cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13670125
title: Influences of physical and biogeochemical variability of the central Red Sea during winter

description: The central Red Sea (CRS) has been characterized by significant eddy activity throughout the year. Weakened wintertime stratification contributes to enhanced vertical exchange. In winter 2014-2015, an extended glider time series in the CRS captured this variability. Surface cooling and stronger winds resulted in deepening of the mixed layer (ML) to nearly 90 m. The vertical distributions of density and oxygen suggest that the ML did not penetrate into the nutricline. However, mixing events dispersed phytoplankton from the deep CHL maximum (DCM) throughout the ML increasing nearsurface chlorophyll. Following the mixing events a mesoscale cyclonic eddy (CE) grew and intensified causing weakening of stratification and a decrease in the ML depth within the eddy. Where the CE interfaced with an adjacent anticyclonic eddy (AE), the CE DCM subducted beneath the shallower AE DCM leading to a local integrated chlorophyll maximum. Low salinity water containing relative high chlorophyll and CDOM concentrations, originating from the Gulf of Aden, appeared in late winter. Mesoscale eddy activity resulted in an 160 m upward displacement of the nutricline to ~60 m, well within the euphotic layer. Remote sensing imagery indicates that these eddies contribute to horizontal dispersion, including exchange between the open sea and coastal coral reefs. When the phytoplankton is distributed through the ML, clear diel variability was evident in the temporal CHL distribution. Because not all of the biogeochemical responses were apparent at the surface, sustained glider observations were essential to understand the temporal and spatial scales and their impact on these processes.
DOI: 10.6084/m9.figshare.13670125.v1
title: Influences of physical and biogeochemical variability of the central Red Sea during winter

description: The central Red Sea (CRS) has been characterized by significant eddy activity throughout the year. Weakened wintertime stratification contributes to enhanced vertical exchange. In winter 2014-2015, an extended glider time series in the CRS captured this variability. Surface cooling and stronger winds resulted in deepening of the mixed layer (ML) to nearly 90 m. The vertical distributions of density and oxygen suggest that the ML did not penetrate into the nutricline. However, mixing events dispersed phytoplankton from the deep CHL maximum (DCM) throughout the ML increasing nearsurface chlorophyll. Following the mixing events a mesoscale cyclonic eddy (CE) grew and intensified causing weakening of stratification and a decrease in the ML depth within the eddy. Where the CE interfaced with an adjacent anticyclonic eddy (AE), the CE DCM subducted beneath the shallower AE DCM leading to a local integrated chlorophyll maximum. Low salinity water containing relative high chlorophyll and CDOM concentrations, originating from the Gulf of Aden, appeared in late winter. Mesoscale eddy activity resulted in an 160 m upward displacement of the nutricline to ~60 m, well within the euphotic layer. Remote sensing imagery indicates that these eddies contribute to horizontal dispersion, including exchange between the open sea and coastal coral reefs. When the phytoplankton is distributed through the ML, clear diel variability was evident in the temporal CHL distribution. Because not all of the biogeochemical responses were apparent at the surface, sustained glider observations were essential to understand the temporal and spatial scales and their impact on these processes.
DOI: 10.25921/sv5c-z350
title: EK80 Water Column Sonar Data Collected During NOAA_MC20_Survey
DOI: 10.6084/m9.figshare.14174807
title: Clinical information of three cohorts-updated

description: Clinical information of three immunotherapeutic cohorts, including age, sex, regimen, survival, and GIPS grouping.<br>
DOI: 10.6084/m9.figshare.14174807.v1
title: Clinical information of three cohorts-updated

description: Clinical information of three immunotherapeutic cohorts, including age, sex, regimen, survival, and GIPS grouping.<br>
DOI: 10.6084/m9.figshare.13550510
title: Cytokines levels

description: The data of Cytokines levels of the article entitled: IL-6 and IL-10 in the serum and exfoliated cervical cells of patients infected with high-risk human papillomavirus
DOI: 10.6084/m9.figshare.13550510.v1
title: Cytokines levels

