Mapping of retardance,diattenuation and polarizance vector on Poincare sphere for diagnosis and classification of cervical precancer

The mapping of diattenuation, polarizance and retardance vector (normalized Stokes vector) on Poincare sphere, evaluated from Mueller matrix of optically anisotropic stromal region of cervical tissues, is presented for cervical precancer detection and its staging. This reveals that the changes in the polarization states shown by these normalized Stokes vectors corresponds to the degradation of linearly arranged collagen fibers, breakage of the collagen cross links in the stromal region and change in the density of scattering sites when cervical cancer evolves. The distinct nature of real and imaginary parts of the refractive index for linear, linear‐45 and circular polarization from the optically anisotropic stromal region underscore the various polarization structures of the connective tissue region which get modified during the pathological changes. It has been found that versatility of these vectors for normal and precancerous cervical tissue of various grades may be utilized as a key distinction for qualitative staging of cervical precancer tissue. Quantitative classification of precancerous stages of cervical precancer has been determined with 95%–100% sensitivity and 93%–100% specificity through the evaluation of linear and circular diattenuation, linear polarizance and linear birefringence from the components of the respective vectors.     

Development of a polarization imaging method to detect paraffin-embedded pathology tissues before applying other techniques

The present article describes the development of a technique, applied to paraffin-embedded tissues, which uses three different wavelengths of monochromatic light (λ1 = 445 nm, λ2 = 540 nm and λ3 = 660 nm) for the measures of the degree of polarization, degree of linear polarization, degree of circular polarization and birefringence, all obtained from measurements of Stokes parameters by using polarized light. The goal of this study was to detect changes in developing embryonic mouse eye when pregnant mice fed diets without folic acid for variable periods compared with a healthy control group. We present a biomedical diagnostic technique based on polarized light detection applied to paraffin-embedded tissues to visualize the structural damage to aid us in the diagnosis before applying other techniques. Through this method, we can visualize and identify which parts of the tissue were altered with respect to the control group.     

Imaging linear and circular polarization features in leaves with complete Mueller matrix polarimetry

Spectropolarimetry of intact plant leaves allows to probe the molecular architecture of vegetation photosynthesis in a non-invasive and non-destructive way and, as such, can offer a wealth of physiological information. In addition to the molecular signals due to the photosynthetic machinery, the cell structure and its arrangement within a leaf can create and modify polarization signals. Using Mueller matrix polarimetry with rotating retarder modulation, we have visualized spatial variations in polarization in transmission around the chlorophyll a absorbance band from 650?nm to 710?nm. We show linear and circular polarization measurements of maple leaves and cultivated maize leaves and discuss the corresponding Mueller matrices and the Mueller matrix decompositions, which show distinct features in diattenuation, polarizance, retardance and depolarization. Importantly, while normal leaf tissue shows a typical split signal with both a negative and a positive peak in the induced fractional circular polarization and circular dichroism, the signals close to the veins only display a negative band. The results are similar to the negative band as reported earlier for single macrodomains. We discuss the possible role of the chloroplast orientation around the veins as a cause of this phenomenon. Systematic artefacts are ruled out as three independent measurements by different instruments gave similar results. These results provide better insight into circular polarization measurements on whole leaves and options for vegetation remote sensing using circular polarization.     

Investigation on the potential of Mueller matrix imaging for digital staining

Digital staining based on Mueller matrix measurements and their derivatives was investigated. Mueller matrix imaging was performed at the microscopic level on gastric tissue sections. Full Mueller matrices (4 × 4) were reconstructed using recorded images, followed by the extraction of polarization parameters. The most effective parameters and their combinations were extracted from Mueller matrix elements, principal component scores and polarization parameters respectively to classify samples into three categories – i.e. cancer, dysplasia and intestinal metaplasia/normal glands for various regions of interest sizes. It was observed that two‐step classification yielded higher classification accuracy than the traditional one‐step classification and that pixel classification based on Mueller matrix elements yielded higher accuracy than that based on polarization parameters and derived principal components. Moreover, Mueller matrix images with a lower spatial resolution generated higher classification accuracy but those with a higher spatial resolution revealed more morphological details.ns.

The original stained image (top) and the digital staining image (bottom).     

