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- ItemCurvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data(Amsterdam [u.a.] : Elsevier, 2022) John, Torsten; Martin, Lisandra L.; Risselada, Herre Jelger; Abel, BerndNanostructured surfaces are widespread in nature and are being further developed in materials science. This makes them highly relevant for biomolecules, such as peptides. In this data article, we present a curvature model and molecular dynamics (MD) simulation data on the influence of nanoparticle size on the stability of amyloid peptide fibrils related to our research article entitled “Mechanistic insights into the size-dependent effects of nanoparticles on inhibiting and accelerating amyloid fibril formation” (John et al., 2022) [1]. We provide the code to perform MD simulations in GROMACS 4.5.7 software of arbitrarily chosen biomolecule oligomers adsorbed on a curved surface of chosen nanoparticle size. We also provide the simulation parameters and data for peptide oligomers of Aß40, NNFGAIL, GNNQQNY, and VQIYVK. The data provided allows researchers to further analyze our MD simulations and the curvature model allows for a better understanding of oligomeric structures on surfaces.
- ItemGrain-size distribution dataset of supercritical flow sediments from a Gilbert-type delta that are associated with disaggregation bands(Amsterdam [u.a.] : Elsevier, 2022) Tanner, David C.; Brandes, Christian; Winsemann, JuttaThis is a dataset of grain-size distribution in sub- and supercritical flow sediments of a Gilbert-type delta from an outcrop in North Germany. Thirteen samples of ca 2.5 kg were dried (at 105°C), and homogenised twice with a sample divider. A representative sample of 1-2 g was then analysed using laser diffraction. The grain-size distribution of the sand has a maximum between fine to medium sand, with a long fine fraction tail down to 0.06 µm and occasional coarse fractions (up to 1.5 mm) in some samples. Specific grain-size distributions correlate with the different sedimentary bedforms from which the samples were taken. This data is important for two reasons: Firstly, sedimentary structures formed by Froude supercritical flows are controlled by grain-size. However, few studies have provided grain-size datasets from the natural record, which often have a much wider grain-size distribution than experimentally-produced supercritical flow deposits. Secondly, the sands were deformed subsequently by disaggregation bands, a type of geological fault that only develops in porous granular materials, i.e. well-sorted, medium sand. The disaggregation bands are indicative of seismic or even aseismic, creeping movement of basement faults.
- ItemGlobal and country-level data of the biodiversity footprints of 175 crops and pasture(Amsterdam [u.a.] : Elsevier, 2021) Beyer, Robert; Manica, AndreaThe destruction of natural habitat for cropland and pasture represents a major threat to global biodiversity. Despite widespread societal concern about biodiversity loss associated with food production, consumer access to quantitative estimates of the impact of crop production on the world's species has been very limited compared to assessments of other environmental variables such as greenhouse gas emissions or water use. Here, we present a consistent dataset of the biodiversity footprints of pasture and 175 crops at the global and national level. The data were generated by combining maps of the global distribution of agricultural areas in the year 2000 with spatially explicit estimates of the biodiversity loss associated with the conversion of natural habitat to farmland. Estimates were derived for three common alternative measures of biodiversity - species richness, threatened species richness, and range rarity - of the world's mammals, birds, and amphibians. Our dataset provides important quantitative information for food consumers and policy makers, allowing them to take evidence-based decisions to reduce the biodiversity footprint of global food production.
- ItemAn extended hybrid input-output model applied to fossil- and bio-based plastics(Amsterdam [u.a.] : Elsevier, 2021) Jander, WiebkeMatrix augmentation method is developed further and described transparently for enabling more specific input-output analyses of bio- vs. fossil-based sectors. A number of economic and environmental effects of substitution can be estimated, compared, and managed. While the model was applied for the first time to the German plastics industry, it can be well integrated into existing bioeconomy monitorings to represent substitution in sectors and countries. • Original matrix augmentation method is described in much detail for the first time considering available data for bio- and fossil-based industries. • Particular attention is paid to balancing cost and benefit in model building so that indicators can be integrated in a continuous monitoring of the bioeconomy. Hence, industry data is prefered to process data whenever possible. • Input structures of bio-based imports are considered in single-region input-output analysis.
