cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5224960
title: Supplementary Material for: Extracellular DNA Contributes to Dental Biofilm Stability

description: Extracellular DNA (eDNA) is a major matrix component of many bacterial biofilms. While the presence of eDNA and its role in biofilm stability have been demonstrated for several laboratory biofilms of oral bacteria, there is no data available on the presence and function of eDNA in in vivo grown dental biofilms. This study aimed to determine whether eDNA was part of the matrix in biofilms grown in situ in the absence of sucrose and whether treatment with DNase dispersed biofilms grown for 2.5, 5, 7.5, 16.5, or 24 h. Three hundred biofilms from 10 study participants were collected and treated with either DNase or heat-inactivated DNase for 1 h. The bacterial biovolume was determined with digital image analysis. Staining with TOTO®-1 allowed visualization of eDNA both on bacterial cell surfaces and, with a cloud-like appearance, in the intercellular space. DNase treatment strongly reduced the amount of biofilm in very early stages of growth (up to 7.5 h), but the treatment effect decreased with increasing biofilm age. This study proves the involvement of eDNA in dental biofilm formation and its importance for biofilm stability in the earliest stages. Further research is required to uncover the interplay of eDNA and other matrix components and to explore the therapeutic potential of DNase treatment for biofilm control.
DOI: 10.6084/m9.figshare.5224933
title: Charlock mustard (<i>Sinapis arvensis</i>): a weed reservoir for begomoviruses and associated betasatellite in Jordan

description: Four crop-infecting begomoviruses were found naturally affecting Charlock mustard (<i>Sinapis arvensis</i> L.) plants in Jordan and characterized at the molecular level. Symptoms included leaf curling and stunting. PCR analysis showed the presence of <i>Tomato yellow leaf curl virus</i> (TYLCV), <i>Tomato yellow leaf curl Sardinia virus</i> (TYLCSV), <i>Squash leaf curl virus</i> (SLCV) and <i>Watermelon chlorotic stunt virus</i> (WmCSV). These viruses were associated with Cotton leaf curl Gezira betasatellite (CLCuGβ). Sequence analysis revealed that TYLCV and TYLCSV had 98.5% and 99.3% nucleotide (nt) sequence identities with a previously described TYLCV strain from Florida and TYLCSV from Sardinia, respectively. The other two viruses, SLCV and WmCSV, shared 99.7% and 99.5% nt identities with previously described strains from Jordan. Sequence analysis also showed that CLCuGβ had 98.8% nt identity with a strain from Israel. To our knowledge, this is the first report of <i>S. arvensis</i> as a natural host of SLCV, WmCSV, TYLCSV and CLCuGβ.
DOI: 10.6084/m9.figshare.5224960.v1
title: Supplementary Material for: Extracellular DNA Contributes to Dental Biofilm Stability

description: Extracellular DNA (eDNA) is a major matrix component of many bacterial biofilms. While the presence of eDNA and its role in biofilm stability have been demonstrated for several laboratory biofilms of oral bacteria, there is no data available on the presence and function of eDNA in in vivo grown dental biofilms. This study aimed to determine whether eDNA was part of the matrix in biofilms grown in situ in the absence of sucrose and whether treatment with DNase dispersed biofilms grown for 2.5, 5, 7.5, 16.5, or 24 h. Three hundred biofilms from 10 study participants were collected and treated with either DNase or heat-inactivated DNase for 1 h. The bacterial biovolume was determined with digital image analysis. Staining with TOTO®-1 allowed visualization of eDNA both on bacterial cell surfaces and, with a cloud-like appearance, in the intercellular space. DNase treatment strongly reduced the amount of biofilm in very early stages of growth (up to 7.5 h), but the treatment effect decreased with increasing biofilm age. This study proves the involvement of eDNA in dental biofilm formation and its importance for biofilm stability in the earliest stages. Further research is required to uncover the interplay of eDNA and other matrix components and to explore the therapeutic potential of DNase treatment for biofilm control.
DOI: 10.6084/m9.figshare.5224936.v1
title: Solar Stormwatch 'Track-it-back' Catalogue

