Detection of Brain Tumor in MRI Image through Fuzzy-Based Approach

The process of accurate detection of edges of MRI images of a brain is always a challenging but interesting problem. Accurate detection is very important and critical for the generation of correct diagnosis. The major problem that comes across while analyzing MRI images of a brain is inaccurate data. The process of segmentation of brain MRI image involves the problem of searching anatomical regions of interest, which can help radiologists to extract shapes, appearance, and other structural features for diagnosis of diseases or treatment evaluation. The brain image segmentation is composed of many stages. During the last few years, preprocessing algorithms, techniques, and operators have emerged as a powerful tool for efficient extraction of regions of interest, performing basic algebraic operations on images, enhancing specific image features, and reducing data on both resolution and brightness. Edge detection is one of the techniques of image segmentation. Here from image segmentation, tumor is located. Finally, we try to retrieve tumor from MRI image of a brain in the form of edge more accurately and efficiently, by enhancing the performance of diffe rent kinds of edge detectors using fuzzy approach

A Collaborative approach for segmentation of probe image for efficient texture recognition

Image processing methodologies and domain is quite wide and really efficient now days for real time applications Our work primarily deals with the domain of image segmentation and using segmentation concept texture recognition has been performed with comparative results and simulations performed over a particular image dataset The initial work in our proposed work is to perform segmentation on each part image then performing extraction We have focused on segmentation followed by extraction so that the classification result may not contain much error The conventional approach has been implemented in this regard first and then the main problem that has been formulated is patch up data pixels together which provide error in getting right and appropriate texture In order to deal with the problem formulated in the existing work we have proposed a new commuted method in which the extraction and segmentation of image depends on the dynamic threshold set by use

Light scattering from a magnetically tunable dense random medium with weak dissipation : ferrofluid

We present a semi-phenomenological treatment of light transmission through and its reflection from a ferrofluid, which we regard as a magnetically tunable system of dense random dielectric scatterers with weak dissipation. Partial spatial ordering is introduced by the application of a transverse magnetic field that superimposes a periodic modulation on the dielectric randomess. This introduces Bragg scattering which effectively enhances the scattering due to disorder alone, and thus reduces the elastic mean free path towards Anderson localization. Our theoretical treatment, based on invariant imbedding, gives a simultaneous decrease of transmission and reflection without change of incident linear polarisation as the spatial order is tuned magnetically to the Bragg condition, namely the light wave vector being equal to half the Bragg vector (Q). Our experimental observations are in qualitative agreement with these results. We have also given expressions for the transit (sojourn) time of light and for the light energy stored in the random medium under steady illumination. The ferrofluid thus provides an interesting physical realization of effectively a "Lossy Anderson-Bragg" (LAB) cavity with which to study the effect of the interplay of spatial disorder, partial order and weak dissipation on light transport. Given the current interest in propagation, optical limiting and storage of light in ferrofluids, the present work seems topical

Molecular control of embryonic stem cell identity

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2008.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references.Embryonic Stem (ES) cells are the in vitro derivatives of the inner cell mass of a developing embryo, and exhibit the property of pluripotency, which is the ability of a cell to give rise to all cell lineages of an organism. Therefore, these cells hold great promise in the treatment of several degenerative diseases through patientspecific cell-based therapy. Consequently, a detailed knowledge of the factors regulating ES cell identity is required in order to exploit this therapeutic potential. In order to address this subject, genome-wide location analysis (or ChIP-chip) has been used to identify downstream genes that are bound, and potentially regulated by the key pluripotency transcription factors, Oct4 and Nanog. The data from this study have also been compared and integrated with Oct4 and Nanog DNA binding data obtained in a different study using the ChIP-PET technology. In order to gain further insight into the mechanisms by which the transcription factor Nanog regulates its downstream targets, an attempt at identifying proteins interacting with Nanog has also been described. Research on ES cells has been plagued with ethical controversies since the creation of these cells requires the destruction of embryos. Recent studies have reported the reprogramming of somatic fibroblasts into an ES cell-like induced pluripotent state (iPS) by virus-mediated transduction of four transcription factors-- Oct4, Sox2, c-Myc and Klf4, thereby circumventing the use of embryos in producing pluripotent cells.In these studies, selection for the activation of the markers Oct4 or Nanog led to completely reprogrammed cells, but selection for fbx15, a downstream target of Oct4, resulted in partially reprogrammed intermediates. An unresolved issue in the field was whether these intermediates were obtained due to early drug selection in the case of fbx15 selection, or because Fbx15 expression is not relevant to pluripotency. Drug selection for fbx15 activation at later time-points, and an examination of the methylation status of the Oct4 locus of Fbx15-iPS cells suggests that the intermediates were obtained due to early drug selection and not due to selection for fbx15. Therefore, these studies have begun to elucidate a framework that governs ES cell identity, and the mechanism by which a differentiated cell can be reprogrammed into a pluripotent state.by Divya Mathur.Ph.D

