cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20362911.v1
title: Structure based virtual screening and molecular dynamics of natural anti-biofilm compounds against SagS response regulator/sensor kinase in <i>Pseudomonas aeruginosa</i>

description: SagS sensor regulator plays a vital role in biofilm development of <i>Pseudomonas aeruginosa</i> which subsequently makes the cells more tolerant to various antimicrobials. The multidrug resistance (MDR) issue has risen substantially in recent years and is considered a global threat. Therefore, alternative compounds should be unearthed immediately to address the issues related to <i>P. aeruginosa</i> drug resistance for which SagS could be a candidate. The present study is an attempt to screen natural anti-biofilm compounds as the potent inhibitors of SagS. Twenty natural anti-biofilm/quorum sensing inhibiting compounds were retrieved from various literatures with significant inhibitory effects against <i>P. aeruginosa</i> biofilm from <i>in-vitro</i> experiments which were screened using various pharmacokinetic parameters. The screened and three standard drugs were docked against SagS-HisKA using AutoDock 4.2 tool, which were further analysed by MD simulations to understand the binding mode of compounds and dynamic behaviour of the complexes. Two potential anti-biofilm natural compounds, pinocembrin with binding affinity (-7.19 kcal/mol), vestitol (-7.18 kcal/mol) and the standard drug ceftazidime (-8.89 kcal/mol) were selected based on filtered parameters and better binding affinity. The trajectory analysis of MD simulations reflected Pinocembrin in stabilizing the system compared to ceftazidime. The existing reports state that the natural products represent promising source of therapy with least or almost nil adverse effect compared to synthetic drugs which is well collated with our <i>in-silico findings</i>. This investigation can save both time and cost required for <i>in-vitro</i> and <i>in-vivo</i> analysis for designing of a novel anti-biofilm agent against <i>P. aeruginosa</i> biofilm-associated infections. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20455641.v1
title: Seasonal variation of the composition of essential oils from <i>Piper cernuum</i> Vell and <i>Piper rivinoides</i> Kunth, ADMET study, DFT calculations, molecular docking and dynamics studies of major components as potent inhibitors of the heterodimer methyltransferase complex NSP16-NSP10 SARS COV-2 protein

description: Coronavirus disease (COVID-19) has the virus that causes the SARS-CoV-2 severe acute respiratory syndrome, which has reached a pandemic proportion, with thousands of deaths worldwide already registered. It has no standardized effective clinical treatment, arousing the urgent need for the discovery of bioactive compounds for the treatment of symptoms of COVID-19. In this context, the present study aimed to evaluate the influence of seasonality on the yield and chemical composition of the essential oils of <i>Piper cernuum</i> and <i>Piper rivinoides</i> as well as to evaluate the anti-SARS-CoV-2 potential of the major components of each oil by molecular docking and quantum chemical calculation (Density Functional Theory method), being possible indicate that the winter and autumn periods, the seasons of the year where it is possible to obtain the highest percentage of <i>Piper cernuum</i> and <i>Piper rivinoides</i> oils, respectively. Regarding the anti-SARS-Cov-2 potential, the present work showed that the dihydroagarofuran present in <i>Piper cernuum</i>, presented a strong interaction with amino acid residues from Mpro, presenting a potential similar to Remdesivir, a drug for clinical use. Regarding methyltransferase, dihydroagarofuran (<i>Piper cernuum</i>) and myristicin (<i>Piper rivinoids</i>) showed better affinity, with important interactions at the active site of the inhibitor Sinefugin, suggesting a potential inhibitory effect of the heterodimer methyltransferase complex NSP16-NSP10 SARS Cov-2. Molecular docking and molecular dynamics studies represent an initial step, being indicative for future <i>in vitro</i> studies of dihydroagarofuran and myristicin, as possible pharmacological tools for COVID-19. Communicated by Ramaswamy H. Sarma Autumn and winter are the most suitable seasons of the year to extract the oils of <i>Piper rivinoides</i> and <i>Piper cernuum</i> respectively. <i>in silico</i> evaluation of majoritary compounds of essential oils against the anti-SARS-Cov-2 potential by Molecular docking. The electronic properties were computed using the Density Functional Theory method to understand the interaction of the molecules and the amino acids. Dihydroagarofuran (<i>Piper cernuum</i>) and myristicin (<i>Piper rivinoids</i>) suggesting a potential inhibitory effect of the heterodimer methyltransferase complex NSP16-NSP10 SARS Cov-2. Dihydroagarofuran present in <i>Piper cernuum</i> suggesting a potential inhibitory effect of the Mpro.
DOI: 10.6084/m9.figshare.20431207
title: Design, dynamic docking, synthesis, and <i>in vitro</i> validation of a novel DNA gyrase B inhibitor