description: A catalogue of CMEs tracking events through the SECCHI COR2, COR1 and EUVI imagers on board NASA's twin STEREO spacecraft, created using data from the 'Track-it-back' activity of the Solar Stormwatch project.<br>
DOI: 10.6084/m9.figshare.5224900
title: cif file of (P)-1-aza[6]helicene, (rac)-N-Methyl-1-aza[6]helicene tetrafluoroborate and (P)-N-Methyl-1-aza[6]helicene tetrafluoroborate

description: cif file of (P)-1-aza[6]helicene (CCDC 921948), (rac)-N-Methyl-1-aza[6]helicene tetrafluoroborate (CCDC 921949) and (P)-N-Methyl-1-aza[6]helicene tetrafluoroborate (CCDC 921950).
DOI: 10.6084/m9.figshare.5224933.v1
title: Charlock mustard (<i>Sinapis arvensis</i>): a weed reservoir for begomoviruses and associated betasatellite in Jordan

description: Four crop-infecting begomoviruses were found naturally affecting Charlock mustard (<i>Sinapis arvensis</i> L.) plants in Jordan and characterized at the molecular level. Symptoms included leaf curling and stunting. PCR analysis showed the presence of <i>Tomato yellow leaf curl virus</i> (TYLCV), <i>Tomato yellow leaf curl Sardinia virus</i> (TYLCSV), <i>Squash leaf curl virus</i> (SLCV) and <i>Watermelon chlorotic stunt virus</i> (WmCSV). These viruses were associated with Cotton leaf curl Gezira betasatellite (CLCuGβ). Sequence analysis revealed that TYLCV and TYLCSV had 98.5% and 99.3% nucleotide (nt) sequence identities with a previously described TYLCV strain from Florida and TYLCSV from Sardinia, respectively. The other two viruses, SLCV and WmCSV, shared 99.7% and 99.5% nt identities with previously described strains from Jordan. Sequence analysis also showed that CLCuGβ had 98.8% nt identity with a strain from Israel. To our knowledge, this is the first report of <i>S. arvensis</i> as a natural host of SLCV, WmCSV, TYLCSV and CLCuGβ.
DOI: 10.6084/m9.figshare.5224609
title: Supplementary Material for: Liquid Biopsy: Value for Melanoma Therapy?

description: Treatment of metastatic melanoma has undergone tremendous changes over the past few years. There are now highly effective systemic therapies available: targeted therapy with BRAF and MEK inhibitors in BRAF-V600-mutant melanoma and immunotherapies, including PD-1 antibodies with or without CTLA-4 antibody, that can be used regardless of mutational status. However, long-term tumor control is only achieved in a minority of patients. Liquid biopsy using circulating tumor cells, circulating tumor DNA (ctDNA), circulating mRNA and micro-RNA might represent valuable biomarkers, e.g. in the setting of systemic treatment for metastatic melanoma. Pre-treatment detection of BRAF V600-mutant ctDNA has been shown to be a prognostic factor in patients receiving BRAF/MEK inhibitor treatment. Furthermore, monitoring of ctDNA of known driver mutations can be used for treatment monitoring and detection of acquired resistance. However, results of the currently available studies need to be interpreted with caution as multiple approaches were used that are hardly comparable. So far, even with advancement of methods, there are only prognostic but no predictive biomarkers available.
DOI: 10.6084/m9.figshare.5224612
title: ECD of monomer and dimer, calculated spectra and dynamic switching

description: Dataset that includes ECD data recorded for pyridinium helicene monomer & dimer plus switching between both states. Also included are individual ECD spectra calculated for different dimers, as well as their (scaled) average.
DOI: 10.6084/m9.figshare.5224603
title: The decline of an urban Hooded Vulture <i>Necrosyrtes monachus</i> population in Dakar, Senegal, over 50 years<sup>§</sup>

