves memory and cognition. <i>Nardostachys jatamansi</i> (D.Don) DC is a medhya plant used in traditional medicine to treat neurological disorders, and its unique pyranocoumarins can be a potential drug candidate for AD. Given its traditional claims, this study aims to find the multi-target potential efficacy of the ligands (drug molecules) against the AD from <i>N. jatamansi</i> pyranocoumarins using computational drug discovery techniques. Drug likeliness analysis confirms that pyranocoumarins of <i>N. jatamansi,</i> such as seselin, jatamansinol, jatamansine, jatamansinone, and dihydrojatamansin are probable drug candidates for AD. Molecular docking, molecular dynamic simulations, and Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) analysis confirm that dihydrojatamansin inhibits acetylcholinesterase (<i>AChE</i>), and jatamansinol inhibits butyrylcholinesterase (<i>BuChE</i>), glycogen synthase kinase 3β <i>(GSK3β</i>), and kelch-like ECH-associating protein 1 (<i>Keap1</i>) AD therapeutic targets. Therefore, this study provides potential multi-target inhibitors that would further validate experimental studies, leading to new treatments for AD. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17111909.v1
title: Jatamansinol from <i>Nardostachys jatamansi</i>: a multi-targeted neuroprotective agent for Alzheimer’s disease

description: Alzheimer’s disease (AD) is a multifactorial progressive and irreversible neurodegenerative disorder characterized by severe memory impairment and cognitive disability in the middle and old-aged human population. There are no proven drugs for AD treatment and prevention. In Ayurveda, medhya plants are used to prepare Rasayana, and its consumption improves memory and cognition. <i>Nardostachys jatamansi</i> (D.Don) DC is a medhya plant used in traditional medicine to treat neurological disorders, and its unique pyranocoumarins can be a potential drug candidate for AD. Given its traditional claims, this study aims to find the multi-target potential efficacy of the ligands (drug molecules) against the AD from <i>N. jatamansi</i> pyranocoumarins using computational drug discovery techniques. Drug likeliness analysis confirms that pyranocoumarins of <i>N. jatamansi,</i> such as seselin, jatamansinol, jatamansine, jatamansinone, and dihydrojatamansin are probable drug candidates for AD. Molecular docking, molecular dynamic simulations, and Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) analysis confirm that dihydrojatamansin inhibits acetylcholinesterase (<i>AChE</i>), and jatamansinol inhibits butyrylcholinesterase (<i>BuChE</i>), glycogen synthase kinase 3β <i>(GSK3β</i>), and kelch-like ECH-associating protein 1 (<i>Keap1</i>) AD therapeutic targets. Therefore, this study provides potential multi-target inhibitors that would further validate experimental studies, leading to new treatments for AD. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20424281
title: <i>In silico</i> screening and epitope mapping of leptospiral outer membrane protein—Lsa46

description: Leptospirosis is one of the neglected diseases caused by the spirochete, <i>Leptospira interrogans</i>. Leptospiral surface adhesion (Lsa) proteins are surface exposed outer membrane proteins present in the pathogen. It acts as laminin and plasminogen binding proteins which enable them to infect host cells. The major target for the development of vaccine in the current era focuses on surface exposed outer membrane proteins, as they can induce strong and fast immune response in hosts. Therefore, the present study mapped the potential epitopes of the Leptospiral outer membrane proteins, mainly the surface adhesion proteins. Protein sequence analysis of Lsa proteins was done by <i>in silico</i> methods. The primary protein sequence analysis revealed Lsa46 as a suitable target which can be a potent Leptospiral vaccine candidate. Its structure was modelled by threading based method in I-TASSER server and validated by Ramachandran plot. The predicted epitope’s interactions with human IgG, IgM(Fab) and T-cell receptor TCR(αβ) were performed by molecular docking studies using Biovia Discovery studio 2018. One of the predicted B-cell epitopes and the IgG showed desirable binding interactions, while four of the predicted B-cell epitopes and T-cell epitopes showed desirable binding interactions with IgM and TCR respectively. The molecular dynamic simulation studies carried out with the molecular docked complexes gave minimized energies indicating stable interactions. The structural analysis of the entire simulated complex showed a stable nature except for one of the Epitope-IgM complex. Further the binding free energy calculation of eight receptor-ligand complex predicted them energetically stable. The results of the study help in elucidating the structural and functional characterization of Lsa46 for epitope-based vaccine design. Communicated by Ramaswamy H. Sarma.
DOI: 10.6084/m9.figshare.20424281.v1
title: <i>In silico</i> screening and epitope mapping of leptospiral outer membrane protein—Lsa46

