Justiceroach7144

Near infrared spectroscopy (NIRS) is an analytical technique for determining the chemical composition or structure of a given sample. For several decades, NIRS has been a frequently used analysis tool in agriculture, pharmacology, medicine, and petrochemistry. The popularity of NIRS is constantly growing as new application areas are discovered. Contrary to mid infrared spectral region, the absorption bands in near infrared spectral region are often non-specific, broad, and overlapping. Analysis of NIR spectra requires multivariate methods which are highly subjective to noise arising from instrumentation, scattering effects, and measurement setup. NIRS measurements are also frequently performed outside of a laboratory which further contributes to the presence of noise. Therefore, preprocessing is a critical step in NIRS as it can vastly improve the performance of multivariate models. While extensive research regarding various preprocessing methods exists, selection of the best preprocessing method is often determined through trial-and-error. A more powerful approach for optimizing preprocessing in NIRS models would be to automatically compare a large number of preprocessing techniques (e.g., through grid-search or hyperparameter tuning). To enable this, we present, nippy, an open-source Python module for semi-automatic comparison of NIRS preprocessing methods (available at https//github.com/uef-bbc/nippy). We provide here a brief overview of the capabilities of nippy and demonstrate the typical usage through two examples with public datasets. Cell-derived extracellular matrices have emerged as promising scaffolds for tissue engineering (TE) strategies due to their ability to create a biomimetic microenvironment providing biochemical and physical cues to cells, without the limitations of availability and potential pathogen transmission associated with tissue-derived extracellular matrix (ECM) scaffolds. Glycosaminoglycans (GAGs) are important components of ECM with a crucial role in the maintenance of the mechanical properties of the tissue and as signaling regulators of several cellular processes, such as cell adhesion, growth and differentiation. However, despite their relevance to the field of TE, little information is available on the GAG composition of cell-derived ECM, mainly due to the lack of appropriate quantitative tools to determine different GAG and disaccharide subtypes in complex biological samples. In this chapter, we describe a highly sensitive and selective liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to characterize decellularized cell-derived ECM generated in vitro in terms of their GAG and disaccharide composition. © 2020 Elsevier Inc. All rights reserved.Tissue elasticity is a critical regulator of cell behavior in normal and diseased conditions like fibrosis and cancer. Since the extracellular matrix (ECM) is a major regulator of tissue elasticity and function, several ECM-based models have emerged in the last decades, including in vitro endogenous ECM, decellularized tissue ECM and ECM hydrogels. The development of such models has urged the need to quantify their elastic properties particularly at the nanometer scale, which is the relevant length scale for cell-ECM interactions. For this purpose, the versatility of atomic force microscopy (AFM) to quantify the nanomechanical properties of soft biomaterials like ECM models has emerged as a very suitable technique. In this chapter we provide a detailed protocol on how to assess the Young's elastic modulus of ECM models by AFM, discuss some of the critical issues, and provide troubleshooting guidelines as well as illustrative examples of AFM measurements, particularly in the context of cancer. © 2020 Elsevier Inc. All rights reserved.Tissue regeneration strategies have been greatly evolving in the last years due to the use of more realistic approaches. These approaches rely in the use of biomaterials for the development of three dimensional (3D) structures that emulate the in vivo microenvironment of different tissues. Recently, extracellular matrices (ECM) secreted by cells have been caught a great deal of attention as an attractive biomaterial for the development 3D structures. In fact, different cells and/or different cellular culture conditions gave rise to different ECM's compositions, which can be used for the development of more physiologically relevant 3D structures. Nevertheless, the recovery of cell-derived ECM requires the use of a proper decellularization protocol. Seliciclib Herein, we report a decellularization protocol to recover the ECM produced by human adipose derived stem cells. This protocol comprises multiple steps (chemical, physical or enzymatic) which are described here in more detail. Furthermore, it is describe the methods that have been used to evaluate the effectiveness of this decellularization protocol. Overall, this protocol enables the production of hASCs-derived matrices that can be further used for the production of more physiologically relevant 3D in vitro models for tissue regeneration strategies. © 2020 Elsevier Inc. All rights reserved.Three-dimensional (3D) in vitro skin and skin cancer models have become an invaluable tool in skin research. They go back to 1979, when Bell and colleagues reported on the establishment of a fibroblast-dependent collagen tissue (Bell, Ivarsson, & Merrill, 1979). On top of such tissue a stratified and differentiated epidermis could be established (Bell, Merrill, & Solomon, 1979). Hydrogel-based dermal equivalents have been generated ever since and upon co-culture with normal human skin keratinocytes, these constructs were then termed skin equivalents. Due to a number of deficiencies, the most important one being their restricted survival time, new developments helped to circumvent premature fibroblast activation and tissue destruction. By avoiding collagen for the dermal equivalent (DE), we proposed, a scaffold-based DE, allowing fibroblasts to reorganize the primary fibrin solution into an "authentic" dermal matrix (Boehnke et al., 2007; Stark et al., 2004, 2006). With this, our goal of a long-term skin equivalent-successful cultivation for several months-was achieved.