description: Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) and vancomycin-intermediate-resistant <i>Staphylococcus aureus</i> (VRSA) are among the WHO's high priority pathogens. Among these two, MRSA is the most globally documented pathogen that necessitates the pressing demand for new classes of anti-MRSA drugs. Bacterial gyrase targeted therapeutics are unique strategies to overcome cross-resistance as they are present only in bacteria and absent in higher eukaryotes. The GyrB subunit is essential for the catalytic functions of the bacterial enzyme DNA Gyrase, thereby constituting a promising druggable target. The current study performed a structure-based virtual screening to designing GyrB target-specific candidate molecules. The <i>de novo</i> ligand design of novel hit molecules was performed using a rhodanine scaffold. Through a systematic <i>in silico</i> screening process, the hit molecules were screened for their synthetic accessibility, drug-likeness and pharmacokinetics properties in addition to its target specific interactions. Of the 374 hit molecules obtained through <i>de novo</i> ligand design, qsl-304 emerged as the most promising ligand. The molecular dynamic simulation studies confirmed the stable interaction between the key residues and qsl-304. qsl-304 was synthesized through a one-step chemical synthesis procedure, and the <i>in vitro</i> activity was proven, with an IC<sub>50</sub> of 31.23 µg/mL against the novobiocin resistant clinical isolate, <i>Staphylococcus aureus sa</i>-P2003. Further studies on time-kill kinetics showed the bacteriostatic nature with the diminished recurrence of resistance. The on-target gyrB inhibition further proved the efficacy of qsl-304. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20431207.v2
title: Design, dynamic docking, synthesis, and <i>in vitro</i> validation of a novel DNA gyrase B inhibitor

description: Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) and vancomycin-intermediate-resistant <i>Staphylococcus aureus</i> (VRSA) are among the WHO's high priority pathogens. Among these two, MRSA is the most globally documented pathogen that necessitates the pressing demand for new classes of anti-MRSA drugs. Bacterial gyrase targeted therapeutics are unique strategies to overcome cross-resistance as they are present only in bacteria and absent in higher eukaryotes. The GyrB subunit is essential for the catalytic functions of the bacterial enzyme DNA Gyrase, thereby constituting a promising druggable target. The current study performed a structure-based virtual screening to designing GyrB target-specific candidate molecules. The <i>de novo</i> ligand design of novel hit molecules was performed using a rhodanine scaffold. Through a systematic <i>in silico</i> screening process, the hit molecules were screened for their synthetic accessibility, drug-likeness and pharmacokinetics properties in addition to its target specific interactions. Of the 374 hit molecules obtained through <i>de novo</i> ligand design, qsl-304 emerged as the most promising ligand. The molecular dynamic simulation studies confirmed the stable interaction between the key residues and qsl-304. qsl-304 was synthesized through a one-step chemical synthesis procedure, and the <i>in vitro</i> activity was proven, with an IC<sub>50</sub> of 31.23 µg/mL against the novobiocin resistant clinical isolate, <i>Staphylococcus aureus sa</i>-P2003. Further studies on time-kill kinetics showed the bacteriostatic nature with the diminished recurrence of resistance. The on-target gyrB inhibition further proved the efficacy of qsl-304. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20431207.v1
title: Design, dynamic docking, synthesis, and <i>in vitro</i> validation of a novel DNA gyrase B inhibitor