- ItemIntegrative programming for simulation of packaging headspace and shelf life of fresh produce(Amsterdam [u.a.] : Elsevier, 2021) Jalali, Ali; Linke, Manfred; Geyer, Martin; Mahajan, PramodFresh horticultural products are exposed to different environmental conditions from farm to fork. Barrier properties of packaging and physiological behaviour of produce, namely respiration and transpiration can affect headspace conditions surrounding produce and consequently remaining shelf life. Packaging material also plays a role in heat and mass transfer, such as thermal conduction and permeation of O2, CO2 and water vapour. All of these behaviours are integrated together in the form of ordinary differential equations and solved using numerical methods in MATLAB. • The simulation program is useful for designing the size and number of perforations to achieve equilibrium modified atmosphere alone or in combination with packaging material having a higher water transmission rate or active moisture absorber. • The simulation program is also useful for predicting the shelf life of fresh produce under the actual supply chain conditions. • The simulation program provides a flexible system to input predefined supply chain conditions and the properties of fresh produce and packaging material, thus, minimizing the costly and time consuming experimental procedures for selecting the optimum packaging material for fresh produce.
- ItemQuantifying sustainable intensification of agriculture: The contribution of metrics and modelling(Amsterdam [u.a.] : Elsevier, 2021) Mouratiadou, Ioanna; Latka, Catharina; van der Hilst, Floor; Müller, Christoph; Berges, Regine; Bodirsky, Benjamin Leon; Ewert, Frank; Faye, Babacar; Heckelei, Thomas; Hoffmann, Munir; Lehtonen, Heikki; Lorite, Ignacio Jesus; Nendel, Claas; Palosuo, Taru; Rodríguez, Alfredo; Rötter, Reimund Paul; Ruiz-Ramos, Margarita; Stella, Tommaso; Webber, Heidi; Wicke, BirkaSustainable intensification (SI) of agriculture is a promising strategy for boosting the capacity of the agricultural sector to meet the growing demands for food and non-food products and services in a sustainable manner. Assessing and quantifying the options for SI remains a challenge due to its multiple dimensions and potential associated trade-offs. We contribute to overcoming this challenge by proposing an approach for the ex-ante evaluation of SI options and trade-offs to facilitate decision making in relation to SI. This approach is based on the utilization of a newly developed SI metrics framework (SIMeF) combined with agricultural systems modelling. We present SIMeF and its operationalization approach with modelling and evaluate the approach’s feasibility by assessing to what extent the SIMeF metrics can be quantified by representative agricultural systems models. SIMeF is based on the integration of academic and policy indicator frameworks, expert opinions, as well as the Sustainable Development Goals. Structured along seven SI domains and consisting of 37 themes, 142 sub-themes and 1128 metrics, it offers a holistic, generic, and policy-relevant dashboard for selecting the SI metrics to be quantified for the assessment of SI options in diverse contexts. The use of SIMeF with agricultural systems modelling allows the ex-ante assessment of SI options with respect to their productivity, resource use efficiency, environmental sustainability and, to a large extent, economic sustainability. However, we identify limitations to the use of modelling to represent several SI aspects related to social sustainability, certain ecological functions, the multi-functionality of agriculture, the management of losses and waste, and security and resilience. We suggest advancements in agricultural systems models and greater interdisciplinary and transdisciplinary integration to improve the ability to quantify SI metrics and to assess trade-offs across the various dimensions of SI.
- ItemMedical gas plasma promotes blood coagulation via platelet activation(Amsterdam [u.a.] : Elsevier, 2021) Bekeschus, Sander; Poschkamp, Broder; van der Linde, JuliaMajor blood loss still is a risk factor during surgery. Electrocauterization often is used for necrotizing the tissue and thereby halts bleeding (hemostasis). However, the carbonized tissue is prone to falling off, putting patients at risk of severe side effects, such as dangerous internal bleeding many hours after surgery. We have developed a medical gas plasma jet technology as an alternative to electrocauterization and investigated its hemostatic (blood clotting) effects and mechanisms of action using whole human blood. The gas plasma efficiently coagulated anticoagulated donor blood, which resulted from the local lysis of red blood cells (hemolysis). Image cytometry further showed enhanced platelet aggregation. Gas plasmas release reactive oxygen species (ROS), but neither scavenging of long-lived ROS nor addition of chemically-generated ROS were able to abrogate or recapitulate the gas plasma effect, respectively. However, platelet activation was markedly impaired in platelet-rich plasma when compared to gas plasma-treated whole blood that moreover contained significant amounts of hemoglobin indicative of red blood cell lysis (hemolysis). Finally, incubation of whole blood with concentration-matched hemolysates phenocopied the gas plasmas-mediated platelet activation. These results will spur the translation of plasma systems for hemolysis into clinical practice.
