475 research outputs found
Two-dimensional segmentation fusion tool: an extensible, free-to-use, user-friendly tool for combining different bidimensional segmentations
Get PDFIntroduction: In several fields, the process of fusing multiple two-dimensional
(2D) closed lines is an important step. For instance, this is fundamental in histology and oncology in general. The treatment of a tumor consists of numerous steps and activities. Among them, segmenting the cancer area, that is, the correct identification of its spatial location by the segmentation technique, is one of the most important and at the same time complex and delicate steps. The difficulty in deriving reliable segmentations stems from the lack of a standard for identifying the edges and surrounding tissues of the tumor area. For this reason, the entire process is affected by considerable subjectivity. Given a tumor image, different practitioners can associate different segmentations with it, and the diagnoses produced may differ. Moreover, experimental data show that the analysis of the same area by the same physician at two separate timepoints may result in different lines being produced. Accordingly, it is challenging to establish which contour line is the ground truth.
Methods: Starting from multiple segmentations related to the same tumor,
statistical metrics and computational procedures could be exploited to
combine them for determining the most reliable contour line. In particular,
numerous algorithms have been developed over time for this procedure, but
none of them is validated yet. Accordingly, in this field, there is no ground truth, and research is still active. Results: In this work, we developed the Two-Dimensional Segmentation Fusion Tool (TDSFT), a user-friendly tool distributed as a free-to-use standalone application for MAC, Linux, and Windows, which offers a simple and extensible interface where numerous algorithms are proposed to “compute the mean” (i.e., the process to fuse, combine, and “average”) multiple 2D lines.
Results: In this work, we developed the Two-Dimensional Segmentation Fusion Tool (TDSFT), a user-friendly tool distributed as a free-to-use standalone application for MAC, Linux, and Windows, which offers a simple and extensible interface where numerous algorithms are proposed to “compute the mean” (i.e., the process to fuse, combine, and “average”) multiple 2D lines.
Conclusions: The TDSFT can support medical specialists, but it can also be used in other fields where it is required to combine 2D close lines. In addition, the TDSFT is designed to be easily extended with new algorithms thanks to a dedicated graphical interface for configuring new parameters. The TDSFT can be downloaded from the following link: https://sourceforge.net/p/tdsft
Surface display of sialyltransferase on the outer membrane of <i>Escherichia coli</i> and ClearColi
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α2,3-Sialyltransferase from Pasteurella multocida (PmST1)is an enzyme that transfers a sialyl group of donor substrates to an acceptor substrate called N-acetyl-D-lactosamine (LacNAc). In this study PmST1 was expressed on the outer membrane of wildtype Escherichia coli (BL21)with lipopolysaccharide (LPS)and ClearColi with no LPS, and then the enzyme activity and expression level of PmST1 were compared. As the first step, the expression levels of PmST1 on the outer membranes of wildtype E. coli (BL21)and ClearColi were compared according to the IPTG induction time, and the absolute amount of surface-displayed PmST1 was calculated using densitometry of SDS-PAGE. As the next step, the influence of LPS on the PmST1 activity was estimated by analyzing Michaelis-Menten plot. The enzyme activity of PmST1 was analyzed by measuring the concentration of CMP, which was a by-product after the transfer of the sialyl group of donor compounds to the acceptor compounds. From a Michaelis–Menten plot, the enzyme activity of the surface-displayed PmST1 and the maximum rate (V
max
)of ClearColi were higher than those of wildtype E. coli (BL21). However, the K
M
value, which represented the concentration of substrate to reach half the maximum rate (V
max
), was similar for both enzymes. These results represented such a difference in enzyme activity was occurred from the interference of LPS on the mass transport of the donor and acceptor to PmST1 for the sialyl group transfer.
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ColorI-DT: An open-source tool for the quantitative evaluation of differences in microscopy color images
Get PDFIn several fields, quantitatively comparing color images is crucial. For instance, this is important in Histopathology, where different microscopes/cameras are typically used for visualizing patient samples by causing significant color variation. No ground-truth metric exists for estimating differences between pairs of color images. A range of possible solutions is available but there is no existing open-source tool that allow clinicians and researchers to apply these metrics to microscopy images through an intuitive, easy-to-use software. In this work, we developed Color Image Difference Tool (ColorI-DT), an open-source tool for measuring quantitative differences between color images of the same subject acquired under different settings. Thanks to a user-friendly graphical user interface, it allows the selection of a pair of color images and a metric from a list of available options, and produces an output 2D pixel-wise color difference matrix between corresponding pixels in the input images. The metrics currently implemented are: (1) Euclidean ΔE; (2) International Commission on Illumination (CIE) 76 (Luv); (3) CIE76 (Lab); (4) CIE94; (5) CIE00; (6) Colour Measurement Committee (CMC). To demonstrate how to use the tool, microscopy images with a predominant color in the red, green, or blue channel were used. In particular, we checked which among the 6 metrics displays the most predictable and linear behavior in the case of controlled primary color alterations. For more pronounced color adjustments, a qualitative comparison would be likely sufficient for analyzing color differences, as a quantitative tool may become unreliable due to the inherent limitations of the implemented metrics
Error Analysis
Get PDFThe Routledge Handbook of Korean as a Second Language aims to define the field and to present the latest research in Korean as a second language (KSL).
