Quantum Black Holes in the Sky

Black Holes are possibly the most enigmatic objects in our Universe. From their detection in gravitational waves upon their mergers, to their snapshot eating at the centres of galaxies, black hole astrophysics has undergone an observational renaissance in the past 4 years. Nevertheless, they remain active playgrounds for strong gravity and quantum effects, where novel aspects of the elusive theory of quantum gravity may be hard at work. In this review article, we provide an overview of the strong motivations for why "Quantum Black Holes" may be radically different from their classical counterparts in Einstein's General Relativity. We then discuss the observational signatures of quantum black holes, focusing on gravitational wave echoes as smoking guns for quantum horizons (or exotic compact objects), which have led to significant recent excitement and activity. We review the theoretical underpinning of gravitational wave echoes and critically examine the seemingly contradictory observational claims regarding their (non-)existence. Finally, we discuss the future theoretical and observational landscape for unraveling the "Quantum Black Holes in the Sky"

G-language genome analysis environment with REST and SOAP web service interfaces

G-language genome analysis environment (G-language GAE) contains more than 100 programs that focus on the analysis of bacterial genomes, including programs for the identification of binding sites by means of information theory, analysis of nucleotide composition bias and the distribution of particular oligonucleotides, calculation of codon bias and prediction of expression levels, and visualization of genomic information. We have provided a collection of web services for these programs by utilizing REST and SOAP technologies. The REST interface, available at http://rest.g-language.org/, provides access to all 145 functions of the G-language GAE. These functions can be accessed from other online resources. All analysis functions are represented by unique universal resource identifiers. Users can access the functions directly via the corresponding universe resource locators (URLs), and biological web sites can readily embed the functions by simply linking to these URLs. The SOAP services, available at http://www.g-language.org/wiki/soap/, provide language-independent programmatic access to 77 analysis programs. The SOAP service Web Services Definition Language file can be readily loaded into graphical clients such as the Taverna workbench to integrate the programs with other services and workflows

Increased expression of integrin-linked kinase is associated with shorter survival in non-small cell lung cancer

BACKGROUND: Integrin-linked kinase (ILK) promotes tumor growth and invasion. Increased ILK expression is correlated with progression of several tumor types, but the expression of ILK has not been investigated in patients with non-small cell lung cancers (NSCLCs). METHODS: We investigated ILK expression in patients with NSCLC by means of immunohistochemistry. RESULTS: ILK expression was significantly associated with tumor grade, T status, lymph node metastasis and stage. (p = 0.0169 for tumor grade; p = 0.0006 for T status; p = 0.0002 for lymph node metastasis; p < 0.0001 for stage). The 5-year survival rates for patients with strong and weak or no ILK expression levels were 20% and 59%, respectively: the difference was statistically significant (p < 0.0001). A multivariate analysis of survival revealed that ILK expression, T status, N status and vascular invasion were statistically significant prognostic factors (p = 0.0218 for ILK; p = 0.0046 for T status; p < 0.0001 for N status; p < 0.0001 for vascular invasion). CONCLUSIONS: Our study demonstrates that increased expression of ILK is a poor prognostic factor in patients with NSCLC

Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API

BACKGROUND: Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage. METHODOLOGY/PRINCIPAL FINDINGS: We have identified five central requirements for a pathway browser: (1) availability of large integrated maps showing genes, enzymes, and metabolites; (2) comprehensive search features and data access; (3) data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4) easy exchange of pathway data; and (5) intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution. CONCLUSIONS/SIGNIFICANCE: Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at (http://www.g-language.org/PathwayProjector/)

The First Result of Global Commissioning of the ATLAS Endcap Muon Trigger System in ATLAS Cavern

We report on the ATLAS commissioning run from the view point of the Thin Gap Chamber (TGC), which is the ATLAS end cap muon trigger detector. All the TGC sectors with on-detector electronics are going to be installed to the ATLAS cavern by the end of September 2007. To integrate all sub-detectors before the physics run starting from early 2008, the global commissioning run together with other sub-detectors has been performed from June 2007. We have evaluated the performance of the complete trigger chain of the TGC electronics and provide the trigger signal using cosmic-ray to the sub-systems in the global run environment

Final Test at the Surface of the ATLAS Endcap Muon Trigger Chamber Electronics

For the detector commissioning planned in 2007, sector assembly of the ATLAS muon-endcap trigger chambers and final test at the surface for the assembled electronics are being done in CERN and almost completed. For the test, we built up the Data Acquisition (DAQ) system using test pulse of two types and cosmic rays in order to check functionality of the various aspects of the electronics mounted on a sector. So far, 99% of all 320,000 channels have been tested and most of them were installed into the ATLAS cavern. In this presentation, we will describe the DAQ systems and mass-test procedure in detail, and report the result of electronics test with some actual experience

Bcl-2 and β1-integrin predict survival in a tissue microarray of small cell lung cancer.

INTRODUCTION: Survival in small cell lung cancer (SCLC) is limited by the development of chemoresistance. Factors associated with chemoresistance in vitro have been difficult to validate in vivo. Both Bcl-2 and β(1)-integrin have been identified as in vitro chemoresistance factors in SCLC but their importance in patients remains uncertain. Tissue microarrays (TMAs) are useful to validate biomarkers but no large TMA exists for SCLC. We designed an SCLC TMA to study potential biomarkers of prognosis and then used it to clarify the role of both Bcl-2 and β(1)-integrin in SCLC. METHODS: A TMA was constructed consisting of 184 cases of SCLC and stained for expression of Bcl-2 and β(1)-integrin. The slides were scored and the role of the proteins in survival was determined using Cox regression analysis. A meta-analysis of the role of Bcl-2 expression in SCLC prognosis was performed based on published results. RESULTS: Both proteins were expressed at high levels in the SCLC cases. For Bcl-2 (n=140), the hazard ratio for death if the staining was weak in intensity was 0.55 (0.33-0.94, P=0.03) and for β(1)-integrin (n=151) was 0.60 (0.39-0.92, P=0.02). The meta-analysis showed an overall hazard ratio for low expression of Bcl-2 of 0.91(0.74-1.09). CONCLUSIONS: Both Bcl-2 and β(1)-integrin are independent prognostic factors in SCLC in this cohort although further validation is required to confirm their importance. A TMA of SCLC cases is feasible but challenging and an important tool for biomarker validation