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Computational breath analysis is a growing research area aiming at identifying volatile organic compounds (VOCs) in human breath to assist medical diagnostics of the next generation. While inexpensive and non-invasive bioanalytical technologies for metabolite detection in exhaled air and bacterial/fungal vapor exist and the first studies on the power of supervised machine learning methods for profiling of the resulting data were conducted, we lack methods to extract hidden data features emerging from confounding factors. Here, we present Carotta, a new cluster analysis framework dedicated to uncovering such hidden substructures by sophisticated unsupervised statistical learning methods. We study the power of transitivity clustering and hierarchical clustering to identify groups of VOCs with similar expression behavior over most patient breath samples and/or groups of patients with a similar VOC intensity pattern. This enables the discovery of dependencies between metabolites. On the one hand, this allows us to eliminate the effect of potential confounding factors hindering disease classification, such as smoking. On the other hand, we may also identify VOCs associated with disease subtypes or concomitant diseases. Carotta is an open source software with an intuitive graphical user interface promoting data handling, analysis and visualization. The back-end is designed to be modular, allowing for easy extensions with plugins in the future, such as new clustering methods and statistics. It does not require much prior knowledge or technical skills to operate. We demonstrate its power and applicability by means of one artificial dataset. We also apply Carotta exemplarily to a real-world example dataset on chronic obstructive pulmonary disease (COPD). While the artificial data are utilized as a proof of concept, we will demonstrate how Carotta finds candidate markers in our real dataset associated with confounders rather than the primary disease (COPD) and bronchial carcinoma (BC). Carotta is publicly available at http://carotta.compbio.sdu.dk.
Blood vessel reconstruction is still an elusive goal for the development of in vitro models as well as artificial vascular grafts. In this study, we used a novel photo curable cytocompatible polyacrylate material (PA) for freeform generation of synthetic vessels. We applied stereolithography for the fabrication of arbitrary 3D tubular structures with total dimensions in the centimeter range, 300 µm wall thickness, inner diameters of 1 to 2 mm and defined pores with a constant diameter of approximately 100 µm or 200 µm. We established a rinsing protocol to remove remaining cytotoxic substances from the photo-cured PA and applied thio-modified heparin and RGDC-peptides to functionalize the PA surface for enhanced endothelial cell adhesion. A rotating seeding procedure was introduced to ensure homogenous endothelial monolayer formation at the inner luminal tube wall. We showed that endothelial cells stayed viable and adherent and aligned along the medium flow under fluid-flow conditions comparable to native capillaries. The combined technology approach comprising of freeform additive manufacturing (AM), biomimetic design, cytocompatible materials which are applicable to AM, and biofunctionalization of AM constructs has been introduced as BioRap® technology by the authors.
Turbidity sensing is very common in the control of drinking water. Furthermore, turbidity measurements are applied in the chemical (e.g., process monitoring), pharmaceutical (e.g., drug discovery), and food industries (e.g., the filtration of wine and beer). The most common measurement technique is nephelometric turbidimetry. A nephelometer is a device for measuring the amount of scattered light of suspended particles in a liquid by using a light source and a light detector orientated in 90°to each other. Commercially available nephelometers cost usually—depending on the measurable range, reliability, and precision —thousands of euros. In contrast, our new developed GRIN-lens-based nephelometer, called GRINephy, combines low costs with excellent reproducibility and precision, even at very low turbidity levels, which is achieved by its ability to rotate the sample. Thereby, many cuvette positions can be measured, which results in a more precise average value for the turbidity calculated by an algorithm, which also eliminates errors caused by scratches and contaminations on the cuvettes. With our compact and cheap Arduino-based sensor, we are able to measure in the range of 0.1–1000 NTU and confirm the ISO 7027-1:2016 for low turbidity values.