description: Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) and vancomycin-intermediate-resistant <i>Staphylococcus aureus</i> (VRSA) are among the WHO's high priority pathogens. Among these two, MRSA is the most globally documented pathogen that necessitates the pressing demand for new classes of anti-MRSA drugs. Bacterial gyrase targeted therapeutics are unique strategies to overcome cross-resistance as they are present only in bacteria and absent in higher eukaryotes. The GyrB subunit is essential for the catalytic functions of the bacterial enzyme DNA Gyrase, thereby constituting a promising druggable target. The current study performed a structure-based virtual screening to designing GyrB target-specific candidate molecules. The <i>de novo</i> ligand design of novel hit molecules was performed using a rhodanine scaffold. Through a systematic <i>in silico</i> screening process, the hit molecules were screened for their synthetic accessibility, drug-likeness and pharmacokinetics properties in addition to its target specific interactions. Of the 374 hit molecules obtained through <i>de novo</i> ligand design, qsl-304 emerged as the most promising ligand. The molecular dynamic simulation studies confirmed the stable interaction between the key residues and qsl-304. qsl-304 was synthesized through a one-step chemical synthesis procedure, and the <i>in vitro</i> activity was proven, with an IC<sub>50</sub> of 31.23 µg/mL against the novobiocin resistant clinical isolate, <i>Staphylococcus aureus sa</i>-P2003. Further studies on time-kill kinetics showed the bacteriostatic nature with the diminished recurrence of resistance. The on-target gyrB inhibition further proved the efficacy of qsl-304. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20440484
title: Insights into the microevolution of SARS-ACE2 interactions: in silico analysis of glycosylation and SNP pattern

description: The prefatory protein–glycan interaction and stabilizing protein–protein interaction of severe acute respiratory syndrome viruses with angiotensin-converting enzyme 2 play a significant role in complex formation thereby promoting endocytosis. The microevolution of SARS-CoV-2 over a period of time has a significant role in increasing the affinity of receptor-binding domain against angiotensin converting-enzyme 2. In this study, we have corroborated the vitality of acquired SNPs over a period of time with increased affinity by using docking studies. The results indicate that the virus modulates the undesirable glycosylation sites by a series of substitution and deletion mutations. It uses bulky residues such as Tyr/Phe for dynamic arrest for quick stabilization of the complex, and Lys residues for stabilizing via hydrogen bond formation besides increasing the binding affinity to ease the cell entry. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20440484.v1
title: Insights into the microevolution of SARS-ACE2 interactions: in silico analysis of glycosylation and SNP pattern

description: The prefatory protein–glycan interaction and stabilizing protein–protein interaction of severe acute respiratory syndrome viruses with angiotensin-converting enzyme 2 play a significant role in complex formation thereby promoting endocytosis. The microevolution of SARS-CoV-2 over a period of time has a significant role in increasing the affinity of receptor-binding domain against angiotensin converting-enzyme 2. In this study, we have corroborated the vitality of acquired SNPs over a period of time with increased affinity by using docking studies. The results indicate that the virus modulates the undesirable glycosylation sites by a series of substitution and deletion mutations. It uses bulky residues such as Tyr/Phe for dynamic arrest for quick stabilization of the complex, and Lys residues for stabilizing via hydrogen bond formation besides increasing the binding affinity to ease the cell entry. Communicated by Ramaswamy H. Sarma
DOI: 10.5519/qd.js21em31
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (5590529 records)
DOI: 10.5281/zenodo.8154897
title: Exploring Psychological Safety in Software Engineering

description: The database used in the article entitled "Exploring Psychological Safety in Software Engineering: Insights from Stack Exchange" consists of two files: "All Results" and "Database Sbes." The "All Results" file includes all search results, while the "Database Sbes" file contains the categorization of selected data.
DOI: 10.5281/zenodo.8154896
title: Exploring Psychological Safety in Software Engineering

description: The database used in the article entitled "Exploring Psychological Safety in Software Engineering: Insights from Stack Exchange" consists of two files: "All Results" and "Database Sbes." The "All Results" file includes all search results, while the "Database Sbes" file contains the categorization of selected data.
DOI: 10.21942/uva.23695308
title: The clinical relevance of subgroups of autistic adults: Stability and predictive value

