Approximate Membership Localization within a Web-Based Join Framework

In this paper, we propose a search-based approach to join two tables in the absence of clean join attributes. Non-structured documents from the web are used to express the correlations between a given query and a reference list. To implement this approach, a major challenge we meet is how to efficiently determine the number of times and the locations of each clean reference from the reference list that is approximately mentioned in the retrieved documents. We formalize the Approximate Membership Localization (AML) problem and propose an efficient partial pruning algorithm to solve it. A study using real-word data sets demonstrates the effectiveness of our search-based approach, and the efficiency of our AML algorithm.

Evidence for three tumor suppressor loci on chromosome 9p involved in melanoma development

Cytogenetic and loss of heterozygosity (LOH) studies have long indicated the presence of a tumor suppressor gene (TSG) on 9p involved in the development of melanoma. Although LOH at 9p has been reported in approximately 60% of melanoma tumors, only 5-10% of these tumors have been shown to carry CDKN2A mutations, raising the possibility that another TSG involved in melanoma maps to chromosome 9p. To investigate this possibility, a panel of 37 melanomas derived from 35 individuals was analyzed for CDKN2A mutations by single-strand conformation polymorphism analysis and sequencing. The melanoma samples were then typed for 15 markers that map to 9p13-24 to investigate LOH trends in this region. In those tumors demonstrating retention of heterozygosity at markers flanking CDKN2A and LOH on one or both sides of the gene, multiplex microsatellite PCR was performed to rule out homozygous deletion of the region encompassing CDKN2A. CDKN2A mutations were found in tumors from 5 patients [5 (14%) of 35], 4 of which demonstrated LOH across the entire region examined. The remaining tumor with no observed LOH carried two point mutations, one on each allele. Although LOH was identified at one or more markers in 22 (59%) of 37 melanoma tumors corresponding to 20 (57%) of 35 individuals, only 11 tumors from 9 individuals [9 (26%) of 35] demonstrated LOH at D9S942 and D9S1748 the markers closest to CDKN2A. Of the remaining 11 tumors with LOH 9 demonstrated LOH at two or more contiguous markers either centromeric and/or telomeric to CDKN2A while retaining heterozygosity at several markers adjacent to CDKN2A. Multiplex PCR revealed one tumor carried a homozygous deletion extending from D9S1748 to the IFN-alpha locus. In the remaining eight tumors, multiplex PCR demonstrated that the observed heterozygosity was not attributable to homozygous deletion and stromal contamination at D9S1748, D9S942, or D9S974, as measured by comparative amplification strengths, which indicates that retention of heterozygosity with flanking LOH does not always indicate a homozygous deletion. This report supports the conclusions of previous studies that a least two TSGs involved in melanoma development in addition to CDKN2A may reside on chromosome 9p.

Deletion mapping suggests that the 1p22 melanoma susceptibility gene is a tumor suppressor localized to a 9-Mb interval

Loss of the short arm of chromosome 1 is frequently observed in many tumor types, including melanoma. We recently localized a third melanoma susceptibility locus to chromosome band 1p22. Critical recombinants in linked families localized the gene to a 15-Mb region between D1S430 and D1S2664. To map the locus more finely we have performed studies to assess allelic loss across the region in a panel of melanomas from 1p22-linked families, sporadic melanomas, and melanoma cell lines. Eighty percent of familial melanomas exhibited loss of heterozygosity (LOH) within the region, with a smallest region of overlapping deletions (SRO) of 9 Mb between D1S207 and D1S435. This high frequency of LOH makes it very likely that the susceptibility locus is a tumor suppressor. In sporadic tumors, four SROs were defined. SRO1 and SRO2 map within the critical recombinant and familial tumor region, indicating that one or the other is likely to harbor the susceptibility gene. However, SRO3 may also be significant because it overlaps with the markers with the highest 2-point LOD score (D1S2776), part of the linkage recombinant region, and the critical region defined in mesothelioma. The candidate genes PRKCL2 and GTF2B, within SRO2, and TGFBR3, CDC7, and EVI5, in a broad region encompassing SRO3, were screened in 1p22-linked melanoma kindreds, but no coding mutations were detected. Allelic loss in melanoma cell lines was significantly less frequent than in fresh tumors, indicating that this gene may not be involved late in progression, such as in overriding cellular senescence, necessary for the propagation of melanoma cells in culture.

Towards a controlled growth of self-assembled nanostructures: shaping, ordering and localization in Ge/Si heteroepitaxy.