USE OF FLUORESCENCE POLARIZATION DETECTION FOR THE MEASUREMENT OF FLUOPEPTIDE™ BINDING TO G PROTEIN-COUPLED RECEPTORS

ABSTRACT

G protein-coupled receptors (GPCRs) represent the single largest molecular target of therapeutic drugs currently on the market, and are also the most common target in high throughput screening assays designed to identify potential new drug candidates. A large percentage of these assays are now formatted as radioligand binding assays. Fluorescence polarization ligand binding assays can offer a non-rad alternative to radioligand binding assays. In addition, fluorescence polarization assays are a homogenous format that is easy to automate for high throughput screening. We have developed a series of peptide ligands labeled with the fluorescent dye BODIPY® TMR whose binding to GPCRs can be detected using fluorescence polarization methodology. BODIPY® TMR has advantages over the more commonly used fluorescein dye in high throughput screening (HTS) assays due to the fact that its excitation and emission spectra are red-shifted approximately 50 nm relative to fluorescein. Assays based on BODIPY® TMR ligands are therefore less susceptible to interference from tissue auto-fluorescence in the assay matrix, or the effects of colored or fluorescent compounds in the screening libraries. A series of BODIPY® TMR labeled peptides have been prepared that bind to a range of GPCRs including melanin concentrating hormone, bradykinin, and melanocortin receptors. Conditions have been optimized in order to utilize a comparable amount of receptor membrane preparation as is used in a radioligand binding assay. The assays are formatted in 384-well microplates with a standard volume of 40 µL. We have compared the assays across the different fluorescence polarization (FP) readers available to determine the parameters for each instrument necessary to achieve the required precision.     

Mueller matrix decomposition for polarized light assessment of biological tissues

The Mueller matrix represents the transfer function of an optical system in its interactions with polarized light and its elements relate to specific biologically or clinically relevant properties. However, when many optical polarization effects occur simultaneously, the resulting matrix elements represent several “lumped” effects, thus hindering their unique interpretation. Currently, no methods exist to extract these individual properties in turbid media. Here, we present a novel application of a Mueller matrix decomposition methodology that achieves this objective. The methodology is validated theoretically via a novel polarized‐light propagation model, and experimentally in tissue simulating phantoms. The potential of the approach is explored for two specific biomedical applications: monitoring of changes in myocardial tissues following regenerative stem cell therapy, through birefringence‐induced retardation of the light's linear and circular polarizations, and non‐invasive blood glucose measurements through chirality‐induced rotation of the light's linear polarization. Results demonstrate potential for both applications. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Strong Near-infrared Avalanche Photoluminescence from Ag Nanowire Arrays

Ag nanowire (NW) arrays with NW diameter d _NW?=?12–120 nm were electrodeposited in anodic aluminum oxide templates. Strong avalanche photoluminescence (PL) from Ag NW arrays with small d _NW were observed near 914 nm by using picosecond laser at the excitation wavelength 808 nm, which is originated from the plasmon-enhanced radiative intraband transitions. The peak PL intensity of the avalanche PL from the sample with small diameter d _NW?=?12 nm is about 10² times stronger than that of the linear PL from the sample with large diameter d _NW?=?120 nm. The opposite excitation polarization dependence and emission polarization distribution of the PL from Ag NW array with d _NW?=?12 nm and d _NW?=?120 nm were also observed.     

Tissue inhibitor of metalloproteinase-4 instigates apoptosis in transformed cardiac fibroblasts

Tumor cells become malignant, in part, because of their activation of matrix metalloproteinases (MMPs) and inactivation of tissue inhibitor of metalloproteinases (TIMPs). Myocardial tumors are rarely malignant. This raises the possibility that the MMPs and TIMPs are differentially regulated in the heart compared to other tissues. Therefore, we hypothesized that a tissue specific tumor suppressor exists in the heart. To test this hypothesis we prepared cardiac tissue extracts from normal (n = 4), ischemic cardiomypathic (ICM) [n = 5], and dilated cardiomyopathic (DCM) [n = 8] human heart end-stage explants. The level of cardiospecific TIMP-4 was determined by SDS-PAGE and Western-blot analysis. The results suggested reduced levels of TIMP-4 in ICM and DCM as compared to normal heart. TIMP-4 was purified by reverse phase HPLC and gelatin-sepharose affinity chromatography. Collagenase inhibitory activity of chromatographic peaks was determined using fluorescein-conjugated collagen as substrate and fluorescence spectroscopy. The activity of TIMP-4 (27 kDa) was characterized by reverse zymography. The role of TIMP-4 in cardiac fibroblast cell migration was examined using Boyden chamber analysis. The results suggested that TIMP-4 inhibited cardiac fibroblast cells migration and collagen gel invasion. To test whether TIMP-4 induces apoptosis, we cultured cardiac normal and polyomavirus transformed fibroblast cells in the presence and absence of TIMP-4. The number of cells were measured and DNA laddering was determined. The results suggested that TIMP-4 controlled normal cardiac fibroblast transformation and induced apoptosis in transformed cells. Cardiospecific TIMP-4 plays a significant role in regulating the normal cell phenotype. The reduced levels of TIMP-4 elicit cellular transformation and may lead to adverse extracellular matrix degradation (remodeling), cardiac hypertrophy and failure. This study suggests a possible protective role of TIMP-4 in other organs which are susceptible to malignancy.     