description: Leptospirosis is one of the neglected diseases caused by the spirochete, <i>Leptospira interrogans</i>. Leptospiral surface adhesion (Lsa) proteins are surface exposed outer membrane proteins present in the pathogen. It acts as laminin and plasminogen binding proteins which enable them to infect host cells. The major target for the development of vaccine in the current era focuses on surface exposed outer membrane proteins, as they can induce strong and fast immune response in hosts. Therefore, the present study mapped the potential epitopes of the Leptospiral outer membrane proteins, mainly the surface adhesion proteins. Protein sequence analysis of Lsa proteins was done by <i>in silico</i> methods. The primary protein sequence analysis revealed Lsa46 as a suitable target which can be a potent Leptospiral vaccine candidate. Its structure was modelled by threading based method in I-TASSER server and validated by Ramachandran plot. The predicted epitope’s interactions with human IgG, IgM(Fab) and T-cell receptor TCR(αβ) were performed by molecular docking studies using Biovia Discovery studio 2018. One of the predicted B-cell epitopes and the IgG showed desirable binding interactions, while four of the predicted B-cell epitopes and T-cell epitopes showed desirable binding interactions with IgM and TCR respectively. The molecular dynamic simulation studies carried out with the molecular docked complexes gave minimized energies indicating stable interactions. The structural analysis of the entire simulated complex showed a stable nature except for one of the Epitope-IgM complex. Further the binding free energy calculation of eight receptor-ligand complex predicted them energetically stable. The results of the study help in elucidating the structural and functional characterization of Lsa46 for epitope-based vaccine design. Communicated by Ramaswamy H. Sarma.
DOI: 10.6084/m9.figshare.17098993
title: <i>In silico</i> screening of phytochemical compounds and FDA drugs as potential inhibitors for NSP16/10 5' methyl transferase activity

description: The recent global pandemic associated with the highly contagious novel coronavirus (SARS-CoV-2) has led to an unpredictable loss of life and economy worldwide, and the discovery of antiviral drugs is an urgent necessity. For the discovery of new drug leads and for the treatment of various diseases, natural products and purified photochemical from medicinal plants are used. The RNA cap was methylated by two S-adenosyl-L-methionine (SAM)-dependent methyltransferases of SARS coronavirus (SARS-CoV-2), catalyzed by NSP16 2′-O-Mtase. Natural substrate SAM, 128 Phytocompounds retrieved from the Phytocompounds database, and 11 standard FDA-approved HIV drugs reclaimed from the PubChem database are subjected to docking analysis. The docking study was done using AutoDock Vina. Further, admetSAR and DruLiTO servers are used to analyze the drug-likeness properties. The NSP16/10 structure and natural substrate SAM, Phytocompounds Withanolide (WTL), and HIV standard drug Dolutegravir (DLT) as hit compounds were identified by molecular dynamics using the Gromacs GPU-enabled package. To examine the effectiveness of the identified drugs versus COVID-19, further <i>in vitro</i> and <i>in vivo</i> studies are required. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17098993.v1
title: <i>In silico</i> screening of phytochemical compounds and FDA drugs as potential inhibitors for NSP16/10 5' methyl transferase activity

description: The recent global pandemic associated with the highly contagious novel coronavirus (SARS-CoV-2) has led to an unpredictable loss of life and economy worldwide, and the discovery of antiviral drugs is an urgent necessity. For the discovery of new drug leads and for the treatment of various diseases, natural products and purified photochemical from medicinal plants are used. The RNA cap was methylated by two S-adenosyl-L-methionine (SAM)-dependent methyltransferases of SARS coronavirus (SARS-CoV-2), catalyzed by NSP16 2′-O-Mtase. Natural substrate SAM, 128 Phytocompounds retrieved from the Phytocompounds database, and 11 standard FDA-approved HIV drugs reclaimed from the PubChem database are subjected to docking analysis. The docking study was done using AutoDock Vina. Further, admetSAR and DruLiTO servers are used to analyze the drug-likeness properties. The NSP16/10 structure and natural substrate SAM, Phytocompounds Withanolide (WTL), and HIV standard drug Dolutegravir (DLT) as hit compounds were identified by molecular dynamics using the Gromacs GPU-enabled package. To examine the effectiveness of the identified drugs versus COVID-19, further <i>in vitro</i> and <i>in vivo</i> studies are required. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17085802
title: Molecular docking and dynamic simulation approach to decipher steroidal sapogenins (genus <i>Trillium</i>) derived agonists for glucocorticoid receptor