The strain-induced self-assembly of suitable semiconductor pairs is an attractive natural route to nanofabrication. To bring to fruition their full potential for actual applications, individual nanostructures need to be combined into ordered patterns in which the location of each single unit is coupled with others and the surrounding environment. Within the Ge/Si model system, we analyze a number of examples of bottom-up strategies in which the shape, positioning, and actual growth mode of epitaxial nanostructures are tailored by manipulating the intrinsic physical processes of heteroepitaxy. The possibility of controlling elastic interactions and, hence, the configuration of self-assembled quantum dots by modulating surface orientation with the miscut angle is discussed. We focus on the use of atomic steps and step bunching as natural templates for nanodot clustering. Then, we consider several different patterning techniques which allow one to harness the natural self-organization dynamics of the system, such as: scanning tunneling nanolithography, focused ion beam and nanoindentation patterning. By analyzing the evolution of the dot assembly by scanning probe microscopy, we follow the pathway which leads to lateral ordering, discussing the thermodynamic and kinetic effects involved in selective nucleation on patterned substrates.

Subcellular localization of proteasomes and their regulatory complexes in mammalian cells

Proteasomes can exist in several different molecular forms in mammalian cells. The core 20S proteasome, containing the proteolytic sites, binds regulatory complexes at the ends of its cylindrical structure. Together with two 19S ATPase regulatory complexes it forms the 26S proteasome, which is involved in ubiquitin-dependent proteolysis. The 20S proteasome can also bind 11S regulatory complexes (REG, PA28) which play a role in antigen processing, as do the three variable c-interferoninducible catalytic b-subunits (e.g. LMP7). In the present study, we have investigated the subcellular distribution of the different forms of proteasomes using subunit speci®c antibodies. Both 20S proteasomes and their 19S regulatory complexes are found in nuclear, cytosolic and microsomal preparations isolated from rat liver. LMP7 was enriched approximately two-fold compared with core a-type proteasome subunits in the microsomal preparations. 20S proteasomes were more abundant than 26S proteasomes, both in liver and cultured cell lines. Interestingly, some signi®cant differences were observed in the distribution of different subunits of the 19S regulatory complexes. S12, and to a lesser extent p45, were found to be relatively enriched in nuclear fractions from rat liver, and immuno¯uorescent labelling of cultured cells with anti-p45 antibodies showed stronger labelling in the nucleus than in the cytoplasm. The REG was found to be localized predominantly in the cytoplasm. Three- to six-fold increases in the level of REG were observed following cinterferon treatment of cultured cells but c-interferon had no obvious effect on its subcellular distribution. These results demonstrate that different regulatory complexes and subpopulations of proteasomes have different distributions within mammalian cells and, therefore, that the distribution is more complex than has been reported for yeast proteasomes.

Aromatic l-amino acid decarboxylase : histochemical localization in rat kidney and lack of effect of dietary potassium or sodium loading on enzyme distribution

Utilizing a mono-specific antiserum produced in rabbits to hog kidney aromatic L-amino acid decarboxylase (AADC), the enzyme was localized in rat kidney by immunoperoxidase staining. AADC was located predominantly in the proximal convoluted tubules; there was also weak staining in the distal convoluted tubules and collecting ducts. An increase in dietary potassium or sodium intake produced no change in density or distribution of AADC staining in kidney. An assay of AADC enzyme activity showed no difference in cortex or medulla with chronic potassium loading. A change in distribution or activity of renal AADC does not explain the postulated dopaminergic modulation of renal function that occurs with potassium or sodium loading.

Towards persistent localization and mapping with a continuous appearance-based topology

Appearance-based localization can provide loop closure detection at vast scales regardless of accumulated metric error. However, the computation time and memory requirements of current appearance-based methods scale not only with the size of the environment but also with the operation time of the platform. Additionally, repeated visits to locations will develop multiple competing representations, which will reduce recall performance over time. These properties impose severe restrictions on long-term autonomy for mobile robots, as loop closure performance will inevitably degrade with increased operation time. In this paper we present a graphical extension to CAT-SLAM, a particle filter-based algorithm for appearance-based localization and mapping, to provide constant computation and memory requirements over time and minimal degradation of recall performance during repeated visits to locations. We demonstrate loop closure detection in a large urban environment with capped computation time and memory requirements and performance exceeding previous appearance-based methods by a factor of 2. We discuss the limitations of the algorithm with respect to environment size, appearance change over time and applications in topological planning and navigation for long-term robot operation.

Capping computation time and storage requirements for appearance-based localization with CAT-SLAM

Appearance-based localization is increasingly used for loop closure detection in metric SLAM systems. Since it relies only upon the appearance-based similarity between images from two locations, it can perform loop closure regardless of accumulated metric error. However, the computation time and memory requirements of current appearance-based methods scale linearly not only with the size of the environment but also with the operation time of the platform. These properties impose severe restrictions on longterm autonomy for mobile robots, as loop closure performance will inevitably degrade with increased operation time. We present a set of improvements to the appearance-based SLAM algorithm CAT-SLAM to constrain computation scaling and memory usage with minimal degradation in performance over time. The appearance-based comparison stage is accelerated by exploiting properties of the particle observation update, and nodes in the continuous trajectory map are removed according to minimal information loss criteria. We demonstrate constant time and space loop closure detection in a large urban environment with recall performance exceeding FAB-MAP by a factor of 3 at 100% precision, and investigate the minimum computational and memory requirements for maintaining mapping performance.