scholarly journals Integrated Cells and Collagen Fibers Spatial Image Analysis

2021 ◽  
Vol 1 ◽  
Author(s):  
Georgii Vasiukov ◽  
Tatiana Novitskaya ◽  
Maria-Fernanda Senosain ◽  
Alex Camai ◽  
Anna Menshikh ◽  
...  

Modern technologies designed for tissue structure visualization like brightfield microscopy, fluorescent microscopy, mass cytometry imaging (MCI) and mass spectrometry imaging (MSI) provide large amounts of quantitative and spatial information about cells and tissue structures like vessels, bronchioles etc. Many published reports have demonstrated that the structural features of cells and extracellular matrix (ECM) and their interactions strongly predict disease development and progression. Computational image analysis methods in combination with spatial analysis and machine learning can reveal novel structural patterns in normal and diseased tissue. Here, we have developed a Python package designed for integrated analysis of cells and ECM in a spatially dependent manner. The package performs segmentation, labeling and feature analysis of ECM fibers, combines this information with pre-generated single-cell based datasets and realizes cell-cell and cell-fiber spatial analysis. To demonstrate performance and compatibility of our computational tool, we integrated it with a pipeline designed for cell segmentation, classification, and feature analysis in the KNIME analytical platform. For validation, we used a set of mouse mammary gland tumors and human lung adenocarcinoma tissue samples stained for multiple cellular markers and collagen as the main ECM protein. The developed package provides sufficient performance and precision to be used as a novel method to investigate cell-ECM relationships in the tissue, as well as detect structural patterns correlated with specific disease outcomes.

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dongxiao Jiang ◽  
Shufei Ding ◽  
Zhujun Mao ◽  
Liyan You ◽  
Yeping Ruan

Abstract Background Colon cancer is a malignant gastrointestinal tumour with high incidence, mortality and metastasis rates worldwide. Aloe-emodin is a monomer compound derived from hydroxyanthraquinone. Aloe-emodin produces a wide range of antitumour effects and is produced by rhubarb, aloe and other herbs. However, the mechanism by which aloe-emodin influences colon cancer is still unclear. We hope these findings will lead to the development of a new therapeutic strategy for the treatment of colon cancer in the clinic. Methods We identified the overlapping targets of aloe-emodin and colon cancer and performed protein–protein interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. In addition, we selected apoptosis pathways for experimental verification with cell viability, cell proliferation, caspase-3 activity, DAPI staining, cell cycle and western blotting analyses to evaluate the apoptotic effect of aloe-emodin on colon cancer cells. Results The MTT assay and cell colony formation assay showed that aloe-emodin inhibited cell proliferation. DAPI staining confirmed that aloe-emodin induced apoptosis. Aloe-emodin upregulated the protein level of Bax and decreased the expression of Bcl-2, which activates caspase-3 and caspase-9. Furthermore, the protein expression level of cytochrome C increased in a time-dependent manner in the cytoplasm but decreased in a time-dependent manner in the mitochondria. Conclusion These results indicate that aloe-emodin may induce the apoptosis of human colon cancer cells through mitochondria-related pathways.


AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hend M. Tag ◽  
Amna A. Saddiq ◽  
Monagi Alkinani ◽  
Nashwa Hagagy

AbstractHaloferax sp strain NRS1 (MT967913) was isolated from a solar saltern on the southern coast of the Red Sea, Jeddah, Saudi Arabia. The present study was designed for estimate the potential capacity of the Haloferax sp strain NRS1 to synthesize (silver nanoparticles) AgNPs. Biological activities such as thrombolysis and cytotoxicity of biosynthesized AgNPs were evaluated. The characterization of silver nanoparticles biosynthesized by Haloferax sp (Hfx-AgNPs) was analyzed using UV–vis spectroscopy, transmission electron microscopy (TEM), X-ray diffraction (XRD), and Fourier-transform infrared spectroscopy (FTIR). The dark brown color of the Hfx-AgNPs colloidal showed maximum absorbance at 458 nm. TEM image analysis revealed that the shape of the Hfx-AgNPs was spherical and a size range was 5.77- 73.14 nm. The XRD spectra showed a crystallographic plane of silver nanoparticles, with a crystalline size of 29.28 nm. The prominent FTIR peaks obtained at 3281, 1644 and 1250 cm− 1 identified the Functional groups involved in the reduction of silver ion reduction to AgNPs. Zeta potential results revealed a negative surface charge and stability of Hfx-AgNPs. Colloidal solution of Hfx-AgNPs with concentrations ranging from 3.125 to 100 μg/mL was used to determine its hemolytic activity. Less than 12.5 μg/mL of tested agent showed no hemolysis with high significant decrease compared with positive control, which confirms that Hfx-AgNPs are considered non-hemolytic (non-toxic) agents according to the ISO/TR 7405-1984(f) protocol. Thrombolysis activity of Hfx-AgNPs was observed in a concentration-dependent manner. Further, Hfx-AgNPs may be considered a promising lead compound for the pharmacological industry.