- ItemLatent Class Cluster Analysis: Selecting the number of clusters(Amsterdam [u.a.] : Elsevier, 2022) Lezhnina, Olga; Kismihók, GáborLatent Class Cluster Analysis (LCCA) is an advanced model-based clustering method, which is increasingly used in social, psychological, and educational research. Selecting the number of clusters in LCCA is a challenging task involving inevitable subjectivity of analytical choices. Researchers often rely excessively on fit indices, as model fit is the main selection criterion in model-based clustering; it was shown, however, that a wider spectrum of criteria needs to be taken into account. In this paper, we suggest an extended analytical strategy for selecting the number of clusters in LCCA based on model fit, cluster separation, and stability of partitions. The suggested procedure is illustrated on simulated data and a real world dataset from the International Computer and Information Literacy Study (ICILS) 2018. For the latter, we provide an example of end-to-end LCCA including data preprocessing. The researcher can use our R script to conduct LCCA in a few easily reproducible steps, or implement the strategy with any other software suitable for clustering. We show that the extended strategy, in comparison to fit indices-based strategy, facilitates the selection of more stable and well-separated clusters in the data. • The suggested strategy aids researchers to select the number of clusters in LCCA • It is based on model fit, cluster separation, and stability of partitions • The strategy is useful for finding separable generalizable clusters in the data.
- ItemGas plasma-spurred wound healing is accompanied by regulation of focal adhesion, matrix remodeling, and tissue oxygenation(Amsterdam [u.a.] : Elsevier, 2021) Schmidt, Anke; Liebelt, Grit; Nießner, Felix; von Woedtke, Thomas; Bekeschus, SanderIn response to injury, efficient migration of skin cells to rapidly close the wound and restore barrier function requires a range of coordinated processes in cell spreading and migration. Gas plasma technology produces therapeutic reactive species that promote skin regeneration by driving proliferation and angiogenesis. However, the underlying molecular mechanisms regulating gas plasma-aided cell adhesion and matrix remodeling essential for wound closure remain elusive. Here, we combined in vitro analyses in primary dermal fibroblasts isolated from murine skin with in vivo studies in a murine wound model to demonstrate that gas plasma treatment changed phosphorylation of signaling molecules such as focal adhesion kinase and paxillin α in adhesion-associated complexes. In addition to cell spreading and migration, gas plasma exposure affected cell surface adhesion receptors (e.g., integrinα5β1, syndecan 4), structural proteins (e.g., vinculin, talin, actin), and transcription of genes associated with differentiation markers of fibroblasts-to-myofibroblasts and epithelial-to-mesenchymal transition, cellular protrusions, fibronectin fibrillogenesis, matrix metabolism, and matrix metalloproteinase activity. Finally, we documented that gas plasma exposure increased tissue oxygenation and skin perfusion during ROS-driven wound healing. Altogether, these results provide critical insights into the molecular machinery of gas plasma-assisted wound healing mechanisms.
- ItemCell cycle-related genes associate with sensitivity to hydrogen peroxide-induced toxicity(Amsterdam [u.a.] : Elsevier, 2022) Bekeschus, Sander; Liebelt, Grit; Menz, Jonas; Singer, Debora; Wende, Kristian; Schmidt, AnkeReactive oxygen species (ROS) such as hydrogen peroxide (H2O2) are well-described agents in physiology and pathology. Chronic inflammation causes incessant H2O2 generation associated with disease occurrences such as diabetes, autoimmunity, and cancer. In cancer, conditioning of the tumor microenvironment, e.g., hypoxia and ROS generation, has been associated with disease outcomes and therapeutic efficacy. Many reports have investigated the roles of the action of H2O2 across many cell lines and disease models. The genes predisposing tumor cell lines to H2O2-mediated demise are less deciphered, however. To this end, we performed in-house transcriptional profiling of 35 cell lines and simultaneously investigated each cell line's H2O2 inhibitory concentration (IC25) based on metabolic activity. More than 100-fold differences were observed between the most resistant and sensitive cell lines. Correlation and gene ontology pathway analysis identified a rigid association with genes intertwined in cell cycle progression and proliferation, as such functional categories dominated the top ten significant processes. The ten most substantially correlating genes (Spearman r > 0.70 or < -0.70) were validated using qPCR, showing complete congruency with microarray analysis findings. Western blotting confirmed the correlation of cell cycle-related proteins negatively correlating with H2O2 IC25. Top genes related to ROS production or antioxidant defense were only modest in correlation (Spearman r > 0.40 or < -0.40). In conclusion, our in-house transcriptomic correlation analysis revealed a set of cell cycle-associated genes associated with a priori resistance or sensitivity to H2O2-induced cellular demise with the detailed and causative roles of individual genes remaining unclear.