Heat Shock Proteins (Hsps) Mediated Signalling Pathways During Abiotic Stress Conditions

The perception of abiotic stress and signal transduction to switch on adaptive innate responses are crucial steps in plant persistence under adverse environmental conditions. The ability of plants to respond to different stresses by maintaining protein in functional active form is of high importance and essential for cell survival. This is possible with the functional activity of heat shock proteins (Hsps), which play a role in maintaining the cellular homeostasis, and preserving the nonnative protein in a competent state for further remodeling as well as in signal transduction. Hsps mediate the stress signals either directly or indirectly, and play an important role in maintaining the homeostasis of plant cells under adverse stress conditions. Much research has been conducted to understand the complex mechanisms of the Hsps including Hsp70/90, ATPase-coupled conformational modifications, and interactions with cochaperones. In addition to this, several signaling proteins including MAP kinases, Ca2+ regulated proteins, Hsfs, reactive oxygen species are seen to be interacting with Hsps. In this study, we discuss the signal transduction of different Hsps, and their role in different signaling mechanisms

Isolation and characterization of stress inducible promoters from Pennisetum glaucum and their role in abiotic stress adaptation

Abiotic stresses including drought, salinity, oxidative stress, extreme temperatures and a combination of these stresses cause immense loss to agricultural crop production. These losses could be immensely reduced if the crops were able to tolerate these above mentioned conditions. This can be overcome by developing transgenic plants with stress inducible promoters with specific genes. Stress-inducible promoters have previously been identified, but there is a shortage of efficient promoters for gene expression that display favorable characteristics in their native plants as well as in xenogeneic species. In the present study five stress inducible promoters PgApx, PgDhn and PgHsc70, PgLea, PgHsp10 were isolated and functionally validated in the tobacco plants. Five stress inducible promoters were isolated using genome-walking method. Further, all five promoters were subjected to cis-motif analysis and identified several stress inducible and tissue specific cis-acting elements. These five full-length promoters were fused with uidA gene in plant transformation vector pMDC164 and transferred to tobacco. Putative transgenic positive plants were confirmed by PCR and positive plants advanced for T1 and T2 generations. Homozygous T2 transgenic plants were analysed for their tolerance to these stresses. The PgApx pro, PgDhn pro, PgHsc70, PgLea, PgHsp10 pro offers advantages over constitutive promoters to produce genetically modified tolerant crops to these adverse conditions. In summary, PgHsc70 pro is active in high temperatures, PgDhn pro in heat, cold and drought and PgApx pro in drought stress, PgLea pro in heat and drought, PgHsp10 pro in control, heat, cold, salt and drought stress treatments

Genome-wide Identification and Characterization of Hsp70 gene family in Pearl millet (Pennisetumglaucum)