Author(s):  
J. Y. Rau ◽  
K. W. Hsiao ◽  
J. P. Jhan ◽  
S. H. Wang ◽  
W. C. Fang ◽  
...  

Bridge is an important infrastructure for human life. Thus, the bridge safety monitoring and maintaining is an important issue to the government. Conventionally, bridge inspection were conducted by human in-situ visual examination. This procedure sometimes require under bridge inspection vehicle or climbing under the bridge personally. Thus, its cost and risk is high as well as labor intensive and time consuming. Particularly, its documentation procedure is subjective without 3D spatial information. In order cope with these challenges, this paper propose the use of a multi-rotary UAV that equipped with a SONY A7r2 high resolution digital camera, 50 mm fixed focus length lens, 135 degrees up-down rotating gimbal. The target bridge contains three spans with a total of 60 meters long, 20 meters width and 8 meters height above the water level. In the end, we took about 10,000 images, but some of them were acquired by hand held method taken on the ground using a pole with 2–8 meters long. Those images were processed by Agisoft PhotoscanPro to obtain exterior and interior orientation parameters. A local coordinate system was defined by using 12 ground control points measured by a total station. After triangulation and camera self-calibration, the RMS of control points is less than 3 cm. A 3D CAD model that describe the bridge surface geometry was manually measured by PhotoscanPro. They were composed of planar polygons and will be used for searching related UAV images. Additionally, a photorealistic 3D model can be produced for 3D visualization. In order to detect cracks on the bridge surface, we utilize object-based image analysis (OBIA) technique to segment the image into objects. Later, we derive several object features, such as density, area/bounding box ratio, length/width ratio, length, etc. Then, we can setup a classification rule set to distinguish cracks. Further, we apply semi-global-matching (SGM) to obtain 3D crack information and based on image scale we can calculate the width of a crack object. For spalling volume calculation, we also apply SGM to obtain dense surface geometry. Assuming the background is a planar surface, we can fit a planar function and convert the surface geometry into a DSM. Thus, for spalling area its height will be lower than the plane and its value will be negative. We can thus apply several image processing technique to segment the spalling area and calculate the spalling volume as well. For bridge inspection and UAV image management within a laboratory, we develop a graphic user interface. The major functions include crack auto-detection using OBIA, crack editing, i.e. delete and add cracks, crack attributing, 3D crack visualization, spalling area/volume calculation, bridge defects documentation, etc.


2017 ◽  
Author(s):  
Dahong Wang ◽  
Lanlan Wei ◽  
Shuaiying Zhang

The biological activities of quinoxalone, a novel small molecular substance isolated from the broth of the myxobacterium Stigmatella eracta WXNXJ-B, was investigated. This study was designed to determine the anti-proliferative, apoptotic property of quinoxalone, using B16 mouse melanoma cells as a model system. The results showed that quinoxalone has antitumor activity and can significantly inhibit the proliferation of B16 cells. The extent and the timing of apoptosis were strongly dependent on the dose. After treating with quinoxalone and staining with Hoechst 33342, B16 cells showed typical apoptotic morphological features such as chromatin condensation by fluorescent microscopy. DNA isolated from B16 cells cultured with quinoxalone showed a typical DNA ladder of apoptosis in agarose gel electrophoresis. Further investigation results showed that the apoptotic machinery of B16 induced by quinoxalone was associated with drop in mitochondrial membrane potential from 5.35% to 23.7%, up-regulation of Bax and down-regulation of Bcl-2 in a dose-dependent manner. And a significant increased activation of caspase-3. Our finding suggests that quinoxalone could suppress the growth of B16 cells and reduces cell survival via disturbing mitochondrial membrane potential and inducing apoptosis of tumor cells.


