Relative expression orderings

It is a basic task in high-throughput gene expression profiling studies to identify differentially expressed genes (DEGs) between two phenotypes. RankComp, an algorithm, could analyze the highly stable withinsample relative expression orderings (REOs) of gene pairs in a particular type of human normal tissue that are widely reversed in the cancer condition, thereby detecting DEGs for individual disease samples measured by a particular platform.

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It is often difficult to obtain sufficient quantity of RNA molecules for gene expression profiling under many practical situations. Amplification from low-input samples may induce artificial signals.

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Due to experimental batch effects, the application of a quantitative transcriptional signature for disease diagnoses commonly requires inter-sample data normalization, which would be hardly applicable under common clinical settings. Many cancers might have qualitative differences with the non-cancer states in the gene expression pattern. Therefore, it is reasonable to explore the power of qualitative diagnostic signatures which are robust against experimental batch effects and other random factors.

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The amount of RNA per cell, namely the transcriptome size, may vary under many biological conditions including tumor. If the transcriptome size of two cells is different, direct comparison of the expression measurements on the same amount of total RNA for two samples can only identify genes with changes in the relative mRNA abundances, i.e., cellular mRNA concentration, rather than genes with changes in the absolute mRNA abundances.

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Microsatellite instability (MSI) accounts for about 15% of colorectal cancer and is associated with prognosis. Today, MSI is usually detected by polymerase chain reaction amplification of specific microsatellite markers.

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Targeted therapy for non-small cell lung cancer is histology dependent. However, histological classification by routine pathological assessment with hematoxylin-eosin staining and immunostaining for poorly differentiated tumors, particularly those from small biopsies, is still challenging.

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Precise diagnosis of the tissue origin for metastatic cancer of unknown primary (CUP) is essential for deciding the treatment scheme to improve patients’ prognoses, since the treatment for the metastases is the same as their primary counterparts.

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This paper describes a compositional semantics for temporal expressions as part of the meaning representation language (MRL) of the JANUS system, a natural language understanding and generation system under joint development by BBN Laboratoires and the Information Sciences Institute. 1 The analysis is based on a higher order intansional logic described in detail in Hinrichs, Ayuso and Scha (1987). Temporal expressions of English are translated into this language as quantifiers over times which bind temporal indices on predicates.

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Temporal reasoners for document understanding typically assume that a document’s creation date is known. Algorithms to ground relative time expressions and order events often rely on this timestamp to assist the learner. Unfortunately, the timestamp is not always known, particularly on the Web.

9p nghetay_1 07-04-2013 44 1   Download

Kihm et al. Nanoscale Research Letters 2011, 6:361 http://www.nanoscalereslett.com/content/6/1/361 NANO EXPRESS Open Access A new heat propagation velocity prevails over Brownian particle velocities in determining the thermal conductivities of nanofluids Kenneth D Kihm1,3*, Chan Hee Chon2, Joon Sik Lee3 and Stephen US Choi4 Abstract An alternative insight is presented concerning heat propagation velocity scales in predicting the effective thermal conductivities of nanofluids.

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The author discusses Packer’s thesis and its flaws in order to (A) contrast the sensuality of Rossetti’s poetry with the relative starkness of her devotional commentary. (B) reveal the secret to which Rossetti alludes in “Winter: My Secret.” (C) call into question the authenticity of recently discovered letters written by Rossetti. (D) compare Woolf’s understanding of Rossetti with a recent, more enlightened view. (E) provide a foundation for the author’s own theory about Rossetti’s life and work. 39.

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The Genetic Map Given the size and complexity of the human genome, initial efforts aimed at developing genetic maps to provide orientation and to delimit where a gene of interest may be located. A genetic map describes the order of genes and defines the position of a gene relative to other loci on the same chromosome. It is constructed by assessing how frequently two markers are inherited together (i.e., linked) by association studies. Distances of the genetic map are expressed in recombination units, or centiMorgans (cM).

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MODEL CHECKING OF FINITE-STATE SYSTEMS One way to show that a program or system meets the designer’s specification is to manually construct a proof using axioms and inference rules in a deductive system such as temporal logic, a first-order logic capable of expressing relative ordering of events. This traditional, manual approach to concurrent program verification is tedious and error-prone even for small programs.

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