Determination of fluoxetine, norfluoxetine and their enantiomers in rat plasma and brain samples by liquid chromatography with fluorescence detection

Fluoxetine (FLX) and norfluoxetine (NFLX) racemic mixtures were determined by reversed-phase liquid chromatography with fluorescence detection (lambda(exc)=227 nm, lambda(em)=305 nm). The calibration curves prepared from drug-free plasma and brain were linear in the range of 5-1000 ng ml(-1) and 100-40,000 ng g(-1) for doped samples, with detection limits of 3.2 and 2.1 ng ml(-1) in plasma and 31.5 and 26.1 ng g(-1) in brain tissue for FLX and NFLX, respectively. Enantiomer determination was carried out through normal phase HPLC-FD (lambda(exc)=224 nm, lambda(em)=336 nm) after precolumn chiral derivatization with R-1-(1-naphthyl)ethyl isocyanate. Standard curves also prepared in a drug-free matrix were linear for each enantiomer over the range of 2-1000 ng ml(-1) and 20-7000 ng g(-1) with detection limits for the four compounds ranging between 0.2 and 0.5 ng ml(-1) in plasma and between 3.0 and 8.2 ng g(-1) in brain tissue. In both methods the analytes were isolated from the biological matrix by a new solid-phase extraction procedure with recovery in plasma and brain over 90 and 87%, respectively. The repeatability of this extraction procedure was satisfactory within-day and between-day with CV<9.1%. This study also offered the opportunity to obtain an assessment of the potential relationships between the concentration of individual enantiomers of FLX and NFLX in plasma and brain tissue after chronic treatment with racemic FLX at a dose intended to mimic the human plasma concentration of FLX in standard clinical conditions, and therefore should make for more reliable extrapolation of neurochemical findings in other species.     

Identifying causal networks linking cancer processes and anti‐tumor immunity using Bayesian network inference and metagene constructs

Cancer arises from a deregulation of both intracellular and intercellular networks that maintain system homeostasis. Identifying the architecture of these networks and how they are changed in cancer is a pre‐requisite for designing drugs to restore homeostasis. Since intercellular networks only appear in intact systems, it is difficult to identify how these networks become altered in human cancer using many of the common experimental models. To overcome this, we used the diversity in normal and malignant human tissue samples from the Cancer Genome Atlas (TCGA) database of human breast cancer to identify the topology associated with intercellular networks in vivo. To improve the underlying biological signals, we constructed Bayesian networks using metagene constructs, which represented groups of genes that are concomitantly associated with different immune and cancer states. We also used bootstrap resampling to establish the significance associated with the inferred networks. In short, we found opposing relationships between cell proliferation and epithelial‐to‐mesenchymal transformation (EMT) with regards to macrophage polarization. These results were consistent across multiple carcinomas in that proliferation was associated with a type 1 cell‐mediated anti‐tumor immune response and EMT was associated with a pro‐tumor anti‐inflammatory response. To address the identifiability of these networks from other datasets, we could identify the relationship between EMT and macrophage polarization with fewer samples when the Bayesian network was generated from malignant samples alone. However, the relationship between proliferation and macrophage polarization was identified with fewer samples when the samples were taken from a combination of the normal and malignant samples. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:470–479, 2016     

Polarized fluorescence spectroscopy of oriented isolated spinach Photosystem I particles

