Indexing multi-dimensional uncertain data with arbitrary probability density functions

Research Session 26: Spatial and Temporal DatabasesIn an "uncertain database", an object o is associated with a multi-dimensional probability density function (pdf), which describes the likelihood that o appears at each position in the data space. A fundamental operation is the "probabilistic range search" which, given a value p q and a rectangular area r q, retrieves the objects that appear in r q with probabilities at least p q. In this paper, we propose the U-tree, an access method designed to optimize both the I/O and CPU time of range retrieval on multi-dimensional imprecise data. The new structure is fully dynamic (i.e., objects can be incrementally inserted/deleted in any order), and does not place any constraints on the data pdfs. We verify the query and update efficiency of U-trees with extensive experiments.postprintThe 31st International Conference on Very Large Data Bases (VLDB 2005), Trondheim, Norway, 30 August-2 September 2005. In Proceedings of 31st VLDB, 2005, v. 3, p. 922-93

MYC functions are specific in biological subtypes of breast cancer and confers resistance to endocrine therapy in luminal tumours.

BACKGROUND: MYC is amplified in approximately 15% of breast cancers (BCs) and is associated with poor outcome. c-MYC protein is multi-faceted and participates in many aspects of cellular function and is linked with therapeutic response in BCs. We hypothesised that the functional role of c-MYC differs between molecular subtypes of BCs. METHODS: We therefore investigated the correlation between c-MYC protein expression and other proteins involved in different cellular functions together with clinicopathological parameters, patients' outcome and treatments in a large early-stage molecularly characterised series of primary invasive BCs (n=1106) using immunohistochemistry. The METABRIC BC cohort (n=1980) was evaluated for MYC mRNA expression and a systems biology approach utilised to identify genes associated with MYC in the different BC molecular subtypes. RESULTS: High MYC and c-MYC expression was significantly associated with poor prognostic factors, including grade and basal-like BCs. In luminal A tumours, c-MYC was associated with ATM (P=0.005), Cyclin B1 (P=0.002), PIK3CA (P=0.009) and Ki67 (P<0.001). In contrast, in basal-like tumours, c-MYC showed positive association with Cyclin E (P=0.003) and p16 (P=0.042) expression only. c-MYC was an independent predictor of a shorter distant metastases-free survival in luminal A LN+ tumours treated with endocrine therapy (ET; P=0.013). In luminal tumours treated with ET, MYC mRNA expression was associated with BC-specific survival (P=0.001). In ER-positive tumours, MYC was associated with expression of translational genes while in ER-negative tumours it was associated with upregulation of glucose metabolism genes. CONCLUSIONS: c-MYC function is associated with specific molecular subtypes of BCs and its overexpression confers resistance to ET. The diverse mechanisms of c-MYC function in the different molecular classes of BCs warrants further investigation particularly as potential therapeutic targets

Mediator complex (MED) 7: a biomarker associated with good prognosis in invasive breast cancer, especially ER+ luminal subtypes

Background: Mediator complex (MED) proteins have a key role in transcriptional regulation, some interacting with the oestrogen receptor (ER). Interrogation of the METABRIC cohort suggested that MED7 may regulate lymphovascular invasion (LVI). Thus MED7 expression was assessed in large breast cancer (BC) cohorts to determine clinicopathological significance. Methods: MED7 gene expression was investigated in the METABRIC cohort (n = 1980) and externally validated using bc-GenExMiner v4.0. Immunohistochemical expression was assessed in the Nottingham primary BC series (n = 1280). Associations with clinicopathological variables and patient outcome were evaluated. Results: High MED7 mRNA and protein expression was associated with good prognostic factors: low grade, smaller tumour size, good NPI, positive hormone receptor status (p < 0.001), and negative LVI (p = 0.04) status. Higher MED7 protein expression was associated with improved BC-specific survival within the whole cohort and ER+/luminal subgroup. Pooled MED7 gene expression data in the external validation cohort confirmed association with better survival, corroborating with the protein expression. On multivariate analysis, MED7 protein was independently predictive of longer BC-specific survival in the whole cohort and Luminal A subtype (p < 0.001). Conclusions: MED7 is an important prognostic marker in BC, particularly in ER+luminal subtypes, associated with improved survival and warrants future functional analysis

Scalar and vector Mathieu transform pairs

A scalar and a vector Mathieu transform pair are developed and their properties are discussed. The orthogonality relationships of the transform kernels are derived in both the spatial and the spectral domains. Finally, Parseval's theorems for the two transforms are derived.link_to_subscribed_fulltex

SIMULTANEOUS RECONSTRUCTION OF PERMITTIVITY AND CONDUCTIVITY PROFILES IN A RADIALLY INHOMOGENEOUS SLAB.

This paper considers the simultaneous reconstruction of permittivity and conductivity profiles in a cylindrically stratified geometry. It is assumed that both the permittivity and conductivity may only vary in the radial direction, and that the unknown region, to be probed, is an annulus of known thickness. An iterative method for the simultaneous inversion of the radial permittivity and conductivity profiles inside this annulus is presented. This method employs a distorted-Born approximation at each iteration step. The inherent nonuniqueness of the problem is circumvented by imposing additional constraints that limit the set of feasible solutions. Numerical simulations show that good results can be obtained for smoothly varying profiles even when a limited number of measurements at a single frequency are used.link_to_subscribed_fulltex

SIMULTANEOUS INVERSION OF RADIALLY VARYING CONDUCTIVITY AND PERMITTIVITY PROFILES.

A hybrid approach to inversion is described that combines the method of characteristics with optimization. In order to test the inversion algorithm, synthetic data was generated by solving the forward problem for the case of a stepwise changing profile. The synthetic data is then input to the inversion algorithm, and the recovered profile is compared to original one for which the forward problem was solved. Numerical experiments with the simplest possible case, a constant tau and stepwise changing sigma , have worked satisfactorily. A simulation is illustrated. Inverting more than one parameter describing the function tau (p) has proven to be possible, but ill-conditioned. The following conjectures are based on extensive numerical experiments; they have not been proved or disproved analytically: The simultaneous inversion of general c(p) and tau (p) profiles from the Cauchy data taken over a finite time interval, for two vertical wave numbers, is generally ill-conditioned; however, if the loss is unknown only up to one parameter, the time-domain inversion procedure described here recovers the one parameter loss and c(p) is a fairly stable manner.link_to_subscribed_fulltex