description: This csv-file includes an anonymized person-to-person correlation matrix based on Sample 2 including autistic and comparison participants. For more information, please read the preprint of this study, that can be found at https://psyarxiv.com/ycp6q/. <br> This correlation matrix was used as input for the Spinglass community detection analysis in the study of Radhoe et al., 2023. The rows and columns represent the study participants (i.e., autistic and non-autistic comparison participants), and the values in the matrix represent the correlations between participants based on fourteen cluster variables.
DOI: 10.21942/uva.23695308.v1
title: The clinical relevance of subgroups of autistic adults: Stability and predictive value

description: This csv-file includes an anonymized person-to-person correlation matrix based on Sample 2 including autistic and comparison participants. For more information, please read the preprint of this study, that can be found at https://psyarxiv.com/ycp6q/. <br> This correlation matrix was used as input for the Spinglass community detection analysis in the study of Radhoe et al., 2023. The rows and columns represent the study participants (i.e., autistic and non-autistic comparison participants), and the values in the matrix represent the correlations between participants based on fourteen cluster variables.
DOI: 10.6084/m9.figshare.23695392
title: U-Pb data

description: Data of the tectonic carbonates dated through U-Pb dating
DOI: 10.6084/m9.figshare.23695392.v1
title: U-Pb data

description: Data of the tectonic carbonates dated through U-Pb dating
DOI: 10.18712/nsd-nsd2720-v1
title: AquaAccept - developing novel socio-environmental indicators and management tools for a sustainable aquaculture

description: Around the world, there is an increasing governmental emphasis on developing the aquaculture industry in an environmentally, economically and socially sustainable manner and Norway is moving in the same direction. The main objective of the proposed project is to investigate the acceptable impacts of aquaculture on marine coastal systems. Focus will be on biological indicators, social acceptability and integrated management in a multidisciplinary approach. The environmental sustainability of aquaculture will be supported through the development of environmental indexes for monitoring, based largely on on-line, real-time tools. The social acceptance for aquaculture will be studied both in Ireland (EU) and in Norway to explore rationalities and priorities present in the different end-user groups and potential conflicts of interests. The environmental and social findings will be merged in a novel managing tool in order to calculate conflict scores, generate matrices of interactions, plot maps, evaluate spatial and/or temporal interactions existing in a specific marine coastal area, calculate overlaps or rank the effects of synergies and conflicts by the calculation of stress levels.
DOI: 10.34740/kaggle/dsv/5917951
title: cardiac-surgery-and-percutaneous
DOI: 10.34740/kaggle/dsv/6149020
title: 2021 World Population (updated daily)
DOI: 10.5281/zenodo.7900161
title: Hypertension and Diabetes Registry Dataset in Addis Ababa, Ethiopia

description: Dataset collected from the “hypertension and diabetes” national registry of the ministry of health of Ethiopia.<br>
DOI: 10.5281/zenodo.7900160
title: Hypertension and Diabetes Registry Dataset in Addis Ababa, Ethiopia

description: Dataset collected from the “hypertension and diabetes” national registry of the ministry of health of Ethiopia.<br>
DOI: 10.34740/kaggle/dsv/6149024
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.5281/zenodo.8151968
title: TelePi: Stitching Dataset

description: TelePi is a camera system based on the Raspberry Pi Zero v1.3 with its High Quality camera module. TelePi functions as a telepathology camera system as well as a standard color microscope camera. To capture a larger field of view, overlapping single images of a hematoxylin and eosin-stained, formalin-fixed, paraffin-embedded ureter specimen were taken (with approximately a 10% overlap) in 20X using an Olympus BX41 microscope (Olympus, Tokyo, Japan). Before each image was taken, any necessary adjustment in the focus was performed, so that the image stayed sharp. Afterwards, the images were stitched together using the bundled Fiji plugin Stitching v1.2 (Preibisch, Saalfeld et al. 2009). The original single images were saved as JPEGs as captured by the camera without editing. The stitched final output is included in the dataset.
description: Formalin-fixed, paraffin-embedded hematoxylin and eosin tissue section from a ureter specimen.
DOI: 10.5281/zenodo.8151967
title: TelePi: Stitching Dataset