description: The data of Cytokines levels of the article entitled: IL-6 and IL-10 in the serum and exfoliated cervical cells of patients infected with high-risk human papillomavirus
DOI: 10.20375/0000-000d-fa8e-a
title: test_upload3.docx
DOI: 10.20375/0000-000d-fa8f-9
title: text_upload3.pdf
DOI: 10.20375/0000-000d-fa90-6
title: text_upload3.xlsx
DOI: 10.48320/4162e388-cca8-45b8-bfb9-d88bdffe3aa0
title: text_upload3
DOI: 10.5281/zenodo.4587406
title: Supplementary data for manuscript "Resampling of ENSO teleconnections."

description: Supplementary data for the manuscript "Resampling: accounting for cold season evolution reduces uncertainty in the North Atlantic". Associated scripts and codes are available in https://github.com/martin-king/kingetal_2020_resamplingenso.
DOI: 10.6084/m9.figshare.14174597
title: Sea level rise impact on intertidal shoals

description: The Delft3D (v 6.02.13.7545M) modeling configurations used to investigate the impact of sea level rise on the morphological evolution of intertidal shoals. Attached also is the Wadden Sea data (bathymetry and sediment composition).<br>
DOI: 10.5281/zenodo.4587448
title: Time-temperature: Bauxite from Turkey and CaO

description: Induction furnace IF75 Time-temperature: Bauxite from Turkey and CaO
DOI: 10.5281/zenodo.4587447
title: Time-temperature: Bauxite from Turkey and CaO

description: Induction furnace IF75 Time-temperature: Bauxite from Turkey and CaO
DOI: 10.6084/m9.figshare.14175401
title: LattanzioBuontempo_Herpetologica - Raw Data and R Code

description: Raw Data and R Code from 'Ecogeographic Divergence Linked to Dorsal Coloration in Eastern Hog-nosed Snakes (<i>Heterodon platirhinos</i>)' by Matthew S. Lattanzio and Michael J. Buontempo.
DOI: 10.6084/m9.figshare.3761562.v1797
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.5281/zenodo.4587487
title: CoVaxxy Tweet IDs data set

description: A collection of Tweet IDs related to Covid-19 Vaccines, gathered from Twitter since Jan 4, 2021. Please see https://arxiv.org/abs/2101.07694 for more information.
DOI: 10.5281/zenodo.4584645
title: Dataset accompanying the paper "Enhancing Euro NCAP Standards with Metamorphic Testing for Verification of Advanced Driver-Assistance Systems"

description: These labpackage files are open for interested readers and researchers to validate, replicate and extend our following paper: M. Iqbal, J. C. Han, Z. Q. Zhou, and D. Towey, “Enhancing Euro NCAP standards with metamorphic testing for verification of advanced driver-assistance systems,” in Proceedings of the IEEE/ACM 6th International Workshop on Metamorphic Testing (MET ’21), in conjunction with the 43rd International Conference on Software Engineering (ICSE ’21), 2021. Here is the abstract of our paper: ADASs have become increasingly popular. To ensure their safety, simulation testing is essential. In this research, we conducted a case study to investigate the fault- detection effectiveness of existing ADAS testing standards: We tested the Lane Keeping Assist System(LKAS), which is a prebuilt ADAS module of MATLAB and Simulink. We first tested LKAS using the European New Car Assessment Programme (Euro NCAP) that contains 40 prebuilt driving scenarios in MATLAB. Our results show that none of the 40 scenarios detected any failure. We then continued the tests by applying a simple metamorphic relation“equivalence under geometric transformation,” and a previously unknown real-life bug in LKAS was immediately revealed. We reported this finding to the MATLAB team in the US, who then confirmed the bug and corrected the LKAS code. This research provides a strong case for incorporating metamorphic testing into ADAS testing standards and protocols. Please refer to the README.pdf file for further instructions on the usage of our test data.
DOI: 10.5281/zenodo.4584644
title: Dataset accompanying the paper "Enhancing Euro NCAP Standards with Metamorphic Testing for Verification of Advanced Driver-Assistance Systems"

