Archon Genomics X PRIZE Validation Protocol

This document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches. The intent for the final version of this Validation Protocol is to become a useful standard by which to gauge the capabilities of whole genome sequencing technologies that emerge even after 2012

Functional genomics of complex cancer genomes.

Cancer functional genomics is the study of how genetic, epigenetic, and transcriptional alterations affect cancer phenotypes, such as growth and therapeutic response. Here, we comment on how, taking advantage of next generation sequencing, functional genomics, often combined with systems biology approaches, has revealed novel cancer vulnerabilities beyond the original paradigm of one gene-one phenotype

The effects of halogen elements on the opening of an icosahedral B12 framework

The fully halogenated or hydrogenated B12X12 (X = H, F, Cl, Br and I) clusters are confirmed to be icosahedral. On the other hand, the bare B12 cluster is shown to have a planar structure. A previous study showed that a transformation from an icosahedron to a plane happens when 5 to 7 iodine atoms are substituted. Later, the transition was confirmed to be seven iodine substitutions based on an infrared spectroscopy study. In this study, we investigated the effects of different halogen atoms on the opening of the B12 icosahedral cage by means of density functional theory calculations. We found that the halogen elements do not have significant effects on the geometries of the clusters. The computed IR spectra show similar representative peaks for all halogen substituted clusters. Interestingly, we found a blue-shift in the IR spectra with the increase in the mass of the halogen atoms. Further, we compared the Gibbs free energies at different temperatures for different halogen atoms. The results show that the Gibbs free energy differences between open and close structures of B12X7 become larger when heavier halogen atoms are present. This interesting finding was subsequently investigated by energy decomposition analysis

Electron heating and acceleration by magnetic reconnection in hot accretion flows

Both analytical and numerical works show that magnetic reconnection must occur in hot accretion flows. This process will effectively heat and accelerate electrons. In this paper we use the numerical hybrid simulation of magnetic reconnection plus test-electron method to investigate the electron acceleration and heating due to magnetic reconnection in hot accretion flows. We consider fiducial values of density, temperature, and magnetic parameter $\beta_e$ (defined as the ratio of the electron pressure to the magnetic pressure) of the accretion flow as $n_{0} \sim 10^{6} {\rm cm^{-3}}$, $T_{e}^0\sim 2\times 10^9 {\rm K}$, and $\beta_e=1$. We find that electrons are heated to a higher temperature $T_{e}=5\times 10^9$K, and a fraction $\eta\sim 8$ of electrons are accelerated into a broken power-law distribution, $dN(\gamma)\propto \gamma^{-p}$, with $p\approx 1.5$ and 4 below and above $\sim 1$ MeV, respectively. We also investigate the effect of varying $\beta$ and $n_0$. We find that when $\beta_e$ is smaller or $n_0$ is larger, i.e, the magnetic field is stronger, $T_e$, $\eta$, and $p$ all become larger.Comment: 6 pages, 6 figure; accepted by Ap