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- 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.
- ItemMedical gas plasma-stimulated wound healing: Evidence and mechanisms(Amsterdam [u.a.] : Elsevier, 2021) Bekeschus, Sander; von Woedtke, Thomas; Emmert, Steffen; Schmidt, AnkeDefective wound healing poses a significant burden on patients and healthcare systems. In recent years, a novel reactive oxygen and nitrogen species (ROS/RNS) based therapy has received considerable attention among dermatologists for targeting chronic wounds. The multifaceted ROS/RNS are generated using gas plasma technology, a partially ionized gas operated at body temperature. This review integrates preclinical and clinical evidence into a set of working hypotheses mainly based on redox processes aiding in elucidating the mechanisms of action and optimizing gas plasmas for therapeutic purposes. These hypotheses include increased wound tissue oxygenation and vascularization, amplified apoptosis of senescent cells, redox signaling, and augmented microbial inactivation. Instead of a dominant role of a single effector, it is proposed that all mechanisms act in concert in gas plasma-stimulated healing, rationalizing the use of this technology in therapy-resistant wounds. Finally, addressable current challenges and future concepts are outlined, which may further promote the clinical utilization, efficacy, and safety of gas plasma technology in wound care in the future.
- ItemStatic and dynamic 3D culture of neural precursor cells on macroporous cryogel microcarriers(Amsterdam [u.a.] : Elsevier, 2020) Newland, Ben; Ehret, Fanny; Hoppe, Franziska; Eigel, Dimitri; Pette, Dagmar; Newland, Heike; Welzel, Petra B.; Kempermann, Gerd; Werner, CarstenNeural precursor cells have been much studied to further our understanding of the far-reaching and controversial question of adult neurogenesis. Currently, differentiation of primary neural precursor cells from the mouse dentate gyrus via 2-dimentional in vitro culture yields low numbers of neurons, a major hindrance to the field of study. 3-dimentional “neurosphere” culture allows better 3D cell-cell contact, but control over cell differentiation is poor because nutrition and oxygen restrictions at the core of the sphere causes spontaneous differentiation, predominantly to glial cells, not neurons. Our group has developed macroporous scaffolds, which overcome the above-mentioned problems, allowing long-term culture of neural stem cells, which can be differentiated into a much higher yield of neurons. Herein we describe a method for culturing neural precursor cells on RGD peptide functionalized-heparin containing cryogel scaffolds, either in standard non-adherent well-plates (static culture) or in spinner flasks (dynamic culture). This method includes: • The synthesis and characterization of heparin based microcarriers. • A “static” 3D culture method for that does not require spinner flask equipment. • “Dynamic” culture in which cell loaded microcarriers are transferred to a spinner flask. © 2020 The Authors
- 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.
- ItemxCT (SLC7A11) expression confers intrinsic resistance to physical plasma treatment in tumor cells(Amsterdam [u.a.] : Elsevier, 2020) Bekeschus, Sander; Eisenmann, Sebastian; Sagwal, Sanjeev Kumar; Bodnar, Yana; Moritz, Juliane; Poschkamp, Broder; Stoffels, Ingo; Emmert, Steffen; Madesh, Muniswamy; Weltmann, Klaus-Dieter; von Woedtke, Thomas; Gandhirajan, Rajesh KumarCold physical plasma is a partially ionized gas investigated as a new anticancer tool in selectively targeting cancer cells in monotherapy or in combination with therapeutic agents. Here, we investigated the intrinsic resistance mechanisms of tumor cells towards physical plasma treatment. When analyzing the dose-response relationship to cold plasma-derived oxidants in 11 human cancer cell lines, we identified four 'resistant' and seven 'sensitive' cell lines. We observed stable intracellular glutathione levels following plasma treatment only in the 'resistant' cell lines indicative of altered antioxidant mechanisms. Assessment of proteins involved in GSH metabolism revealed cystine-glutamate antiporter xCT (SLC7A11) to be significantly more abundant in the 'resistant' cell lines as compared to 'sensitive' cell lines. This decisive role of xCT was confirmed by pharmacological and genetic inhibition, followed by cold physical plasma treatment. Finally, microscopy analysis of ex vivo plasma-treated human melanoma punch biopsies suggested a correlation between apoptosis and basal xCT protein abundance. Taken together, our results demonstrate that xCT holds the potential as a biomarker predicting the sensitivity of tumor cells towards plasma treatment.
- 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.
- 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.
- ItemMeasuring and evaluating colorimetric properties of samples from loess-paleosol sequences(Amsterdam [u.a.] : Elsevier, 2023) Laag, Christian; Lagroix, France; Kreutzer, Sebastian; Chapkanski, Stoil; Zeeden, Christian; Guyodo, YohanColorimetric measurements are valuable in studying paleoenvironmental changes in sediment archives such as loess-paleosol sequences. These measurements allow for the identification of climate-sensitive minerals such as hematite, goethite, and secondary carbonates, as well as the observation of stratigraphic changes influenced by paleoclimate variations. Herein, a detailed workflow protocol emphasizing mineral abundance extraction by determining true band amplitudes is presented. Moreover, we present a protocol for colorimetric measurements that eliminates container bias, allowing the analysis and re-analysis of stored sediment quickly and inexpensively. Finally, we introduce a new R-package ('LESLIE') for graphical data display and enhancement. The protocol and its validation are demonstrated on the Suhia Kladenetz loess-paleosol sequence of northern Bulgaria. • A detailed workflow protocol eliminating container bias in colorimetric measurements and extracting mineral abundances is presented. • The protocol is independently validated with aid of Attenuated Total Reflectance Fourier Transform mid-infrared (ATR-FTIR) spectroscopic experiments. • Stratigraphic color enhancement using the R-package 'LESLIE' is facilitated by a user-friendly R-shiny application.
- ItemLaser induced diffuse reflectance imaging – Monte Carlo simulation of backscattering measured on the surface(Amsterdam [u.a.] : Elsevier, 2020) Baranyai, LászlóThe Monte Carlo simulation algorithm of photon trajectory computation is implemented in object oriented R code. Diffuse reflectance, also called backscattering, is modeled in semi-infinite homogeneous media. Spatial photon flux leaving the surface of the media is collected. The profile of intensity along radii relative to the incident point is used to simulate measurement of computer vision systems. Four optical parameters of the media are used: absorption coefficient, scattering coefficient, anisotropy factor and refractive index. Five parameters are used to describe configuration of the vision system: number of photons, radius of circular light beam, limiting energy level of photons, radius of observed area, spatial resolution of the vision system. • The incident angle of the light beam is included in the photon launch procedure. Initial direction is typically assumed to be normal with x,y,z coordinates of 0,0,1. In the proposed modification, initial move vector is calculated based on the incident angle and refractive index of the media. Additionally, elliptic distortion of the circular light beam on the surface is calculated based on the incident angle. • Photon flux leaving media through the surface is corrected with Lambertian method to measure intensity captured by an imaging device in normal position. • The software implementing the method is written in R language, the R code is available as standard package.
- 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.