description: These labpackage files are open for interested readers and researchers to validate, replicate and extend our following paper: M. Iqbal, J. C. Han, Z. Q. Zhou, and D. Towey, “Enhancing Euro NCAP standards with metamorphic testing for verification of advanced driver-assistance systems,” in Proceedings of the IEEE/ACM 6th International Workshop on Metamorphic Testing (MET ’21), in conjunction with the 43rd International Conference on Software Engineering (ICSE ’21), 2021. Here is the abstract of our paper: ADASs have become increasingly popular. To ensure their safety, simulation testing is essential. In this research, we conducted a case study to investigate the fault- detection effectiveness of existing ADAS testing standards: We tested the Lane Keeping Assist System(LKAS), which is a prebuilt ADAS module of MATLAB and Simulink. We first tested LKAS using the European New Car Assessment Programme (Euro NCAP) that contains 40 prebuilt driving scenarios in MATLAB. Our results show that none of the 40 scenarios detected any failure. We then continued the tests by applying a simple metamorphic relation“equivalence under geometric transformation,” and a previously unknown real-life bug in LKAS was immediately revealed. We reported this finding to the MATLAB team in the US, who then confirmed the bug and corrected the LKAS code. This research provides a strong case for incorporating metamorphic testing into ADAS testing standards and protocols. Please refer to the README.pdf file for further instructions on the usage of our test data.
DOI: 10.3886/e116215v1-80680
title: Replication data for: The Effects of Rent Control Expansion on Tenants, Landlords, and Inequality: Evidence from San Francisco

description: Using a 1994 law change, we exploit quasi-experimental variation in the assignment of rent control in San Francisco to study its impacts on tenants and landlords. Leveraging new data tracking individuals' migration, we find rent control limits renters' mobility by 20 percent and lowers displacement from San Francisco. Landlords treated by rent control reduce rental housing supplies by 15 percent by selling to owner-occupants and redeveloping buildings. Thus, while rent control prevents displacement of incumbent renters in the short run, the lost rental housing supply likely drove up market rents in the long run, ultimately undermining the goals of the law.
DOI: 10.6084/m9.figshare.12853362.v1
title: <i>In silico</i> designing of multi-epitope vaccine construct against human coronavirus infections

description: Single stranded RNA viruses were known to cause variety of diseases since many years and are gaining much importance due to pandemic after the identification of a novel corona virus (severe acute respiratory syndrome-coronavirus (SARS-CoV-2)). Seven coronaviruses (CoVs) are known to infect humans and they are OC43 CoV, NL63 CoV, HKU1 CoV, Middle East respiratory syndrome, SARS CoV, and SARS CoV-2. Virus replication weakens the immune system of host thereby altering T-cell count and much of interferon response. Although no vaccine or therapeutic treatment has been approved till now for CoV infection, trials of vaccine against SARS CoV-2 are in progress. One of the epitopes used for vaccine production is of the spike protein on the surface of virus. The work focuses on designing of multi-epitope vaccine construct for treatment of seven human CoV infections using the epitopes present on the spike protein of human CoVs. To address this, immuno-informatics techniques have been employed to design multi-epitope vaccine construct. B- and T-cell epitopes of the spike proteins have been predicted and designed into a multi-epitope vaccine construct. The tertiary structure of the vaccine construct along with the adjuvant has been modelled and the physiochemical properties have been predicted. The multi-epitope vaccine construct has antigenic and non-allergenic property. After validation, refinement and disulphide engineering of the vaccine construct, molecular docking with toll-like receptors (TLRs) have been performed. Molecular dynamics simulation in aqueous environment predicted that the vaccine-TLRs complexes were stable. The vaccine construct is predicted to be able to trigger primary immune response <i>in silico</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853359
title: Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study