This chapter of Error Analysis provides a general critique of core issues, such as data sampling and identification, description, and explanation of errors, as well as key findings from EA studies in Korean. It then offers a discussion of pedagogical implications and makes suggestions for future developments of EA in Korean
Monocarboxylate transporter-1 (MCT-1) inhibitors screened from autodisplayed FV-antibody library
No full text: Monocarboxylate transporter-1 (MCT-1) inhibitors were screened from the Fv-antibody library, which contained complementary determining region 3 with randomized amino acid sequences (11 residues) through site-directed mutagenesis. Fv-antibodies against MCT-1 were screened from the autodisplayed Fv-antibody library. Two clones were screened, and the binding affinity (KD) against MCT-1 was estimated using flow cytometry. The screened Fv-antibodies were expressed as soluble fusion proteins (Fv-1 and Fv-2) and the KD for MCT-1 was estimated using the SPR biosensor. The inhibitory activity of the expressed Fv-antibodies was observed in HEK293T and Jurkat cell lines by measuring intracellular pH and lactate accumulation. The level of cell viability in HEK293T and Jurkat cell lines was decreased by the inhibitory activity of the expressed Fv-antibodies. The binding properties of the Fv-antibodies to MCT-1 were analyzed using molecular docking simulations. Overall, the results showed that the screened Fv-antibodies against MCT-1 from the Fv-antibody library had high binding affinity and inhibitory activity against MCT-1, which could be used as potential therapeutic drug candidates for the MCT-1 inhibitor
DS4H Image Alignment (DS4H-IA), an open-source ImageJ/Fiji plugin for aligning multimodality 2D microscopy images.
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Overexpression of VlPRX21 and VlPRX35 genes in Arabidopsis plants leads to bioconversion of trans-resveratrol to δ-viniferin
No full textStilbenes, including resveratrol and viniferins, a small family of polyphenols, are considered the most important phytoalexin group in Vitis species. In a previous study, we found that co-treatment of methyl jasmonate (MJ) and stevioside (STE) resulted in enhanced extracellular production of viniferins in grapevine cell suspension cultures. Thus, to further understand the mechanisms of viniferin production in grapevine cell cultures, we performed transcriptome analysis and isolated seven candidates of grapevine peroxidase genes (VlAPX6, VlGPX5, VlPRX13, VlPRX21, VlPRX35, VlPRX40, and VlPRX50). Bioconversion of trans-resveratrol to δ-viniferin was examined using crude protein extracts isolated from agroinfiltration-based transient expression of VlPRXs in Nicotiana benthamiana. In addition, we found that crude protein extracts from VlPRX21-, VlPRX35-, and VlPRX40-overexpressing (OX) transgenic Arabidopsis plants led to the conversion of trans-resveratrol to δ-viniferin. We found that in vitro experiments with crude protein extracts from VlPRX21-OX and VlPRX35-OX Arabidopsis plants catalyzed the dimerization of trans-resveratrol to δ-viniferin. Our results suggest that VlPRX21 and VlPRX35 encode functional grapevine class III peroxidases and catalyze the oxidative dimerization of trans-resveratrol to form δ-viniferin in grapevine.
Radiomic analysis of 3D spheroids using 2D brightfield images
Get PDFBackground and Objective: Radiomics is a field of quantitative imaging involving the extraction of features from medical images transforming them into mineable data for diagnostic, prognostic, and predictive purposes. In this work, we focused on the analysis of 2D brightfield images acquired with standard microscopes today available in all biological laboratories. Methods: We analysed images of 3D multicellular spheroids, an in vitro model commonly used in Regenerative Medicine and Oncology. Besides describing Analysis of Spheroid version 3.0 (AnaSP 3.0), a new release of an open-source software suite specifically designed for segmenting and extracting features from 2D brightfield spheroid images. To validate the tool, spheroids generated with U-shape bottom multi-well plates and different concentrations of mesenchymal stem cells and osteosarcoma cell lines have been used. Results: We demonstrated how advanced features included in AnaSP 3.0, i.e. sphericity, volume, and image gradient, may be used to indirectly assess the spheroidization of the spheroids over time, the number of cells composing the spheroids, and the extension of a possible central necrotic core. Conclusions: AnaSP 3.0 is freely available at https://sourceforge.net/p/anasp. Compared to the previous versions, it includes a new algorithm for volume estimation and introduces new modules to extract advanced features using the original grey-level image values, rather than just relying on binary masks
Development of a wash-free immunoassay using Escherichia coli cells with autodisplayed Z-domains
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Escherichia coli cells that autodisplay Z-domains have been used to improve the sensitivity and limit of detection (LOD) of immunoassays by controlling antibody orientation.</p
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