Author(s):  
Shilin Wang ◽  
Wing Hong Lau ◽  
Alan Wee-Chung Liew ◽  
Shu Hung Leung

Recently, lip image analysis has received much attention because the visual information extracted has been shown to provide significant improvement for speech recognition and speaker authentication, especially in noisy environments. Lip image segmentation plays an important role in lip image analysis. This chapter will describe different lip image segmentation techniques, with emphasis on segmenting color lip images. In addition to providing a review of different approaches, we will describe in detail the state-of-the-art classification-based techniques recently proposed by our group for color lip segmentation: “Spatial fuzzy c-mean clustering” (SFCM) and “fuzzy c-means with shape function” (FCMS). These methods integrate the color information along with different kinds of spatial information into a fuzzy clustering structure and demonstrate superiority in segmenting color lip images with natural low contrast in comparison with many traditional image segmentation techniques.


2018 ◽  
Vol 10 (11) ◽  
pp. 4235 ◽  
Author(s):  
Yu Sun ◽  
Elisabete Silva ◽  
Wei Tian ◽  
Ruchi Choudhary ◽  
Hong Leng

In this paper, we developed a new integrated analysis environment in order to thoroughly analyses urban-building energy patterns, named IUBEA (integrated urban building energy analysis), which focuses on energy modeling and analysis of a city’s building stock to support district or city-scale efficiency programs. It is argued that cities and towns account for more than two-thirds of world energy consumption. Thus, this paper explores techniques to integrate a spatial analysis environment in the field of urban building energy assessment in cites to make full use of current spatial data relevant to urban-building energy consumption and energy efficiency policies. We illustrate how multi-scale sampling and analysis for energy consumption and simulate the energy-saving scenarios by taking as an example of Greater London. In the final part, is an application of an agent-based model (ABM) in IUBEA regarding behavioral and economic characteristics of building stocks in the context of building energy efficiency. This paper first describes the basic concept for this integrated spatial analysis environment IUBEA. Then, this paper discusses the main functions for this new environment in detail. The research serves a new paradigm of the multi-scale integrated analysis that can lead to an efficient energy model, which contributes the body of knowledge of energy modeling beyond the single building scale. Findings also proved that ABM is a feasible tool to tackle intellectual challenges in energy modeling. The final adoption example of Greater London demonstrated that the integrated analysis environment as a feasible tool for building energy consumption have unique advantages and wide applicability.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3994-3994
Author(s):  
Thomas H. Fischer ◽  
Alisa S. Wolberg ◽  
Arthur P. Bode ◽  
Kevin J. Ramer ◽  
Timothy C. Nichols

Abstract The experiments presented here were undertaken to determine if factor VIIa (rFVIIa, the Novo Nordisk product NovoSeven™) will directly bind to rehydrated, lyophilized (RL) platelets (Stasix™ platelets, Entegrion, Inc. trade) for the formation of a catalytic surface with an enhanced ability to generate thrombin. The relationship of rFVIIa to the RL platelet surface was examined by measuring equilibrium and non-equilibrium binding of the coagulation factor to the cells, by studying the subcellular localization of the coagulation factor on RL platelets, and by following the effects of the surface modification on the kinetics of thrombin generation. The association of rFVIIa with RL platelets occurred with an on rate of 3.6x103 sec−1moles−1. Saturation occurred in minutes and was calcium dependent. Disassociation (in plasma or citrated saline) was slow, with over half of the coagulation factor remaining bound after two hours (with slow and fast rate constants of 5.0x10−5 and 4.1x10−4 sec−5 respectively). These results define a binding site with an apparent equilibrium constants of 110 nM. Equilibrium binding of rFVIIa to RL platelets was analyzed with flow cytometry and Western analysis. The rFVIIa was bound to RL platelets in a dose-dependent manner when incubated at concentrations of 0.3 to 10.0 uM rFVIIa and 3x104 to 106 RL platelets/ul in citrated saline. When high concentrations of rFVIIa were bound to RL platelets densities of over one million molecules of rFVIIa per RL platelet was obtained. Fluorescent microscopy analysis revealed that the rFVIIa was localized to the surface membrane and that some rFVIIa localized internally to the outer surface of the surface connected open canalicular system and/or sites of internal trafficking. Flow cytometric analysis with annexin V demonstrated that considerable quantities of phosphatidylserine were present on the external surface of the RL platelet membrane for potential facilitation of rFVIIa binding. The effect of RL platelet surface modification by rFVIIa on thrombin generation was investigated by following the hydrolysis of the thrombin-specific fluorogenic substate D-phe-pro-arg-ANSNHin plasma. rFVIIa and RL platelets accelerated thrombin generation in this system with rFVIIa being approximately twice as effective (per molecule of the recombinant protein) when added to the assay system pre-bound to RL platelets as compared to being initially free in the plasma. Similar results were obtained when free and RL platelet bound rFVIIa were tested in factor IX-deficient plasma. These experiments show that rFVIIa retains activity when super-saturated on the RL platelet membrane. The results of the studies presented here suggest that RL platelets can be used to concentrate rFVIIa at sites of vascular injury.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 3509-3509 ◽  
Author(s):  
Miki Nakamura ◽  
Takahiro Kamimoto ◽  
Tamotsu Yoshimori ◽  
Hiroaki Mitsuya ◽  
Hiroyuki Hata