description: The spread of novel coronavirus strain, Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) causes Coronavirus disease (COVID-19) has now spread worldwide and effecting the entire human race. The viral genetic material is transcripted and replicated by 3 C-like protease, as a result, it is an important drug target for COVID-19. Hydroxychloroquine (HCQ) report promising results against this drug target so, we perform molecular docking followed by MD-simulation studies of HCQ and modelled some ligand (Mod-I and Mod-II) molecules with SARS-CoV-2-main protease which reveals the structural organization of the active site residues and presence of a conserve water-mediated catalytic triad that helps in the recognition of Mod-I/II ligand molecules. The study may be helpful to gain a detailed structural insight on the presence of water-mediated catalytic triad which could be useful for inhibitor modelling. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853359.v1
title: Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study

description: The spread of novel coronavirus strain, Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) causes Coronavirus disease (COVID-19) has now spread worldwide and effecting the entire human race. The viral genetic material is transcripted and replicated by 3 C-like protease, as a result, it is an important drug target for COVID-19. Hydroxychloroquine (HCQ) report promising results against this drug target so, we perform molecular docking followed by MD-simulation studies of HCQ and modelled some ligand (Mod-I and Mod-II) molecules with SARS-CoV-2-main protease which reveals the structural organization of the active site residues and presence of a conserve water-mediated catalytic triad that helps in the recognition of Mod-I/II ligand molecules. The study may be helpful to gain a detailed structural insight on the presence of water-mediated catalytic triad which could be useful for inhibitor modelling. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853368
title: A comparative pan-genomic analysis of 53 <i>C. pseudotuberculosis</i> strains based on functional domains

description: <i>Corynebacterium pseudotuberculosis</i> is a pathogenic bacterium with great veterinary and economic importance. It is classified into two biovars: <i>ovis</i>, nitrate-negative, that causes lymphadenitis in small ruminants and <i>equi</i>, nitrate-positive, causing ulcerative lymphangitis in equines. With the explosive growth of available genomes of several strains, pan-genome analysis has opened new opportunities for understanding the dynamics and evolution of <i>C. pseudotuberculosis</i>. However, few pan-genomic studies have compared biovars <i>equi</i> and <i>ovis.</i> Such studies have considered a reduced number of strains and compared entire genomes. Here we conducted an original pan-genome analysis based on protein sequences and their functional domains. We considered 53 <i>C. pseudotuberculosis</i> strains from both biovars isolated from different hosts and countries. We have analysed conserved domains, common domains more frequently found in each biovar and biovar-specific (unique) domains. Our results demonstrated that biovar <i>equi</i> is more variable; there is a significant difference in the number of proteins per strains, probably indicating the occurrence of more gene loss/gain events. Moreover, strains of biovar <i>equi</i> presented a higher number of biovar-specific domains, 77 against only eight in biovar <i>ovis</i>, most of them are associated with virulence mechanisms. With this domain analysis, we have identified functional differences among strains of biovars <i>ovis</i> and <i>equi</i> that could be related to niche-adaptation and probably help to better understanding mechanisms of virulence and pathogenesis. The distribution patterns of functional domains identified in this work might have impacts on bacterial physiology and lifestyle, encouraging the development of new diagnoses, vaccines, and treatments for <i>C. pseudotuberculosis</i> diseases. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853368.v1
title: A comparative pan-genomic analysis of 53 <i>C. pseudotuberculosis</i> strains based on functional domains

