Journal of the American Chemical SocietyDOI: 10.1021/ja312610j

Journal of the American Chemical SocietyDOI: 10.1021/ja312503y

Journal of the American Chemical SocietyDOI: 10.1021/ja310929s

Wasted energy

Nature 495, 7441 (2013). doi:10.1038/495281a

The burning off of gas during oil extraction is environmentally unsound and unjustifiable. The United States should instead be seeking to make use of this natural resource.

CITES for sore eyes

Nature 495, 7441 (2013). doi:10.1038/495281b

Successes at last week’s wildlife-trade treaty meeting must be backed up with action.

A pope for today

Nature 495, 7441 (2013). doi:10.1038/495282a

Latest pontiff looks to enhance social relevance of Catholic Church.

Time called on chimp work

Nature 495, 7441 (2013). http://www.nature.com/doifinder/10.1038/495289a

Author: Meredith Wadman

NIH likely to retire hundreds of government-owned chimpanzees.

Oil boom raises burning issues

Nature 495, 7441 (2013). http://www.nature.com/doifinder/10.1038/495290a

Author: Jeff Tollefson

Unburned methane could be adding to the environmental impact of gas flares in North Dakota.

Mars rover under pressure to reach mountain goal

Nature 495, 7441 (2013). http://www.nature.com/doifinder/10.1038/495292a

Author: Alexandra Witze

Curiosity’s memory glitch prompts mission scientists to pick up the pace.

Gene-analysis firms reach for the cloud

Nature 495, 7441 (2013). http://www.nature.com/doifinder/10.1038/495293a

Author: Erika Check Hayden

Online bioinformatics companies rush to provide genomics platforms and software for hospitals.

UK company pursues deep-sea bonanza

Nature 495, 7441 (2013). http://www.nature.com/doifinder/10.1038/495294a

Author: Mark Schrope

After decades of preparation, firm moves forward with plans to harvest mineral-rich nuggets from sea floor.

Background: Microarray technology can acquire information about thousands of genes simultaneously. We analyzed published breast cancer microarray databases to predict five-year recurrence and compared the performance of three data mining algorithms of artificial neural networks (ANN), decision trees (DT) and logistic regression (LR) and two composite models of DT-ANN and DT-LR. The collection of microarray datasets from the Gene Expression Omnibus, four breast cancer datasets were pooled for predicting five-year breast cancer relapse. After data compilation, 757 subjects, 5 clinical variables and 13,452 genetic variables were aggregated. The bootstrap method, Mann--Whitney U test and 20-fold cross-validation were performed to investigate candidate genes with 100 most-significant p-values. The predictive powers of DT, LR and ANN models were assessed using accuracy and the area under ROC curve. The associated genes were evaluated using Cox regression. Results: The DT models exhibited the lowest predictive power and the poorest extrapolation when applied to the test samples. The ANN models displayed the best predictive power and showed the best extrapolation. The 21 most-associated genes, as determined by integration of each model, were analyzed using Cox regression with a 3.53-fold (95% CI: 2.24-5.58) increased risk of breast cancer five-year recurrence... Conclusions: The 21 selected genes can predict breast cancer recurrence. Among these genes, CCNB1, PLK1 and TOP2A are in the cell cycle G2/M DNA damage checkpoint pathway. Oncologists can offer the genetic information for patients when understanding the gene expression profiles on breast cancer recurrence.

Background This paper introduces a new constrained model and thecorresponding algorithm, called unsupervised Bayesian linearunmixing (uBLU), to identify biological signatures from highdimensional assays like gene expression microarrays. Thebasis for uBLU is a Bayesian model for the data sampleswhich are represented as an additive mixture of randompositive gene signatures, called factors, with randompositive mixing coefficients, called factor scores,that specify the relative contribution of each signature toa specific sample. The particularity of the proposed methodis that uBLU constrains the factor loadings to benon-negative and the factor scores to be probabilitydistributions over the factors. Furthermore, it also providesestimates of the number of factors.A Gibbs sampling strategy is adopted here to generate randomsamples according to the posterior distribution of thefactors, factor scores, and number of factors.These samples are then used to estimate all the unknownparameters.Results Firstly, the proposed uBLU method is applied to severalsimulated datasets with known ground truth and compared withprevious factor decomposition methods, such as principalcomponent analysis (PCA), non negative matrix factorization(NMF), Bayesian factor regression modeling (BFRM), and thegradient-based algorithm for general matrix factorization(GB-GMF).Secondly, we illustrate the application of uBLU on a realtime-evolving gene expression dataset from a recent viralchallenge study in which individuals have been inoculatedwith influenza A/H3N2/Wisconsin. We show that the uBLUmethod significantly outperforms the other methods on thesimulated and real data sets considered here.Conclusions The results obtained on synthetic and real data illustratethe accuracy of the proposed uBLU method when compared toother factor decomposition methods from the literature (PCA,NMF, BFRM, and GB-GMF).The uBLU method identifies an inflammatory component closelyassociated with clinical symptom scores collected during thestudy. Using a constrained model allows recovery of all theinflammatory genes in a single factor.

Erik Strandberg, Jonathan Zerweck, Parvesh Wadhwani, Anne S. Ulrich. PGLa and magainin 2 (MAG2) are amphiphilic antimicrobial peptides from frog skin with known synergistic activity. The orientation of the two helices in membranes was studied using solid-state

Magnus Andersson, Jakob P. Ulmschneider, Martin B. Ulmschneider, Stephen H. White. The distribution of peptide conformations in the membrane interface is central to partitioning energetics. Molecular-dynamics simulations enable characterization of in-membrane structural dynamics....

Francesca M. Marassi.

Denis Wirtz.

Christopher L. Berger.

Yinghao Wu, Barry Honig, Avinoam Ben-Shaul. The equilibrium constants of trans and cis dimerization of membrane bound (2D) and freely moving (3D) adhesion receptors are expressed and compared using elementary statistical-therm....

Olga Gaiko, Robert E. Dempski. Channelrhodopsin-2 (ChR2) is a light-activated nonselective cation channel that is found in the eyespot of the unicellular green alga Chlamydomonas reinhardtii. Despite the wide employment ....