description: TelePi is a camera system based on the Raspberry Pi Zero v1.3 with its High Quality camera module. TelePi functions as a telepathology camera system as well as a standard color microscope camera. To capture a larger field of view, overlapping single images of a hematoxylin and eosin-stained, formalin-fixed, paraffin-embedded ureter specimen were taken (with approximately a 10% overlap) in 20X using an Olympus BX41 microscope (Olympus, Tokyo, Japan). Before each image was taken, any necessary adjustment in the focus was performed, so that the image stayed sharp. Afterwards, the images were stitched together using the bundled Fiji plugin Stitching v1.2 (Preibisch, Saalfeld et al. 2009). The original single images were saved as JPEGs as captured by the camera without editing. The stitched final output is included in the dataset.
description: Formalin-fixed, paraffin-embedded hematoxylin and eosin tissue section from a ureter specimen.
DOI: 10.5281/zenodo.7312102
title: Supporting Data -- Evaluating Mask R-CNN Models to Extract Terracing across Oceanic High Islands: an example from Sāmoa.

description: This dataset provides supplemental information for the manuscript, "Diverse terracing practices revealed by automated lidar analysis across the Sāmoan islands", submitted to Archaeological Prospection. The dataset contains a trained Mask R-CNN deep learning model designed for detecting archaeological terracing features on the islands of American Samoa, associated training data, and the raw and cleaned output of detected terraces.
DOI: 10.5281/zenodo.7312103
title: Supporting Data -- Evaluating Mask R-CNN Models to Extract Terracing across Oceanic High Islands: an example from Sāmoa.

description: This dataset provides supplemental information for the manuscript, "Diverse terracing practices revealed by automated lidar analysis across the Sāmoan islands", submitted to Archaeological Prospection. The dataset contains a trained Mask R-CNN deep learning model designed for detecting archaeological terracing features on the islands of American Samoa, associated training data, and the raw and cleaned output of detected terraces.
DOI: 10.6084/m9.figshare.19518937
title: Impact of host stress on the replication rate of Plasmodium: Take it easy to avoid malaria recurrence

description: This dataset is associated with a study where we explored the impact of increasing the concentration of corticosterone in the blood of birds on the within-host infection dynamic of malaria parasite (i.e. Plasmodium relictum). The birds were in a chronic stage of infection. We manipulated the corticosterone concentration of the birds either artificially (corticosterone ingestion, experiment 1) or naturally (handling stress, experiment 2). We also exposed treated and controlled birds to mosquitoes to determine if increased stress hormone levels in vertebrate hosts impacted Plasmodium transmission. We conducted a third experiment to study the impact of mosquito bites on stress hormone levels in vertebrate hosts.
DOI: 10.6084/m9.figshare.19518937.v1
title: Impact of host stress on the replication rate of Plasmodium: Take it easy to avoid malaria recurrence

description: This dataset is associated with a study where we explored the impact of increasing the concentration of corticosterone in the blood of birds on the within-host infection dynamic of malaria parasite (i.e. Plasmodium relictum). The birds were in a chronic stage of infection. We manipulated the corticosterone concentration of the birds either artificially (corticosterone ingestion, experiment 1) or naturally (handling stress, experiment 2). We also exposed treated and controlled birds to mosquitoes to determine if increased stress hormone levels in vertebrate hosts impacted Plasmodium transmission. We conducted a third experiment to study the impact of mosquito bites on stress hormone levels in vertebrate hosts.
DOI: 10.5281/zenodo.7515880
title: Plasma etching for fabrication of complex nanophotonic lasers from bonded InP semiconductor layers

description: Integrating optically active III-V materials on silicon/insulator platforms is one potential path towards improving the energy efficiency and performance of modern computing. Here we demonstrate the applicability of direct wafer bonding combined with plasma etching to the fabrication of complex nanophotonic systems out of InP layers. We explore and optimise the plasma etching of InP, validating existing processes and developing improved ones. We explore the use of microdisk lasing as a way to evaluate fabrication fidelity, and demonstrate that we can create complex lasing systems of interest to us: coupled disk cavities and random network lasers. <strong>This repository contains data used to generate figures in https://doi.org/10.1016/j.mne.2023.100196.</strong>