An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Influence of infiltration temperature on the microstructure and oxidation behavior of SiC-ZrC ceramic coating on C/C composites prepared by reactive melt infiltration

SiC–ZrC ceramic coating on C/C composites was prepared by reactive melt infiltration (RMI) using a powder mixture composed of Zr, Si and C as the infiltrator. The phase composition and microstructure of the ceramic coating were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The oxidation resistance of the as-prepared composites was tested at 1550 °C in static air. The results indicate that the infiltration temperature has remarkable effects on the phase composition and microstructure of the ceramic coating, as well as on the oxidation resistance of the composites. The SiC–ZrC coated C/C composites prepared at 2000 °C exhibit an excellent oxidation resistance. They gain weight about 5.9 wt% after oxidation at 1550 °C in static air for 5 h, whereas the SiC–ZrC coated C/C composites prepared at 1800 °C lose weight about 3.2 wt%. As a comparison, SiC coated C/C composites prepared at 2000 °C by RMI show an inferior oxidation resistance. After 5 h oxidation, SiC coated C/C composites are severely damaged and their weight loss reaches up to 44.3 wt%. The outstanding oxidation resistance of the SiC–ZrC coated C/C composites prepared at 2000 °C can be attributed to the rapid formation of a continuous glass-like layer composed of ZrO2, ZrSiO4 and SiO2, which covers the surface of the composites and retards the oxygen diffusion and the attack on the underlying C/C substrate. For SiC coated C/C composites, the large SiC particles formed on the surface of the composites are difficult to oxidize rapidly and so a continuous and dense SiO2 layer cannot be formed in time to significantly hinder fast oxygen diffusion leading to the consequent severe oxidation of the C/C substrate

Prunella vulgaris: A comprehensive review of chemical constituents, pharmacological effects and clinical applications.

Prunella vulgaris (PV) is a perennial herb belonging to the Labiate family and is widely distributed in northeastern Asian countries such as Korea, Japan, and China. It is reported to display diverse biological activities including anti-microbial, anti-cancer, and anti-inflammation as determined by in vitro or in vivo studies. So far, about 200 compounds have been isolated from PV plant and majority of these have been characterized mainly as triterpenoids, sterols and flavonoids, followed by coumarins, phenylpropanoids, polysaccharides and volatile oils. This review summarizes and analyzes the current knowledge on the chemical constituents, pharmacological activities, mechanisms of action and clinical applications of the PV plant including its potential as a future medicinal plant. Although some of the chemical constituents of the PV plant and their mechanism of action have been investigated the biological activities of many of these remain unknown and further clinical trials are required to further enhance its reputation as a medicinal plant

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Search for supersymmetry in events with photons and low missing transverse energy in pp collisions at √s=7 TeV

This is the pre-print version of the Article. The official published version can be accessed from the links below - Copyright @ 2013 Elsevier.Many models of new physics, including versions of supersymmetry (SUSY), predict production of events with low missing transverse energy, electroweak gauge bosons, and many energetic final-state particles. The stealth SUSY model yields this signature while conserving R-parity by means of a new hidden sector in which SUSY is approximately conserved. The results of a general search for new physics, with no requirement on missing transverse energy, in events with two photons and four or more hadronic jets are reported. The study is based on a sample of proton–proton collisions at √s=7 TeV corresponding to 4.96 fb−1 of integrated luminosity collected with the CMS detector in 2011. Based on good agreement between the data and the standard model expectation, the data are used to determine model-independent cross-section limits and a limit on the squark mass in the framework of stealth SUSY. With this first study of its kind, squark masses less than 1430 GeV are excluded at the 95% confidence level.This study is supported by the BMWF and FWF (Austria); FNRS and FWO (Belgium); CNPq, CAPES, FAPERJ, and FAPESP (Brazil); MES (Bulgaria); CERN; CAS, MoST, and NSFC (China); COLCIENCIAS (Colombia); MSES (Croatia); RPF (Cyprus); MEYS (Czech Republic); MoER, SF0690030s09 and ERDF (Estonia); Academy of Finland, MEC, and HIP (Finland); CEA and CNRS/IN2P3 (France); BMBF, DFG, and HGF (Germany); GSRT (Greece); OTKA and NKTH (Hungary); DAE and DST (India); IPM (Iran); SFI (Ireland); INFN (Italy); NRF and WCU (Korea); LAS (Lithuania); CINVESTAV, CONACYT, SEP, and UASLP-FAI (Mexico); MSI (New Zealand); PAEC (Pakistan); MSHE and NSC (Poland); FCT (Portugal); JINR (Armenia, Belarus, Georgia, Ukraine, Uzbekistan); MON, RosAtom, RAS and RFBR (Russia); MSTD (Serbia); SEIDI and CPAN (Spain); Swiss Funding Agencies (Switzerland); NSC (Taipei); ThEP, IPST and NECTEC (Thailand); TUBITAK and TAEK (Turkey); NASU (Ukraine); STFC (United Kingdom); DOE and NSF (USA)

Observation of a new Xi(b) baryon

The first observation of a new b baryon via its strong decay into Xi(b)^- pi^+ (plus charge conjugates) is reported. The measurement uses a data sample of pp collisions at sqrt(s) = 7 TeV collected by the CMS experiment at the LHC, corresponding to an integrated luminosity of 5.3 inverse femtobarns. The known Xi(b)^- baryon is reconstructed via the decay chain Xi(b)^- to J/psi Xi^- to mu^+ mu^- Lambda^0 pi^-, with Lambda^0 to p pi^-. A peak is observed in the distribution of the difference between the mass of the Xi(b)^- pi^+ system and the sum of the masses of the Xi(b)^- and pi^+, with a significance exceeding five standard deviations. The mass difference of the peak is 14.84 +/- 0.74 (stat.) +/- 0.28 (syst.) MeV. The new state most likely corresponds to the J^P=3/2^+ companion of the Xi(b).Comment: Submitted to Physical Review Letter