Visual Execution and Data Visualisation in Natural Language Processing

We describe GGI, a visual system that allows the user to execute an automatically generated data flow graph containing code modules that perform natural language processing tasks. These code modules operate on text documents. GGI has a suite of text visualisation tools that allows the user useful views of the annotation data that is produced by the modules in the executable graph. GGI forms part of the GATE natural language engineering system

Self-Calibration Technique for 3-point Intrinsic Alignment Correlations in Weak Lensing Surveys

The intrinsic alignment (IA) of galaxies has been shown to be a significant barrier to precision cosmic shear measurements. (Zhang, 2010, ApJ, 720, 1090) proposed a self-calibration technique for the power spectrum to calculate the induced gravitational shear-galaxy intrinsic ellipticity correlation (GI) in weak lensing surveys with photo-z measurements which is expected to reduce the IA contamination by at least a factor of 10 for currently proposed surveys. We confirm this using an independent analysis and propose an expansion to the self-calibration technique for the bispectrum in order to calculate the dominant IA gravitational shear-gravitational shear-intrinsic ellipticity correlation (GGI) contamination. We first establish an estimator to extract the galaxy density-density-intrinsic ellipticity (ggI) correlation from the galaxy ellipticity-density-density measurement for a photo-z galaxy sample. We then develop a relation between the GGI and ggI bispectra, which allows for the estimation and removal of the GGI correlation from the cosmic shear signal. We explore the performance of these two methods, compare to other possible sources of error, and show that the GGI self-calibration technique can potentially reduce the IA contamination by up to a factor of 5-10 for all but a few bin choices, thus reducing the contamination to the percent level. The self-calibration is less accurate for adjacent bins, but still allows for a factor of three reduction in the IA contamination. The self-calibration thus promises to be an efficient technique to isolate both the 2-point and 3-point intrinsic alignment signals from weak lensing measurements.Comment: 22 pages, 5 figures, matches version published in MNRAS. Published online December 5, 201

Improvement of the clinical applicability of the Genomic Grade Index through a qRT-PCR test performed on frozen and formalin-fixed paraffin-embedded tissues

BACKGROUND: Proliferation and tumor differentiation captured by the genomic grade index (GGI) are important prognostic indicators in breast cancer (BC) especially for the estrogen receptor positive (ER+) disease. The aims of this study were to convert this microarray index to a qRT-PCR assay (PCR-GGI), which could be realized on formalin fixed paraffin embedded samples (FFPE), and to assess its prognostic performance and predictive value of clinical benefit in early and advanced ER+ BC patients treated with tamoxifen. METHODS: The accuracy and concordance of the PCR-GGI with the GGI was assessed using BC patients for which frozen and FFPE tissues as well as microarray data were available (n = 19). The evaluation of the prognostic value of the PCR-GGI was assessed on FFPE material using a consecutive series of 212 systemically treated early BC patients. The predictive performance for tamoxifen benefit was assessed using two ER+ BC populations treated either with adjuvant tamoxifen only (n = 77+139) or first-line tamoxifen for advanced disease (n = 270). RESULTS: The PCR-GGI is based on the expression of 8 genes (4 representative of the GGI and 4 reference genes). A significant correlation was observed between the microarray-derived GGI and the qRT-PCR assay using frozen (rho = 0.95, p < 10E-06) and FFPE material (rho = 0.89, p < 10E-06). The prognostic performance of the PCR-GGI was confirmed on FFPE samples (HRunivar. = 1.89; [95CI:1.01-3.54], p = 0.05). The PCR-GGI further identified two subgroups of patients with statistically different time to distant metastasis free survival (DMFS) across the two cohorts of ER+ BC patients treated with adjuvant tamoxifen. Additionally, the PCR-GGI was associated with response to tamoxifen in the advanced setting (HRunivar. = 1.98; [95CI:1.51-2.59], p = 6.9E-07). CONCLUSION: PCR-GGI recapitulates in an accurate and reproducible manner the performances of the GGI using frozen and FFPE samples

HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions

Gene-gene interaction (GGI) analysis is known to play an important role in explain missing heritability issue. Many previous studies have already proposed software to analyze GGI, but most methods focus on a binary phenotype in case-control design. In this study, we developed 'Hierarchical structural CoMponent analysis of Gene-Gene Interactions' (HisCoM-GGI) software for gene-gene interaction analysis with a continuous phenotype. The HisCoM-GGI method considers hierarchical structural relationships between genes and SNPs, that enables both gene-level and SNP-level interaction analysis in a single model. Furthermore, this software accepts various type of genomic data, and supports a data management and multithreading to improve the efficiency of GWAS data analysis. We expect that the HisCoM-GGI software provides advanced accessibility to the researchers on the genetic interaction studies and a more effective way to understand biological mechanisms of complex diseases.ope

The Gene expression Grade Index: a potential predictor of relapse for endocrine-treated breast cancer patients in the BIG 1–98 trial