description: As in many West African cities, in Dakar Hooded Vultures <i>Necrosyrtes monachus</i> have always been characteristic urban scavengers. The recent decline of Hooded Vultures in other parts of Africa, mainly eastern Africa, has been the reason in 2015 for up-listing of its status by the IUCN in the Red List of Threatened Species to Critically Endangered. As the Hooded Vulture is still common in the Lower Casamance, Senegal, in the Western Region of The Gambia and in Guinea-Bissau, without clear signs of a recent decrease, a survey of its current status in Dakar was undertaken and compared with historical data over the past 50 years. A strong decrease of &gt;85% was noted from 3 000 individuals in 1969 to 400 in 2016. This decline is on the high end of the decline noticed over much of its range but in striking contrast with the apparently stable populations along the West African coast more to the south (The Gambia to Guinea). Likely causes are (1) exponential urbanisation resulting in loss of feeding sites and reduced food availability, (2) increased poisoning of feral dogs with strychnine sulphate due to an upsurge of rabies and (3) increased disappearance of suitable trees for nesting and roosting.
DOI: 10.6084/m9.figshare.5224603.v1
title: The decline of an urban Hooded Vulture <i>Necrosyrtes monachus</i> population in Dakar, Senegal, over 50 years<sup>§</sup>

description: As in many West African cities, in Dakar Hooded Vultures <i>Necrosyrtes monachus</i> have always been characteristic urban scavengers. The recent decline of Hooded Vultures in other parts of Africa, mainly eastern Africa, has been the reason in 2015 for up-listing of its status by the IUCN in the Red List of Threatened Species to Critically Endangered. As the Hooded Vulture is still common in the Lower Casamance, Senegal, in the Western Region of The Gambia and in Guinea-Bissau, without clear signs of a recent decrease, a survey of its current status in Dakar was undertaken and compared with historical data over the past 50 years. A strong decrease of &gt;85% was noted from 3 000 individuals in 1969 to 400 in 2016. This decline is on the high end of the decline noticed over much of its range but in striking contrast with the apparently stable populations along the West African coast more to the south (The Gambia to Guinea). Likely causes are (1) exponential urbanisation resulting in loss of feeding sites and reduced food availability, (2) increased poisoning of feral dogs with strychnine sulphate due to an upsurge of rabies and (3) increased disappearance of suitable trees for nesting and roosting.
DOI: 10.6084/m9.figshare.5224612.v1
title: ECD of monomer and dimer, calculated spectra and dynamic switching

description: Dataset that includes ECD data recorded for pyridinium helicene monomer & dimer plus switching between both states. Also included are individual ECD spectra calculated for different dimers, as well as their (scaled) average.
DOI: 10.6084/m9.figshare.5224534
title: Data file 4 from Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions

description: Calculation of Vcmax and Jmax using the data presented in Figure 3.
DOI: 10.6084/m9.figshare.5224531
title: Data file 3 from Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions

description: The raw data output from the Licor 6400 for results presented in Figure 4.
DOI: 10.6084/m9.figshare.5224534.v1
title: Data file 4 from Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions

description: Calculation of Vcmax and Jmax using the data presented in Figure 3.
DOI: 10.6084/m9.figshare.5224528
title: Data file 5 from Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions

description: To meet the growing demand for food, substantial improvements in yields are needed. This is particularly the case for wheat, where global yield has stagnated in recent years. Increasing photosynthesis has been identified as a primary target to achieve yield improvements. To increase leaf photosynthesis in wheat, the level of the Calvin–Benson cycle enzyme sedoheptulose-1,7-biphosphatase (SBPase) has been increased through transformation and expression of a <i>Brachypodium distachyon</i> SBPase gene construct. Transgenic lines with increased SBPase protein levels and activity were grown under greenhouse conditions and showed enhanced leaf photosynthesis and increased total biomass and dry seed yield. This showed the potential of improving yield potential by increasing leaf photosynthesis in a crop species such as wheat. The results are discussed with regards to future strategies for further improvement of photosynthesis in wheat.This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
DOI: 10.6084/m9.figshare.5224531.v1
title: Data file 3 from Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions

description: The raw data output from the Licor 6400 for results presented in Figure 4.
DOI: 10.6084/m9.figshare.5224525
title: Data file 1 from Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions

description: The raw data output from the Licor 6400 for results presented in Figure 3.
DOI: 10.6084/m9.figshare.5224519
title: Data file 2 from Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions

description: Calculation of Vcmax and Jmax using the data presented in Figure 3.
DOI: 10.6084/m9.figshare.5224525.v1
title: Data file 1 from Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions

description: The raw data output from the Licor 6400 for results presented in Figure 3.
DOI: 10.6084/m9.figshare.5224528.v1
title: Data file 5 from Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions

description: To meet the growing demand for food, substantial improvements in yields are needed. This is particularly the case for wheat, where global yield has stagnated in recent years. Increasing photosynthesis has been identified as a primary target to achieve yield improvements. To increase leaf photosynthesis in wheat, the level of the Calvin–Benson cycle enzyme sedoheptulose-1,7-biphosphatase (SBPase) has been increased through transformation and expression of a <i>Brachypodium distachyon</i> SBPase gene construct. Transgenic lines with increased SBPase protein levels and activity were grown under greenhouse conditions and showed enhanced leaf photosynthesis and increased total biomass and dry seed yield. This showed the potential of improving yield potential by increasing leaf photosynthesis in a crop species such as wheat. The results are discussed with regards to future strategies for further improvement of photosynthesis in wheat.This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
DOI: 10.6084/m9.figshare.5224501
title: Text-mined disease–lifestyle associations

description: Diseases–lifestyle associations text mined from PubMed abstracts. The associations were filtered to include only those with a z-score greater than 3 and related to ICD-10 level 3.
DOI: 10.6084/m9.figshare.5224501.v1
title: Text-mined disease–lifestyle associations

description: Diseases–lifestyle associations text mined from PubMed abstracts. The associations were filtered to include only those with a z-score greater than 3 and related to ICD-10 level 3.
DOI: 10.6084/m9.figshare.5224519.v1
title: Data file 2 from Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions

description: Calculation of Vcmax and Jmax using the data presented in Figure 3.
DOI: 10.6084/m9.figshare.5224456
title: Dynamic programming and mixed integer programming based algorithms for the online glass cutting problem with defects and production targets

description: In flat glass manufacturing, glass products of various dimensions are cut from a glass ribbon that runs continuously on a conveyor belt. Placement of glass products on the glass ribbon is restricted by the defects of varying severity located on the ribbon as well as the quality grades of the products to be cut. In addition to cutting products, a common practice is to remove defective parts of the glass ribbon as scrap glass. As the glass ribbon moves continuously, cutting decisions need to be made within seconds, which makes this online problem very challenging. A simplifying assumption is to limit scrap cuts to those made immediately behind a defect (a cut-behind-fault or CBF). We propose an online algorithm for the glass cutting problem that solves a series of static cutting problems over a rolling horizon. We solve the static problem using two methods: a dynamic programming algorithm (DP) that utilises the CBF assumption and a mixed integer programming (MIP) formulation with no CBF restriction. While both methods improve the process yield substantially, the results indicate that MIP significantly outperforms DP, which suggests that the computational benefit of the CBF assumption comes at a cost of inferior solution quality.
DOI: 10.6084/m9.figshare.5224456.v1
title: Dynamic programming and mixed integer programming based algorithms for the online glass cutting problem with defects and production targets

description: In flat glass manufacturing, glass products of various dimensions are cut from a glass ribbon that runs continuously on a conveyor belt. Placement of glass products on the glass ribbon is restricted by the defects of varying severity located on the ribbon as well as the quality grades of the products to be cut. In addition to cutting products, a common practice is to remove defective parts of the glass ribbon as scrap glass. As the glass ribbon moves continuously, cutting decisions need to be made within seconds, which makes this online problem very challenging. A simplifying assumption is to limit scrap cuts to those made immediately behind a defect (a cut-behind-fault or CBF). We propose an online algorithm for the glass cutting problem that solves a series of static cutting problems over a rolling horizon. We solve the static problem using two methods: a dynamic programming algorithm (DP) that utilises the CBF assumption and a mixed integer programming (MIP) formulation with no CBF restriction. While both methods improve the process yield substantially, the results indicate that MIP significantly outperforms DP, which suggests that the computational benefit of the CBF assumption comes at a cost of inferior solution quality.
DOI: 10.15128/r1g732d901w
title: Nanostructured alkali-metal vapor cells [dataset]

