A Novel GBM Saliency Detection Model Using Multi-Channel MRI

The automatic computerized detection of regions of interest (ROI) is an important step in the process of medical image processing and analysis. The reasons are many, and include an increasing amount of available medical imaging data, existence of inter-observer and inter-scanner variability, and to improve the accuracy in automatic detection in order to assist doctors in diagnosing faster and on time. A novel algorithm, based on visual saliency, is developed here for the identification of tumor regions from MR images of the brain. The GBM saliency detection model is designed by taking cue from the concept of visual saliency in natural scenes. A visually salient region is typically rare in an image, and contains highly discriminating information, with attention getting immediately focused upon it. Although color is typically considered as the most important feature in a bottom-up saliency detection model, we circumvent this issue in the inherently gray scale MR framework. We develop a novel pseudo-coloring scheme, based on the three MRI sequences, viz. FLAIR, T2 and T1C (contrast enhanced with Gadolinium). A bottom-up strategy, based on a new pseudo-color distance and spatial distance between image patches, is defined for highlighting the salient regions in the image. This multi-channel representation of the image and saliency detection model help in automatically and quickly isolating the tumor region, for subsequent delineation, as is necessary in medical diagnosis. The effectiveness of the proposed model is evaluated on MRI of 80 subjects from the BRATS database in terms of the saliency map values. Using ground truth of the tumor regions for both high- and low- grade gliomas, the results are compared with four highly referred saliency detection models from literature. In all cases the AUC scores from the ROC analysis are found to be more than 0.999 ± 0.001 over different tumor grades, sizes and positions.     

Comparative study of the chondrogenic potential of human bone marrow stromal cells, neonatal chondrocytes and adult chondrocytes

Cartilage tissue engineering is still a major clinical challenge with optimisation of a suitable source of cells for cartilage repair/regeneration not yet fully addressed. The aims of this study were to compare and contrast the differences in chondrogenic behaviour between human bone marrow stromal cells (HBMSCs), human neonatal and adult chondrocytes to further our understanding of chondroinduction relative to cell maturity and to identify factors that promote chondrogenesis and maintain functional homoeostasis. Cells were cultured in monolayer in either chondrogenic or basal medium, recapitulating procedures used in existing clinical procedures for cell-based therapies. Cell doubling time, morphology and alkaline phosphatase specific activity (ALPSA) were determined at different time points. Expression of chondrogenic markers (SOX9, ACAN and COL2A1) was compared via real time polymerase chain reaction. Amongst the three cell types studied, HBMSCs had the highest ALPSA in basal culture and lowest ALPSA in chondrogenic media. Neonatal chondrocytes were the most proliferative and adult chondrocytes had the lowest ALPSA in basal media. Gene expression analysis revealed a difference in the temporal expression of chondrogenic markers which were up regulated in chondrogenic medium compared to levels in basal medium. Of the three cell types studied, adult chondrocytes offer a more promising cell source for cartilage tissue engineering. This comparative study revealed differences between the microenvironment of all three cell types and provides useful information to inform cell-based therapies for cartilage regeneration.     

First-Order Assessment of the Influence of Three EPS and Calcite-Producing Microbes Isolated from a Cemented Sand Site on Soil Shear Strength

Subsurface geotechnical data from a cemented tailings sand site in eastern India indicated that the cementation was at least partially biogenic. Three strains of aerobic soil-residing bacteria from this site exhibited capabilities of producing extracellular polymeric substance, calcite and struvite when grown in minimal mineral salt media. These strains grew easily under a variety of physical, chemical and nutritional conditions. Drained triaxial testing of loose sand samples indicated that they became stronger upon hosting these strains. No details on EPS and calcite production of these isolates and the effects of these products on soil behavior were found in the literature.     

Enzymes of PEP-succinate pathway in Setaria cervi and effect of anthelmintic drugs

Localization of different enzymes of PEP-succinate pathway has been done in Setaria cervi, a bovine filarial worm. Succinate dehydrogenase and fumarate reductase were localized in mitochondria rich particulate fraction while all other enzymes were cytosolic. The in vitro effect of certain antifilarial/anthelmintic agents on these enzymes was also investigated. Sumarmin, at low concentration, could cause a marked inhibition of most of the enzymes of this pathway. Centperazine, an antifilarial drug being developed by CDRI showed significant inhibitory action on pyruvate kinase, lactate dehydrogenase, fumarase and succinate dehydrogenase while CDRI compound 72/70 showed significant inhibition of PEP-carboxykinase activity. Diethylcarbamazine and levamisole, however, were found to be more or less ineffective at lower concentrations against all the enzymes of this pathway.     