<p>Abstract</p> <p>Background</p> <p>We have previously shown that the Gene expression Grade Index (GGI) was able to identify two subtypes of estrogen receptor (ER)-positive tumors that were associated with statistically distinct clinical outcomes in both untreated and tamoxifen-treated patients. Here, we aim to investigate the ability of the GGI to predict relapses in postmenopausal women who were treated with tamoxifen (T) or letrozole (L) within the BIG 1–98 trial.</p> <p>Methods</p> <p>We generated gene expression profiles (Affymetrix) and computed the GGI for a matched, case-control sample of patients enrolled in the BIG 1–98 trial from the two hospitals where frozen samples were available. All relapses (cases) were identified from patients randomized to receive monotherapy or from the switching treatment arms for whom relapse occurred before the switch. Each case was randomly matched with four controls based upon nodal status and treatment (T or L). The prognostic value of GGI was assessed as a continuous predictor and divided at the median. Predictive accuracy of GGI was estimated using time-dependent area under the curve (AUC) of the ROC curves.</p> <p>Results</p> <p>Frozen samples were analyzable for 48 patients (10 cases and 38 controls). Seven of the 10 cases had been assigned to receive L. Cases and controls were comparable with respect to menopausal and nodal status, local and chemotherapy, and HER2 positivity. Cases were slightly older than controls and had a larger proportion of large, poorly differentiated ER+/PgR- tumors. The GGI was significantly and linearly related to risk of relapse: each 10-unit increase in GGI resulted in an increase of approximately 11% in the hazard rate (p = 0.02). Within the subgroups of patients with node-positive disease or who were treated with L, the hazard of relapse was significantly greater for patients with GGI at or above the median. AUC reached a maximum of 78% at 27 months.</p> <p>Conclusion</p> <p>This analysis supports the GGI as a good predictor of relapse for ER-positive patients, even among patients who receive L. Validation of these results, in a larger series from BIG 1–98, is planned using the simplified GGI represented by a smaller set of genes and tested by qRT-PCR on paraffin-embedded tissues.</p

The Gonococcal Genetic Island and Type IV Secretion in the Pathogenic Neisseria

Eighty percent of Neisseria gonorrhoeae strains and some Neisseria meningitidis strains encode a 57-kb gonococcal genetic island (GGI). The GGI was horizontally acquired and is inserted in the chromosome at the replication terminus. The GGI is flanked by direct repeats, and site-specific recombination at these sites results in excision of the GGI and may be responsible for its original acquisition. Although the role of the GGI in N. meningitidis is unclear, the GGI in N. gonorrhoeae encodes a type IV secretion system (T4SS). T4SS are versatile multi-protein complexes and include both conjugation systems as well as effector systems that translocate either proteins or DNA–protein complexes. In N. gonorrhoeae, the T4SS secretes single-stranded chromosomal DNA into the extracellular milieu in a contact-independent manner. Importantly, the DNA secreted through the T4SS is effective in natural transformation and therefore contributes to the spread of genetic information through Neisseria populations. Mutagenesis experiments have identified genes for DNA secretion including those encoding putative structural components of the apparatus, peptidoglycanases which may act in assembly, and relaxosome components for processing the DNA and delivering it to the apparatus. The T4SS may also play a role in infection by N. gonorrhoeae. During intracellular infection, N. gonorrhoeae requires the Ton complex for iron acquisition and survival. However, N. gonorrhoeae strains that do not express the Ton complex can survive intracellularly if they express structural components of the T4SS. These data provide evidence that the T4SS is expressed during intracellular infection and suggest that the T4SS may provide an advantage for intracellular survival. Here we review our current understanding of how the GGI and type IV secretion affect natural transformation and pathogenesis in N. gonorrhoeae and N. meningitidis

An Investigation into the Feasibility of Using a Modern Gravity Gradient Instrument for Passive Aircraft Navigation and Terrain Avoidance

Recently, Gravity Gradient Instruments (GGIs) - devices which measure the spatial derivatives of gravity, have improved remarkably due to development of accelerometer technologies. Specialized GGIs are currently flown on aircraft for geological purposes in the mining industries. As such, gravity gradient data is recorded in flight and detailed gradient maps are created after post mission processing. These maps, if stored in a database onboard an aircraft and combined with a GGI, form the basis for a covert navigation system using a map matching process. This system is completely passive and essentially unjammable. To determine feasibility of this method, a GGI sensor model was developed to investigate signal levels at representative flight conditions. Aircraft trajectories were simulated over modeled gravity gradient maps to determine the utility of flying modern GGIs in the roles of navigation and terrain avoidance. It was shown that the GGI based map-matching navigation system can likely provide a marked improvement over a non-aided INS but is limited by decreasing gravity gradient strength at higher altitudes, particularly over smooth terrain. Additionally, GGI output rate and bandwidth limitations, along with the inverse nature of the terrain avoidance problem, rendered GGI aided terrain avoidance unfeasible for the time being

Dark matter and the LHC

Cosmological and astrophysical measurements indicate that the universe contains a large amount of dark matter. A number of weak scale dark matter candidates have been proposed in extensions of the standard model. The potential to discover the dark matter particle and determine its properties at the upcoming LHC is summarized.Comment: 6 pages, 4 figures, Talk at Dark matter and dark energy, GGI, Florence, Italy, March 200