The fluorescence anisotropy of Photosystem I (PS I) particles, isolated from spinach chloroplasts and containing approximately 200 chlorophyll molecules per reaction center, is investigated at low temperatures. The particles are oriented by squeezing in polyacrylamid gels with different macroscopic deformation parameters. Fluorescence anisotropy is measured upon steady state excitation with a laser line at 632.8 nm. A formula for the fluorescence anisotropy in oriented Photosystem I particles is applied for a different polarization of the linearly polarized exciting light. Our calculations are based on the consideration of the Photosystem I complex as a triple-chromophore complex: the absorbing chlorophyll molecules (chl), belonging to the light-harvesting complex of PS I (LHC), and two fluorophores, emitting at 720 nm (F720) and at 735 nm (F735), respectively. Using polarized fluorescence spectroscopy with a different polarization of the linearly polarized exciting light, the experimental dependence of the fluorescence anisotropy on this polarization is obtained. Based on this dependence and applying the derived formula, as a first approximation, both the orientation of the photosynthetic pigments with respect to the membrane and their mutual orientation are determined in PS I particles. As the most probable average orientational angles in PS I particles, we obtained the values 35°÷ 50°, 50°÷ 60°, and 65°÷ 67° for the absorbing dipoles of chl and for the emission dipoles of F720 and F735, respectively, with the normal of the plane of the membrane. For their mutual orientation, the following limits are determined: 10°÷ 20°, 40 ± 2°, 20°÷ 30° for the angles between chl and F720, chl and F735; and F720 and F735, correspondingly. Of course, the values of the angles estimated as a result of our study are an average value of all angles of the excited transitions and must be considered as their first approximation valid for the idealized case when all PS I particles are oriented in gel. This revised version was published online in June 2006 with corrections to the Cover Date.     

Colon cancer detection by using Poincaré sphere and 2D polarimetric mapping of ex vivo colon samples

This work is dedicated to the diagnosis and grading of colon cancer by a combined use of Poincaré sphere and 2D Stokes vector polarimetry mapping approaches. The major challenge consists in exploring the applicability of polarized light for noninvasive screening of the histological abnormalities within the samples of biological tissues. Experimental studies were conducted in ex vivo colon sample, excised after surgical procedure for colon tumor removal of G2‐adenocarcinoma lesion. Polarimetric measurements in linear and circular regime were carried via personally developed polarimetric, optical set‐up, using supercontinuous fiber laser with irradiation fixed at 635 nm. We apply the Poincaré sphere and two‐dimensional Stokes vector scanning approach for screening the corresponding tissue samples. A comparison between linear and circular polarization states is made both for quantitative and qualitative evaluations. It is shown that circular polarization has better diagnostic capabilities than linear polarization, with higher dynamic ranges of the polarimetric parameters and better values of the diagnostic quantities. In addition to the standard polarimetry parameters, utilized as essential diagnostic markers, we apply statistical analysis to obtain more detailed information in frame of the applied diagnostic approach.     

Anisotropy of the emission and absorption bands of spinach chloroplasts measured by fluorescence polarization and polarized excitation spectra at low temperature

Spectra of fluorescence polarization were measured between 4 and 120 K of spinach chloroplasts, oriented in a magnetic field. At least seven emission bands were observed. The well known bands near 685 nm (‘F-685’) and 735–740 nm (‘F-735’) and the band near 680 nm (‘F-680’) were strongly polarized parallel to the plane of the thylakoid membrane, whereas emission bands near 695 nm (‘F-695’), 710, 730–735 and 760 nm showed perpendicular polarization. Assuming perfect orientation of the thylakoid membranes, we calculated orientation angles of 64, 47 and 66.5° for the emission dipoles of F-685, F-695 and F-735, respectively, with respect to the normal of the membrane. Excitation spectra of F-695 and F-735 in polarized light at 4 K provided information about the orientation of the absorption dipoles of chlorophylls a and b. The spectra thus obtained were in very good agreement with the linear dichroism spectrum. Moreover, they allowed us to distinguish between the pigments associated with Photosystems I and Ii, which is not possible from measurement of linear dichroism alone. The results indicate that a high degree of orientation is not confined to the long-wave absorbing bands, but also bands at shorter wavelength show a clear anisotropy. The calculated orientations were in quantitative agreement with the hypothesis that F-685 and F-735 are associated with chlorophylls absorbing at 676 and 710–715 nm, respectively.     

生物组织的折射和折射率

光在生物组织中的传播与组织的光学性质有关。光通过组织时,光强和光的偏振状态会发生变化。而折射率是组织光学用来评价组织改变光线行进方向的基本参量。本文以菲涅耳公式为理论依据,用空气一组织界面的反射率、生物组织薄膜的反射率和生物组织反射光的倔振分量,推算生物组织的折射率。     

Biochemical changes induced by grape seed extract and low level laser therapy administration during intraoral wound healing in rat liver: an experimental and in silico study

