Integrative Analysis of Survival-Associated Gene Sets in Breast Cancer

Patient gene expression information has recently become a clinical feature used to evaluate breast cancer prognosis. The emergence of prognostic gene sets that take advantage of these data has led to a rich library of information that can be used to characterize the molecular nature of a patient’s cancer. Identifying robust gene sets that are consistently predictive of a patient’s clinical outcome has become one of the main challenges in the field. We inputted our previously established BASE algorithm with patient gene expression data and gene sets from MSigDB to develop the gene set activity score (GSAS), a metric that quantitatively assesses a gene set’s activity level in a given patient. We utilized this metric, along with patient time-to-event data, to perform survival analyses to identify the gene sets that were significantly correlated with patient survival. We then performed cross-dataset analyses to identify robust prognostic gene sets and to classify patients by metastasis status. Additionally, we created a gene set network based on component gene overlap to explore the relationship between gene sets derived from MSigDB. We developed a novel gene set based on this network’s topology and applied the GSAS metric to characterize its role in patient survival

An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database)

<p>Abstract</p> <p>Background</p> <p>Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically dependent on the use of genuine materials. For time to time, life-threatening poisoning is found because toxic adulterant or substitute is administered. DNA barcoding provides a definitive means of authentication and for conducting molecular systematics studies. Owing to the reduced cost in DNA authentication, the volume of the DNA barcodes produced for medicinal materials is on the rise and necessitates the development of an integrated DNA database.</p> <p>Description</p> <p>We have developed an integrated DNA barcode multimedia information platform- Medicinal Materials DNA Barcode Database (MMDBD) for data retrieval and similarity search. MMDBD contains over 1000 species of medicinal materials listed in the Chinese Pharmacopoeia and American Herbal Pharmacopoeia. MMDBD also contains useful information of the medicinal material, including resources, adulterant information, medical parts, photographs, primers used for obtaining the barcodes and key references. MMDBD can be accessed at <url>http://www.cuhk.edu.hk/icm/mmdbd.htm</url>.</p> <p>Conclusions</p> <p>This work provides a centralized medicinal materials DNA barcode database and bioinformatics tools for data storage, analysis and exchange for promoting the identification of medicinal materials. MMDBD has the largest collection of DNA barcodes of medicinal materials and is a useful resource for researchers in conservation, systematic study, forensic and herbal industry.</p

Measurement of the Inclusive Charm Cross Section at 4.03 GeV and 4.14 GeV

The cross section for charmed meson production at $\sqrt{s} = 4.03$ and 4.14 GeV has been measured with the Beijing Spectrometer. The measurement was made using 22.3 $pb^{-1}$ of $e^+e^-$ data collected at 4.03 GeV and 1.5 $pb^{-1}$ of $e^+e^-$ data collected at 4.14 GeV. Inclusive observed cross sections for the production of charged and neutral D mesons and momentum spectra are presented. Observed cross sections were radiatively corrected to obtain tree level cross sections. Measurements of the total hadronic cross section are obtained from the charmed meson cross section and an extrapolation of results from below the charm threshold.Comment: 11 pages, 13 figures. The top level tex file is paper.tex. It builds the paper from other tex files in this .tar and the .eps file

Measurement of the Total Cross Section for Hadronic Production by e+e- Annihilation at Energies between 2.6-5 Gev

Using the upgraded Beijing Spectrometer (BESII), we have measured the total cross section for $e^+e^-$ annihilation into hadronic final states at center-of-mass energies of 2.6, 3.2, 3.4, 3.55, 4.6 and 5.0 GeV. Values of $R$, $\sigma(e^+e^-\to {hadrons})/\sigma(e^+e^-\to\mu^+\mu^-)$, are determined.Comment: Submitted to Phys. Rev. Let

Measurements of the Cross Section for e+e- -> hadrons at Center-of-Mass Energies from 2 to 5 GeV

We report values of $R = \sigma(e^+e^-\to {hadrons})/\sigma(e^+e^-\to\mu^+\mu^-)$ for 85 center-of-mass energies between 2 and 5 GeV measured with the upgraded Beijing Spectrometer at the Beijing Electron-Positron Collider.Comment: 5 pages, 3 figure

Measurement of ψ(2S)\psi(2S) decays to baryon pairs

A sample of 3.95M $\psi(2S)$ decays registered in the BES detector are used to study final states containing pairs of octet and decuplet baryons. We report branching fractions for $\psi(2S)\to p\bar{p}$, $\Lambda\bar{\Lambda}$, $\Sigma^0\bar{\Sigma}{}^0$, $\Xi^-\bar{\Xi}{}^+$, $\Delta^{++}\bar{\Delta}{}^{--}$, $\Sigma^+(1385)\bar{\Sigma}{}^-(1385)$, $\Xi^0(1530)\bar{\Xi}{}^0(1530)$, and $\Omega^-\bar{\Omega}{}^+$. These results are compared to expectations based on the SU(3)-flavor symmetry, factorization, and perturbative QCD.Comment: 22 pages, 21 figures, 4 table

Study of the P-wave charmonium state \chi_{cJ} in \psi(2S) decays

The processes $\psi(2S)\to \gamma \pi^+ \pi^-$, $\gamma K^+ K^-$ and $\gamma p \bar{p}$ have been studied using a sample of $3.7 \times 10^6$ produced $\psi(2S)$ decays. We determine the total width of the $\chi_{c0}$ to be $\Gamma^{tot}_{\chi_{c0}} = 14.3\pm 2.0\pm 3.0$ MeV. We present the first measurement of the branching fraction $B(\chi_{c0} \to p \bar{p}) = (16.3 \pm 4.4 \pm 5.4)\times 10^{-5}$, where the first error is statistical and the second one systematic. Branching fractions of $\chi_{c0,2} \to \pi^+ \pi^-$ and $K^+ K^-$ are also reported.Comment: 10 pages, revtex, 3 figures, 2 table

First Measurement of the Branching Fraction of the Decay psi(2S) --> tau tau

The branching fraction of the psi(2S) decay into tau pair has been measured for the first time using the BES detector at the Beijing Electron-Positron Collider. The result is $B_{\tau\tau}=(2.71\pm 0.43 \pm 0.55) \times 10^{-3}$, where the first error is statistical and the second is systematic. This value, along with those for the branching fractions into e+e- and mu+mu of this resonance, satisfy well the relation predicted by the sequential lepton hypothesis. Combining all these values with the leptonic width of the resonance the total width of the psi(2S) is determined to be $(252 \pm 37)$ keV.Comment: 9 pages, 2 figure

Observation of ηc→ωω\eta_c\to\omega\omega in J/ψ→γωωJ/\psi\to\gamma\omega\omega

Using a sample of $(1310.6\pm7.0)\times10^6$ $J/\psi$ events recorded with the BESIII detector at the symmetric electron positron collider BEPCII, we report the observation of the decay of the $(1^1 S_0)$ charmonium state $\eta_c$ into a pair of $\omega$ mesons in the process $J/\psi\to\gamma\omega\omega$. The branching fraction is measured for the first time to be $\mathcal{B}(\eta_c\to\omega\omega)= (2.88\pm0.10\pm0.46\pm0.68)\times10^{-3}$, where the first uncertainty is statistical, the second systematic and the third is from the uncertainty of $\mathcal{B}(J/\psi\to\gamma\eta_c)$. The mass and width of the $\eta_c$ are determined as $M=(2985.9\pm0.7\pm2.1)\,$MeV/$c^2$ and $\Gamma=(33.8\pm1.6\pm4.1)\,$MeV.Comment: 13 pages, 6 figure