The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures

As yeast cultures enter stationary phase in rich, glucose-based medium, differentiation of two major subpopulations of cells, termed quiescent and nonquiescent, is observed. Differences in mRNA abundance between exponentially growing and stationary-phase cultures and quiescent and nonquiescent cells are known, but little was known about protein abundance in these cells. To measure protein abundance in exponential and stationary-phase cultures, the yeast GFP-fusion library (4159 strains) was examined during exponential and stationary phases, using high-throughput flow cytometry (HyperCyt). Approximately 5% of proteins in the library showed twofold or greater changes in median fluorescence intensity (abundance) between the two conditions. We examined 38 strains exhibiting two distinct fluorescence-intensity peaks in stationary phase and determined that the two fluorescence peaks distinguished quiescent and nonquiescent cells, the two major subpopulations of cells in stationary-phase cultures. GFP-fusion proteins in this group were more abundant in quiescent cells, and half were involved in mitochondrial function, consistent with the sixfold increase in respiration observed in quiescent cells and the relative absence of Cit1p:GFP in nonquiescent cells. Finally, examination of quiescent cell-specific GFP-fusion proteins revealed symmetry in protein accumulation in dividing quiescent and nonquiescent cells after glucose exhaustion, leading to a new model for the differentiation of these cells.     

Quantitative Immunohistochemical Analysis Reveals Association between Sodium Iodide Symporter and Estrogen Receptor Expression in Breast Cancer

Background

Human sodium iodide symporter (hNIS) gene over-expression is under active consideration worldwide as an alternative target molecule for breast cancer (BC) diagnosis and targeted radio-iodine treatment. However, the field demands better stratified analysis of endogenous hNIS expression across major BC subtypes. Therefore, we have analyzed subtype-specific variation of hNIS overexpression in breast tumor tissue samples by immunohistochemistry (IHC) and also report the development of a homogeneous, quantitative analysis method of digital IHC images.

Methods

hNIS expression was analyzed from 108 BC tissue samples by IHC. Sub-cellular localization of hNIS protein was analyzed by dual immunofluorescence (IF) staining method using hNIS and HER2 antibodies. An ImageJ based two-step digital analysis method was developed and applied for the bias-free analysis of the images.

Results

Staining of the tumor samples show 70% cases are hNIS positive indicating high incidence of hNIS positive cases in BC. More importantly, a subtype specific analysis done for the first time shows that hNIS expression is overly dominated in estrogen receptor (ER) positive cases than the receptor negative cases. Further, 56% of the ER+ve, PgR+ve, HER2-ve and 36% of ER+ve, PgR+ve, HER2+ve cases show highest intensity staining equivalent to the thyroid tissue. A significant positive correlation is also observed between hNIS and estrogen receptor expression (p = 0.0033, CI = 95%) suggesting hNIS mediated targeted radio-iodine therapy procedures may benefit both ER+ve, PgR+ve, HER2–ve as well as HER2+ve cases. Further, in a few cases, hNIS and HER2 protein localization is demonstrated by overlapping membrane co-expression. ImageJ based image analysis method shows over 70% match with manual pathological scoring method.

Conclusion

The study indicates a positive link between hNIS and ER expression in BC. The quantitative IHC image analysis method reported here will further help in patient stratification and potentially benefit global clinical assessment where hNIS mediated targeted ¹³¹I radio-ablative therapy is aimed.     

Periostin Induces Intracellular Cross-talk between Kinases and Hyaluronan in Atrioventricular Valvulogenesis

Periostin (PN), a novel fasciclin-related matricellular protein, has been implicated in cardiac development and postnatal remodeling, but the mechanism remains unknown. We examined the role of PN in mediating intracellular kinase activation for atrioventricular valve morphogenesis using well defined explant cultures, gene transfection systems, and Western blotting. The results show that valve progenitor (cushion) cells secrete PN into the extracellular matrix, where it can bind to INTEGRINs and activate INTEGRIN/focal adhesion kinase signaling pathways and downstream kinases, PI3K/AKT and ERK. Functional assays with prevalvular progenitor cells showed that activating these signaling pathways promoted adhesion, migration, and anti-apoptosis. Through activation of PI3K/ERK, PN directly enhanced collagen expression. Comparing PN-null to WT mice also revealed that expression of hyaluronan (HA) and activation of hyaluronan synthase-2 (Has2) are also enhanced upon PN/INTEGRIN/focal adhesion kinase-mediated activation of PI3K and/or ERK, an effect confirmed by the reduction of HA synthase-2 in PN-null mice. We also identified in valve progenitor cells a potential autocrine signaling feedback loop between PN and HA through PI3K and/or ERK. Finally, in a three-dimensional assay to simulate normal valve maturation in vitro, PN promoted collagen compaction in a kinase-dependent fashion. In summary, this study provides the first direct evidence that PN can act to stimulate a valvulogenic signaling pathway.