Heat shock proteins (Hsps) are a class of molecular chaperons which are crucial for protein folding, assembly, and translocation in many normal cellular processes. They stabilize proteins and membranes, and can assist in protein refolding under stress conditions in plants. Pearl millet (Pennisetum glaucum) is highly abiotic stress tolerant, but its Hsps have not been characterized. In the present study, PgHsp70 genes were retrieved and gene information analyzed in order to characterize their structure, localization and functions. Genome-wide screening using the tools of bioinformatics identified 18 PgHsp70 genes in the pearl millet genome which have been categorized into four subfamilies depending on their cellular localization such as endoplasmic reticulum, mitochondria, chloroplast and cytoplasm. Number of introns ranged from 0-11 in PgHsp70 family genes and the genes are located across 1 to 7 chromosomes. Phylogenetic analysis of Hsp70s revealed that they are closely related to Sorghum Hsp70s. Promoter analysis showed the presence of cisacting elements such as GCN4, HSE, LTR, MBS, ABRE, MYB, and TC Aassociated with abiotic stress conditions indicating the involvement of these genes in the abiotic stress. Under vapour pressure deficit (VPD) conditions, leaf and root tissues of VPD-sensitive ICMR 1152 line, showed mild expression and in the presence of high VPD, VPD-insensitive ICMR1122 PgHsp70 genes showed high expression in leaf and root tissues in comparison with VPD-sensitive line. Gene PgcHsp70-1 displayed high transcript level under high VPD conditions. These results expand our horizon of understanding of the structure and function of Hsp70s, especially under abiotic stress conditions which can further be validated and employed in breeding programs and genetic engineering

Isolation and functional characterization of three abiotic stress-inducible (Apx, Dhn and Hsc70) promoters from pearl millet (Pennisetum glaucum L.)

Pearl millet is a C4 cereal crop that grows in arid and semi-arid climatic conditions with the remarkable abiotic stress tolerance. It contributed to the understanding of stress tolerance not only at the physiological level but also at the genetic level. In the present study, we functionally cloned and characterized three abiotic stress-inducible promoters namely cytoplasmic Apx1 (Ascorbate peroxidase), Dhn (Dehydrin), and Hsc70 (Heat shock cognate) from pearl millet. Sequence analysis revealed that all three promoters have several cis-acting elements specific for temporal and spatial expression. PgApx pro, PgDhn pro and PgHsc70 pro were fused with uidA gene in Gateway-based plant transformation pMDC164 vector and transferred into tobacco through leaf-disc method. While PgApx pro and PgDhn pro were active in seedling stages, PgHsc70 pro was active in stem and root tissues of the T2 transgenic tobacco plants under control conditions. Higher activity was observed under high temperature and drought, and less in salt and cold stress conditions. Further, all three promoters displayed higher GUS gene expression in the stem, moderate expression in roots, and less expression in leaves under similar conditions. While RT-qPCR data showed that PgApx pro and PgDhn pro were expressed highly in high temperature, salt and drought, PgHsc70 pro was fairly expressed during high temperature stress only. Histochemical and RT-qPCR assays showed that all three promoters are inducible under abiotic stress conditions. Thus, these promoters appear to be immediate candidates for developing abiotic stress tolerant crops as these promoter-driven transgenics confer high degree of tolerance in comparison with the wild-type (WT) plants

Comprehensive evaluation of candidate reference genes for real-time quantitative PCR (RT-qPCR) data normalization in nutri-cereal finger millet [Eleusine Coracana (L.)]

Finger millet (Eleusine coracana L.) is an annual herbaceous self-pollinating C4 cereal crop of the arid and semi-arid regions of the world. Finger millet is a food security crop proven to have resilience to changing climate and scores very high in nutrition. In the current study, we have assessed sixteen candidate reference genes for their appropriateness for the normalization studies in finger millet subjected to experimental regimes and treatments. Ten candidate reference genes (GAPDH, β-TUB, CYP, EIF4α, TIP41, UBC, G6PD, S24, MACP and MDH) were cloned and six (ACT, ELF1α, PP2A, PT, S21 and TFIID) were mined from the NCBI database as well as from the literature. Expression stability ranking of the finger millet reference genes was validated using four different statistical tools i.e., geNorm, NormFinder, BestKeeper, ΔCt and RefFinder. From the study, we endorse MACP, CYP, EIF4α to be most stable candidate reference genes in all ‘tissues’, whereas PT, TFIID, MACP ranked high across genotypes, β-TUB, CYP, ELF1α were found to be best under abiotic stresses and ‘all samples set’. The study recommends using minimum of two reference genes for RT-qPCR data normalizations in finger millet. All in all, CYP, β-TUB, and EF1α, in combination were found to be best for robust normalizations under most experimental conditions. The best and the least stable genes were validated for confirmation by assessing their appropriateness for normalization studies using EcNAC1 gene. The report provides the first comprehensive list of suitable stable candidate reference genes for nutritional rich cereal finger millet that will be advantageous to gene expression studies in this crop