description: Open access datasets used in the Physical Review Applied manuscript entitled "Nanostructured alkali-metal vapor cells".
description: Laser spectroscopy.
DOI: 10.6084/m9.figshare.5223928
title: Air Traffic Management Case Study SecBPMN2 models

description: The bpmn models that are provided in <em>my.example</em> directory represnts a SecBPMN2 models for our <em>Air Traffic Management System</em> case study. Please note that you can not open or modify these models directly from your Eclipse. These models are designed by using the Socio-Technical-System (STS) tool. To view and modify these bpmn models please follow the provided in the README file.
DOI: 10.6084/m9.figshare.5223928.v1
title: Air Traffic Management Case Study SecBPMN2 models

description: The bpmn models that are provided in <em>my.example</em> directory represnts a SecBPMN2 models for our <em>Air Traffic Management System</em> case study. Please note that you can not open or modify these models directly from your Eclipse. These models are designed by using the Socio-Technical-System (STS) tool. To view and modify these bpmn models please follow the provided in the README file.
DOI: 10.6084/m9.figshare.5223901
title: Dataset for: Meta-analytical synthesis of regression coefficients under different categorization scheme of continuous covariates

description: Recently, the number of clinical prediction models sharing the same regression task has increased in the medical literature. However, evidence synthesis methodologies that utilize the results of these regression models have not been sufficiently studied, particularly in meta-analysis settings where only regression coefficients are available. One of the difficulties lies in the differences between the categorization schemes of continuous covariates across different studies. In general, categorization methods using cutoff-values are study-specific across available models, even if they focus on the same covariates of interest. Differences in the categorization of covariates could lead to serious bias in the estimated regression coefficients, and thus in subsequent syntheses. To tackle this issue, we developed synthesis methods for linear regression models with different categorization schemes of covariates. A two-step approach to aggregate the regression coefficient estimates is proposed. The first step is to estimate the joint distribution of covariates by introducing a latent sampling distribution, which uses one set of individual participant data to estimate the marginal distribution of covariates with categorization. The second step is to use a non-linear mixed-effects model with correction terms for the bias due to categorization to estimate the overall regression coefficients. Especially in terms of precision, numerical simulations show that our approach outperforms conventional methods, which only use studies with common covariates or ignore the differences between categorization schemes. The method developed in this study is also applied to a series of WHO epidemiologic studies on white blood cell counts.
DOI: 10.6084/m9.figshare.5223898
title: README

description: In this link, we present an information about usage of the artifact submission for our paper of the same name, to be presented at the MoDELS conference 2017 in Austin, TX. Our submission includes the model transformation from SecBPMN2 to UMLsec models as well as four examples models from the Air Traffic Management System case study. We explain the process of using the transformation, and the verification of the generated UMLsec models using the CARiSMA tool.
DOI: 10.6084/m9.figshare.5223901.v1
title: Dataset for: Meta-analytical synthesis of regression coefficients under different categorization scheme of continuous covariates

description: Recently, the number of clinical prediction models sharing the same regression task has increased in the medical literature. However, evidence synthesis methodologies that utilize the results of these regression models have not been sufficiently studied, particularly in meta-analysis settings where only regression coefficients are available. One of the difficulties lies in the differences between the categorization schemes of continuous covariates across different studies. In general, categorization methods using cutoff-values are study-specific across available models, even if they focus on the same covariates of interest. Differences in the categorization of covariates could lead to serious bias in the estimated regression coefficients, and thus in subsequent syntheses. To tackle this issue, we developed synthesis methods for linear regression models with different categorization schemes of covariates. A two-step approach to aggregate the regression coefficient estimates is proposed. The first step is to estimate the joint distribution of covariates by introducing a latent sampling distribution, which uses one set of individual participant data to estimate the marginal distribution of covariates with categorization. The second step is to use a non-linear mixed-effects model with correction terms for the bias due to categorization to estimate the overall regression coefficients. Especially in terms of precision, numerical simulations show that our approach outperforms conventional methods, which only use studies with common covariates or ignore the differences between categorization schemes. The method developed in this study is also applied to a series of WHO epidemiologic studies on white blood cell counts.