Bone remodeling can be mimicked in vitro by co-culture models. Based on bone cells, such co-cultures help to study synergistic morphological changes and the impact of materials and applied substances. Hence, we examined the formation of osteoclasts on bovine bone materials to prove the bone resorption functionality of the osteoclasts in three different co-culture set-ups using human monocytes (hMCs) and (I) human mesenchymal stem cells (hMSCs), (II) osteogenic differentiated hMSCs (hOBs), and (III) hOBs in addition of soluble monocyte-colony stimulating factor (M CSF) and cytokine receptor activator of NFkB ligand (RANKL).We detected osteoclast-specific actin morphology, as well as the expression of cathepsin K and CD51/61 in single cells in set-up II and in numerous cells in set-up III. Resorption pits on bone material as characteristic proof of functional osteoclasts were not found in set-up I and II, but we detected such resorption pits in set–up III. We conclude in co culture models without M-CSF and RANKL that monocytes can differentiate into osteoclasts that show the characteristic actin structures and protein expression. However, to receive functional bone resorbing osteoclasts in vitro, the addition of M-CSF and RANKL is needed. Moreover, we suggest the use of bone or bone-like materials for future studies evaluating osteoclastogenesis.
Water jacket systems are routinely used to control the temperature of Petri dish cell culture chambers. Despite their widespread use, the thermal characteristics of such systems have not been fully investigated. In this study, we conducted a comprehensive set of theoretical, numerical and experimental analyses to investigate the thermal characteristics of Petri dish chambers under stable and transient conditions. In particular, we investigated the temperature gradient along the radial axis of the Petri dish under stable conditions, and the transition period under transient conditions. Our studies indicate a radial temperature gradient of 3.3 °C along with a transition period of 27.5 min when increasing the sample temperature from 37 to 45 °C for a standard 35 mm diameter Petri dish. We characterized the temperature gradient and transition period under various operational, geometric, and environmental conditions. Under stable conditions, reducing the diameter of the Petri dish and incorporating a heater underneath the Petri dish can effectively reduce the temperature gradient across the sample. In comparison, under transient conditions, reducing the diameter of the Petri dish, reducing sample volume, and using glass Petri dish chambers can reduce the transition period.
Human adipose-derived mesenchymal stem/stromal cells (Ad-MSCs) have great potential for bone tissue engineering. Cryogels, mimicking the three-dimensional structure of spongy bone, represent ideal carriers for these cells. We developed poly(2-hydroxyethyl methacrylate) cryogels, containing hydroxyapatite to mimic inorganic bone matrix. Cryogels were additionally supplemented with different types of proteins, namely collagen (Coll), platelet rich plasma (PRP), immune cells-conditioned medium (CM), and RGD peptides (RGD). The different protein components did not affect scaffolds’ porosity or water-uptake capacity, but altered pore size and stiffness. Stiffness was highest in scaffolds with PRP (82.3 kPa), followed by Coll (55.3 kPa), CM (45.6 kPa), and RGD (32.8 kPa). Scaffolds with PRP, CM, and Coll had the largest pore diameters (~60 µm). Ad MSCs were osteogenically differentiated on these scafffolds for 14 days. Cell attachment and survival rates were comparable for all four scaffolds. Runx2 and osteocalcin levels only increased in Ad-MSCs on Coll, PRP and CM cryogels. Osterix levels increased slightly in Ad-MSCs differentiated on Coll and PRP cryogels. With differentiation alkaline phosphatase activity decreased under all four conditions. In summary, besides Coll cryogel our PRP cryogel constitutes as an especially suitable carrier for bone tissue engineering. This is of special interest, as this scaffold can be generated with patients’ PRP.
The present publication reports the purification effort of two natural bone blocks, that is, an allogeneic bone block (maxgraft®, botiss biomaterials GmbH, Zossen, Germany) and a xenogeneic block (SMARTBONE®, IBI S.A., Mezzovico Vira, Switzerland) in addition to previously published results based on histology. Furthermore, specialized scanning electron microscopy (SEM) and in vitro analyses (XTT, BrdU, LDH) for testing of the cytocompatibility based on ISO 10993-5/-12 have been conducted. The microscopic analyses showed that both bone blocks possess a trabecular structure with a lamellar subarrangement. In the case of the xenogeneic bone block, only minor remnants of collagenous structures were found, while in contrast high amounts of collagen were found associated with the allogeneic bone matrix. Furthermore, only island-like remnants of the polymer coating in case of the xenogeneic bone substitute seemed to be detectable. Finally, no remaining cells or cellular remnants were found in both bone blocks. The in vitro analyses showed that both bone blocks are biocompatible. Altogether, the purification level of both bone blocks seems to be favorable for bone tissue regeneration without the risk for inflammatory responses or graft rejection. Moreover, the analysis of the maxgraft® bone block showed that the underlying purification process allows for preserving not only the calcified bone matrix but also high amounts of the intertrabecular collagen matrix.