description: <i>Corynebacterium pseudotuberculosis</i> is a pathogenic bacterium with great veterinary and economic importance. It is classified into two biovars: <i>ovis</i>, nitrate-negative, that causes lymphadenitis in small ruminants and <i>equi</i>, nitrate-positive, causing ulcerative lymphangitis in equines. With the explosive growth of available genomes of several strains, pan-genome analysis has opened new opportunities for understanding the dynamics and evolution of <i>C. pseudotuberculosis</i>. However, few pan-genomic studies have compared biovars <i>equi</i> and <i>ovis.</i> Such studies have considered a reduced number of strains and compared entire genomes. Here we conducted an original pan-genome analysis based on protein sequences and their functional domains. We considered 53 <i>C. pseudotuberculosis</i> strains from both biovars isolated from different hosts and countries. We have analysed conserved domains, common domains more frequently found in each biovar and biovar-specific (unique) domains. Our results demonstrated that biovar <i>equi</i> is more variable; there is a significant difference in the number of proteins per strains, probably indicating the occurrence of more gene loss/gain events. Moreover, strains of biovar <i>equi</i> presented a higher number of biovar-specific domains, 77 against only eight in biovar <i>ovis</i>, most of them are associated with virulence mechanisms. With this domain analysis, we have identified functional differences among strains of biovars <i>ovis</i> and <i>equi</i> that could be related to niche-adaptation and probably help to better understanding mechanisms of virulence and pathogenesis. The distribution patterns of functional domains identified in this work might have impacts on bacterial physiology and lifestyle, encouraging the development of new diagnoses, vaccines, and treatments for <i>C. pseudotuberculosis</i> diseases. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12853371
title: Computational studies on bacterial secondary metabolites against breast cancer

description: Microbes exist in the human body provide more benefits by modulating metabolic processes, immunity, and signal transduction. However, microbial dysbiosis with harmful bacterial species can cause chronic inflammation and cancers. Hence human probiotics were recently paid more attention to immune responses, therapy, and diagnosis. Breast cancer is the second leading cancer worldwide and causes more death in women. The role of breast microbiome secondary metabolites in breast cancer is poorly studied. Research shows that breast has a specific microbiome inhabited with particular bacterial species. More significantly probiotics produced from breast microbiomes may act as a potential biomarker for breast cancer diagnosis. Hence this computational research aimed at the effect of chosen metabolites on breast cancer cell receptor G-protein-coupled bile acid receptor, Gpbar1 (<i>TGR5</i>). The current research suggested that cadaverine, succinate, <i>p</i>-cresol, and its derivatives could be used as a molecular marker in the diagnosis of breast cancer.
DOI: 10.6084/m9.figshare.12853371.v1
title: Computational studies on bacterial secondary metabolites against breast cancer

description: Microbes exist in the human body provide more benefits by modulating metabolic processes, immunity, and signal transduction. However, microbial dysbiosis with harmful bacterial species can cause chronic inflammation and cancers. Hence human probiotics were recently paid more attention to immune responses, therapy, and diagnosis. Breast cancer is the second leading cancer worldwide and causes more death in women. The role of breast microbiome secondary metabolites in breast cancer is poorly studied. Research shows that breast has a specific microbiome inhabited with particular bacterial species. More significantly probiotics produced from breast microbiomes may act as a potential biomarker for breast cancer diagnosis. Hence this computational research aimed at the effect of chosen metabolites on breast cancer cell receptor G-protein-coupled bile acid receptor, Gpbar1 (<i>TGR5</i>). The current research suggested that cadaverine, succinate, <i>p</i>-cresol, and its derivatives could be used as a molecular marker in the diagnosis of breast cancer.
DOI: 10.6084/m9.figshare.12932819
title: Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting

description: The genomic ssRNA of coronaviruses is packaged within a helical nucleocapsid. Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Such signals coordinated with the nucleocapsid helical structure were detected and reconstructed in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2. The main period of the signals for both viruses was about 54 nt, that implies 6.75 nt per N protein. The complete coverage of the ssRNA genome of length about 30,000 nt by the nucleocapsid would need 4.4 × 10<sup>3</sup> N proteins, that makes them the most abundant among the structural proteins. The repertoires of motifs for SARS-CoV and SARS-CoV-2 were divergent but nearly coincided for different isolates of SARS-CoV-2. We obtained the distributions of assembly/packaging signals over the genomes with nonoverlapping windows of width 432 nt. Finally, using the spectral entropy, we compared the load from point mutations and indels during virus age for SARS-CoV and SARS-CoV-2. We found the higher mutational load on SARS-CoV. In this sense, SARS-CoV-2 can be treated as a ‘newborn’ virus. These observations may be helpful in practical medical applications and are of basic interest. Communicated by Ramaswamy H. Sarma