In the present study, the changes that occur in rat liver tissue as a result of the use of grape seed extract (GSE) and low level laser therapy (LLLT) in intraoral wound (IW) healing are analyzed using biochemical parameters. Diode laser application groups received 8 J/cm² dose LLLT once a day for 4 days (810 nm wavelength, continuous mode, 0.25 W, 9 s). As a result of the biological parameter analysis, it was determined that the oxidative damage caused by the IWs and recovery period on 7th and 14th days could be substantially removed with GSE applications that have antioxidant capacity especially in rat liver tissue. In addition, the active compound of grape seed, catechin is studied in the active site of glycogen synthase kinase 3 (GSK3) target using molecular modeling approaches. Post-processing molecular dynamics (MD) results for catechin is compared with a standard GSK3 inhibitor. MD simulations assisted for better understanding of inhibition mechanism and the crucial amino acids contributing in the ligand binding. These results along with a through free energy analysis of ligands using sophisticated simulations methods are quite striking and it suggests a greater future role for simulation in deciphering complex patterns of molecular mechanism in combination with methods for understanding drug-receptor interactions.     

Principal component analysis and artificial neural network analysis of oral tissue fluorescence spectra: classification of normal premalignant and malignant pathological conditions

Pulsed laser-induced autofluorescence spectroscopic studies of pathologically certified normal, premalignant, and malignant oral tissues were carried out at 325 nm excitation. The spectral analysis and classification for discrimination among normal, premalignant, and malignant conditions were performed using principal component analysis (PCA) and artificial neural network (ANN) separately on the same set of spectral data. In case of PCA, spectral residuals, Mahalanobis distance, and scores of factors were used for discrimination among normal, premalignant, and malignant cases. In ANN, parameters like mean, spectral residual, standard deviation, and total energy were used to train the network. The ANN used in this study is a classical multiplayer feed-forward type with a back-propagation algorithm for the training of the network. The specificity and sensitivity were determined in both classification schemes. In the case of PCA, they are 100 and 92.9%, respectively, whereas for ANN they are 100 and 96.5% for the data set considered.     

Plasmon Resonances in V-Shaped Gold Nanostructures

Using numerical simulations, we examine the change in plasmon resonance behavior in gold nanorod structures that have a V shape. The reduction in symmetry compared to linear rods causes two different longitudinal-type resonances to appear in a single structure, and the relative intensity and hybridization of these can be controlled by varying the angle of the arms of the ??V.?? The resonances may also be selectively excited by controlling the polarization of the incident light, thereby providing a convenient way to control a nanoscale optical electric field using far-field parameters. For example, the wavelength at which a strong resonance occurs in the V-shaped structures studied can be switched between 630 and 900?nm by a 90° rotation of the polarization of the incident light. Due to the symmetry of the targets, there will be three types of special near-field location; a location at which the electric field intensity is enhanced by either resonance, a location at which the electric field intensity is enhanced by the 630?nm resonance but not by the 890?nm resonance, and a location at which the electric field intensity is enhanced by the 890?nm resonance but not by the 630?nm one.     

Synthesis rates and binding kinetics of matrix products in engineered cartilage constructs using chondrocyte-seeded agarose gels

Large-sized cartilage constructs suffer from inhomogeneous extracellular matrix deposition due to insufficient nutrient availability. Computational models of nutrient consumption and tissue growth can be utilized as an efficient alternative to experimental trials to optimize the culture of large constructs; models require system-specific growth and consumption parameters. To inform models of the [bovine chondrocyte]−[agarose gel] system, total synthesis rate (matrix accumulation rate+matrix release rate) and matrix retention fractions of glycosaminoglycans (GAG), collagen, and cartilage oligomeric matrix protein (COMP) were measured either in the presence (continuous or transient) or absence of TGF-β3 supplementation. TGF-β3's influences on pyridinoline content and mechanical properties were also measured. Reversible binding kinetic parameters were characterized using computational models. Based on our recent nutrient supplementation work, we measured glucose consumption and critical glucose concentration for tissue growth to computationally simulate the culture of a human patella-sized tissue construct, reproducing the experiment of Hung et al. (2003). Transient TGF-β3 produced the highest GAG synthesis rate, highest GAG retention ratio, and the highest binding affinity; collagen synthesis was elevated in TGF-β3 supplementation groups over control, with the highest binding affinity observed in the transient supplementation group; both COMP synthesis and retention were lower than those for GAG and collagen. These results informed the modeling of GAG deposition within a large patella construct; this computational example was similar to the previous experimental results without further adjustments to modeling parameters. These results suggest that these nutrient consumption and matrix synthesis models are an attractive alternative for optimizing the culture of large-sized constructs.