Abstract Introduction Some macrolide antibiotics exert effects other than anti-bacterial activity on the growth and viability of certain cancer cells. The presence of cytoplasmic vacuoles is one the salient features of autophagy, a cellular event believed to recycle cellular ingredients under nutrient-starved conditions. Such vacuoles (autophagosomes) fuse with lysozomes, generating autolysozomes toward later stages of autophagy, digesting organelles and degenerated proteins. Our own and others’ findings that a macrolide antibiotic clarithromicin (CAM) occasionally shows anti-myeloma effects when combined with thalidomide and/or dexamethasone prompted us to examine CAM for its effects on myeloma cells in vitro. Methods Four myeloma cell lines (12PE, KHM-11, KMM-1 and U266) and primary myeloma cells purified by CD138-conjugated immune-magnetic beads (Miltenvi Biotec, Auburn, CA) were utilized. Clarithromicin was obtained from Taisho-Toyama pharmaceuticals (Tokyo, JAPAN). Morphology was analyzed either by May-Giemza staining or electron microscopy. Autolysozome was stained with Lysotracker (Invitrogen, Carlsbad, CA) and analyzed using fluorescent microscopy. Antibody to LC3 was obtained from Dr. T. Yoshimori (Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University). Results and discussion CAM induced vacuoles in the cytoplasm of both myeloma cell lines and primary myeloma cells at concentrations ranging from 10 to 50 mg/ml at a dose-dependent manner after ~18 hours treatment. Electron microscopy revealed that those vacuoles morphologically resemble autolysozomes. To further confirm the identity of autolysozomes, cells were stained with Lysotracker, which specifically stains acid lysozome. After the treatment with CAM, the accumulation of vacuoles in the cytoplasm, stained with Lysotacker, was observed. Since initiation of autophagy depends on PI3-kinase, we investigated whether CAM induced AKT phosphorylation. AKT phosphorylation was readily observed, and moreover, the emergence of vacuoles stainable with Lysotracker was inhibited when the cells were pretreated with PI3-kinase inhibitors, 3MA or LY294002, strongly suggesting that vacuolation is indeed mediated with PI3-kinase. To further confirm that autopahgy is induced by CAM, the process of LC3-I to LC3-II, a hallmark of autophagy, was examined. We found that the induction of LC3-II by CAM occurred at a dose-dependent manner. Taken together, these findings strongly suggest that CAM induces autolysozome accumulation through activating PI3-kinase. Finally, we examined whether CAM induced apoptosis when combined with thalidomide. Three myeloma cells lines, which abundantly expressed Bcl-2, showed no growth inhibition, while KHM-11, which was defective in Bcl-2, showed marked apoptosis and growth inhibition with the combination of CAM and thalidomide, suggesting that CAM might potentially augment anti-myeloma activity of thalidomide although the mechanisms are to be determined. Taken these observations together, the manipulation of certain autophagy processes with reagents such as macrolides (i.e., CAM) might represent a new therapeutic approach in the treatment of myeloma. We hypothesize that CAM dually functions in the event of autophagy, i.e., it initiates autophagy while it suppresses autophagy at later stages. Further study under the hypothesis is currently underway.


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