The aim of this study was to predefine the pore structure of β-tricalcium phosphate (β-TCP) scaffolds with different macro pore sizes (500, 750, and 1000 µm), to characterize β-TCP scaffolds, and to investigate the growth behavior of cells within these scaffolds. The lead structures for directional bone growth (sacrificial structures) were produced from polylactide (PLA) using the fused deposition modeling techniques. The molds were then filled with β-TCP slurry and sintered at 1250° C, whereby the lead structures (voids) were burnt out. The scaffolds were mechanically characterized (native and after incubation in simulated body fluid (SBF) for 28 d). In addition, biocompatibility was investigated by live/dead, cell proliferation and lactate dehydrogenase assays.
The chemical synthesis of polysiloxanes from monomeric starting materials involves a series of hydrolysis, condensation and modification reactions with complex monomeric and oligomeric reaction mixtures. Real-time monitoring and precise process control of the synthesis process is of great importance to ensure reproducible intermediates and products and can readily be performed by optical spectroscopy. In chemical reactions involving rapid and simultaneous functional group transformations and complex reaction mixtures, however, the spectroscopic signals are often ambiguous due to overlapping bands, shifting peaks and changing baselines. The univariate analysis of individual absorbance signals is hence often only of limited use. In contrast, batch modelling based on the multivariate analysis of the time course of principal components (PCs) derived from the reaction spectra provides a more efficient tool for real time monitoring. In batch modelling, not only single absorbance bands are used but information over a broad range of wavelengths is extracted from the evolving spectral fingerprints and used for analysis. Thereby, process control can be based on numerous chemical and morphological changes taking place during synthesis. “Bad” (or abnormal) batches can quickly be distinguished from “normal” ones by comparing the respective reaction trajectories in real time. In this work, FTIR spectroscopy was combined with multivariate data analysis for the in-line process characterization and batch modelling of polysiloxane formation. The synthesis was conducted under different starting conditions using various reactant concentrations. The complex spectral information was evaluated using chemometrics (principal component analysis, PCA). Specific spectral features at different stages of the reaction were assigned to the corresponding reaction steps. Reaction trajectories were derived based on batch modelling using a wide range of wavelengths. Subsequently, complexity was reduced again to the most relevant absorbance signals in order to derive a concept for a low-cost process spectroscopic set-up which could be used for real-time process monitoring and reaction control.
Here, we study resin cure and network formation of solid melamine formaldehyde pre-polymer over a large temperature range viadynamic temperature curing profiles. Real-time infrared spectroscopy is used to analyze the chemical changes during network formation and network hardening. By applying chemometrics (multivariate curve resolution,MCR), the essential chemical functionalities that constitute the network at a given stage of curing are mathematically extracted and tracked over time. The three spectral components identified by MCR were methylol-rich, ether linkages-rich and methylene linkages-rich resin entities. Based on dynamic changes of their characteristic spectral patterns in dependence of temperature, curing is divided into five phases: (I) stationary phase with free methylols as main chemical feature, (II) formation of flexible network cross-linked by ether linkages, (III) formation of rigid, ether-cross-linked network, (IV) further hardening via transformation of methylols and ethers into methylene-cross-linkages, and (V) network consolidation via transformation of ether into methylene bridges. The presented spectroscopic/chemometric approach can be used as methodological basis for the functionality design of MF-based surface films at the stage of laminate pressing, i.e., for tailoring the technological property profile of cured MF films using a causal understanding of the underlying chemistry based on molecular markers and spectroscopic fingerprints.