http://ee.sharif.edu/~miap/Files/A%20Survey%20of%20Medical%20Image%20Registration.pdf

A survey of medical image registration.

https://www.cs.princeton.edu/courses/archive/spr05/cos598E/bib/rui99_cbir_survey.pdf

Image Retrieval

The expression of genes is regulated at many levels. Perhaps the area in which least is known is how nuclear organization influences gene expression. Studies of higher-order chromatin arrangements and their dynamic interactions with other nuclear components have been boosted by recent technical advances. The emerging view is that chromosomes are compartmentalized into discrete territories. The location of a gene within a chromosome territory seems to influence its access to the machinery responsible for specific nuclear functions, such as transcription and splicing. This view is consistent with a topological model for gene regulation.

/pdf/chromosome-territories-nuclear-architecture-and-gene-36775rhtfg.pdf

Chromosome territories, nuclear architecture and gene regulation in mammalian cells.

tion of gene expression and other nuclear functions — namely the architecture of the nucleus as a whole. In particular, we describe evidence for a compartmentalized nuclear architecture in the mammalian cell nucleus based on chromosome territories (CTs) and an interchromatin compartment (IC) that contains macromolecular complexes that are required for replication, transcription, splicing and repair (summarized in FIG. 1). Other nuclear components, such as the nucleolus, nuclear lamina and pores, are not reviewed here (for reviews, see REFS 15,16), and although the focus of this review is the mammalian nucleus, the nuclear architecture of other organisms will be mentioned where appropriate. During the past two decades, various new methods have expanded the cell biologist’s ‘toolkit’ for the study of nuclear architecture and function (BOX 1). These methods have provided the basis for detailed studies of CTs, as well as for studies of the topology and dynamics of non-chromatin domains in the nucleus of fixed and, more recently, living cells. Computer simulations of CTs and nuclear architecture are also being used to make quantitative predictions that can be tested experimentally. On the basis of Despite all the celebrations associated with the sequencing of the human genome, and the genomes of other model organisms, our abilities to interpret genome sequences are quite limited. For example, we cannot understand the orchestrated activity — and the silencing — of many thousands of genes in any given cell just on the basis of DNA sequences, such as promoter and enhancer elements. How are the profound differences in gene activities established and maintained in a large number of cell types to ensure the development and functioning of a complex multicellular organism? To answer this question fully, we need to understand how genomes are organized in the nucleus, the basic principles of nuclear architecture and the changes in nuclear organization that occur during cellular differentiation. During recent years, EPIGENETIC mechanisms of gene regulation, such as DNA methylation and histone modification, have entered the centre stage of chromatin research. Modifications of DNA and nucleosomes, however, as well as boundaries and insulators, that affect gene regulation at the chromatin level are not the focus of this article. Instead, we review experimental data and models for a higher level of the regulaCHROMOSOME TERRITORIES, NUCLEAR ARCHITECTURE AND GENE REGULATION IN MAMMALIAN CELLS

Nuclear architecture and gene regulation in mammalian cells

Content-based image retrieval (CBIR) has become one of the most active research areas in the past few years. Many visual feature representations have been explored and many systems built. While these research efforts establish the basis of CBIR, the usefulness of the proposed approaches is limited. Specifically, these efforts have relatively ignored two distinct characteristics of CBIR systems: (1) the gap between high-level concepts and low-level features, and (2) the subjectivity of human perception of visual content. This paper proposes a relevance feedback based interactive retrieval approach, which effectively takes into account the above two characteristics in CBIR. During the retrieval process, the user's high-level query and perception subjectivity are captured by dynamically updated weights based on the user's feedback. The experimental results over more than 70000 images show that the proposed approach greatly reduces the user's effort of composing a query, and captures the user's information need more precisely.

Relevance feedback: a power tool for interactive content-based image retrieval

Fluorescence microscopic analysis of newly replicated DNA has revealed discrete granular sites of replication (RS). The average size and number of replication sites from early to mid S-phase suggest that each RS contains numerous replicons clustered together. We are using fluorescence laser scanning confocal microscopy in conjunction with multidimensional image analysis to gain more precise information about RS and their spatial-temporal dynamics. Using a newly improved imaging segmentation program, we report an average of ∼1,100 RS after a 5-min pulse labeling of 3T3 mouse fibroblast cells in early S-phase. Pulse-chase-pulse double labeling experiments reveal that RS take ∼45 min to complete replication. Appropriate calculations suggest that each RS contains an average of 1 mbp of DNA or ∼6 average-sized replicons. Double pulse–double chase experiments demonstrate that the DNA sequences replicated at individual RS are precisely maintained temporally and spatially as the cell progresses through the cell cycle and into subsequent generations. By labeling replicated DNA at the G1/S borders for two consecutive cell generations, we show that the DNA synthesized at early S-phase is replicated at the same time and sites in the next round of replication.

https://rupress.org/jcb/article-pdf/143/6/1415/1282483/9807091.pdf

Spatial and Temporal Dynamics of DNA Replication Sites in Mammalian Cells

Microscopy shows that individual sites of DNA replication and transcription of mammalian nuclei segregate into sets of roughly 22 and 16 higher order domains, respectively. Each domain set displayed a distinct network-like appearance, including regions of individual domains and interdigitation of domains between the two networks. These data support a dynamic mosaic model for the higher order arrangement of genomic function inside the cell nuclei.

https://science.sciencemag.org/content/sci/281/5382/1502.full.pdf

Segregation of Transcription and Replication Sites Into Higher Order Domains

Discrete analytical hyperplanes

Image retrieval based on color content is an auxiliary function for traditional text-annotated image databases. Most color-based image retrieval systems adopt color histograms as the feature of color content. One of the most important steps in these systems is to reduce histogram dimensions with the least loss in color content. A good clustering technique is vital for this purpose. This paper examines the color conservation property by applying different clustering techniques in perceptually uniform color spaces and different images. For studying color spaces, the perceptual uniform spaces, such as Mathematical Transformation to Munsell system (MTM) and C.I.E. L*a*b*, are investigated. For evaluating clustering techniques, the equalized quantization approach, the hierarchical clustering approach, and the Color-Naming-System (CNS) supervised clustering approach are studied. For analyzing color loss, the error bound, the quantized error in color space conversion, and the average quantized error of 400 color images are explored. An image retrieval application based on color content is shown to demonstrate the difference in applying these clustering techniques. These simulation results suggest that good clustering techniques usually lead to more effective retrieval.

Raj S. Acharya

Papers

Spatial and Temporal Dynamics of DNA Replication Sites in Mammalian Cells

Segregation of Transcription and Replication Sites Into Higher Order Domains

Discrete analytical hyperplanes

Color clustering techniques for color-content-based image retrieval from image databases

Biomedical imaging modalities: a tutorial