description: Steroidal sapogenins (SS) are structural analogues of steroidal drugs, which are frequently used for the treatment of several diseases including reproductive, malignancies, neurological, and inflammation-related diseases. The glucocorticoid receptor (GR) is a nuclear receptor that regulates development, metabolism, and inflammation, in response to steroidal ligands. Therefore, GR is considered as a potential therapeutic target for steroidal agents to the treatment of inflammation-related diseases. We hypothesized that SS may act as an agonist for GR due to structural similarity with corticosteroids. In this study, we carried out <i>in silico</i> screening of various SS from the genus <i>Trillium</i> to check their potential as an agonist for GR. Our data suggest that out of 42 SS, only 7 molecules have interacted with GR. However, molecular mechanics with generalized Born and surface area (MM-GBSA) analysis revealed that only two SS (SS <b>38</b> and SS <b>39</b>) molecules bind favorably to GR. Among these, SS <b>38</b> (docking score: –9.722 Kcal/mol and MM-GBSA ΔG<sub>bind</sub>: –50.192 Kcal/mol) and SS <b>39</b> (docking score: –11.20 Kcal/mol and MM-GBSA ΔG<sub>bind</sub>: –58.937 Kcal/mol) have best docking and MM-GBSA scores. Molecular dynamics (MD) simulation studies of SS <b>38</b>, SS <b>39</b>, and dexamethasone-GR complex revealed that both SS shows hydrogen bonding and hydrophobic interaction with GR over the 120 ns simulation with mild fluctuations. The current study suggests that SS <b>38</b> and SS <b>39</b> may be further explored as a potential agonist to treat several disease conditions mediated by GR. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17085802.v1
title: Molecular docking and dynamic simulation approach to decipher steroidal sapogenins (genus <i>Trillium</i>) derived agonists for glucocorticoid receptor

description: Steroidal sapogenins (SS) are structural analogues of steroidal drugs, which are frequently used for the treatment of several diseases including reproductive, malignancies, neurological, and inflammation-related diseases. The glucocorticoid receptor (GR) is a nuclear receptor that regulates development, metabolism, and inflammation, in response to steroidal ligands. Therefore, GR is considered as a potential therapeutic target for steroidal agents to the treatment of inflammation-related diseases. We hypothesized that SS may act as an agonist for GR due to structural similarity with corticosteroids. In this study, we carried out <i>in silico</i> screening of various SS from the genus <i>Trillium</i> to check their potential as an agonist for GR. Our data suggest that out of 42 SS, only 7 molecules have interacted with GR. However, molecular mechanics with generalized Born and surface area (MM-GBSA) analysis revealed that only two SS (SS <b>38</b> and SS <b>39</b>) molecules bind favorably to GR. Among these, SS <b>38</b> (docking score: –9.722 Kcal/mol and MM-GBSA ΔG<sub>bind</sub>: –50.192 Kcal/mol) and SS <b>39</b> (docking score: –11.20 Kcal/mol and MM-GBSA ΔG<sub>bind</sub>: –58.937 Kcal/mol) have best docking and MM-GBSA scores. Molecular dynamics (MD) simulation studies of SS <b>38</b>, SS <b>39</b>, and dexamethasone-GR complex revealed that both SS shows hydrogen bonding and hydrophobic interaction with GR over the 120 ns simulation with mild fluctuations. The current study suggests that SS <b>38</b> and SS <b>39</b> may be further explored as a potential agonist to treat several disease conditions mediated by GR. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22829159
title: Does Inflation matter article dataset

description: Prepared using: <br> The data on inflation perception are openly available in https://www.ecb.europa.eu/stats/ecb_surveys/consumer_exp_survey/html/data_methodological.en.html <br> The Eurobarometer survey data are openly available in at https://doi.org/10.4232 <br> Macroeconomic data are sourced from the Eurostat database
DOI: 10.17030/uclan.data.00000377
title: Data and Code for Thesis - An Examination of Observed Coronal Structures Through Automated Techniques Across Solar Cycle 24