Composite WO₃/TiO₂ Nanostructures for High Electrochromic Activity

A composite material consisting of TiO₂ nanotubes (NT) with WO₃ electrodeposited on its surface has been fabricated, detached from its Ti substrate, and attached to a fluorine-doped tin oxide (FTO) film on glass for application to electrochromic (EC) reactions. Several adhesion layers were tested, finding that a paste of TiO₂ made from commercially available TiO₂ nanoparticles creates an interface for the TiO₂ NT film to attach to the FTO glass, which is conductive and does not cause solution-phase ions in an electrolyte to bind irreversibly with the material. The effect of NT length and WO₃ concentration on the EC performance were studied. The composite WO₃/TiO₂ nanostructures showed higher ion storage capacity, better stability, enhanced EC contrast, and longer memory time compared with the pure WO₃ and TiO₂ materials

Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

<div><p>An obstacle to validating and benchmarking methods for genome analysis is that there are few reference datasets available for which the “ground truth” about the mutational landscape of the sample genome is known and fully validated. Additionally, the free and public availability of real human genome datasets is incompatible with the preservation of donor privacy. In order to better analyze and understand genomic data, we need test datasets that model all variants, reflecting known biology as well as sequencing artifacts. Read simulators can fulfill this requirement, but are often criticized for limited resemblance to true data and overall inflexibility. We present NEAT (NExt-generation sequencing Analysis Toolkit), a set of tools that not only includes an easy-to-use read simulator, but also scripts to facilitate variant comparison and tool evaluation. NEAT has a wide variety of tunable parameters which can be set manually on the default model or parameterized using real datasets. The software is freely available at <a href="http://github.com/zstephens/neat-genreads" target="_blank">github.com/zstephens/neat-genreads</a>.</p></div

SNP substitution frequency matrices for Melanoma model.

<p>Note the strong preference for G → A and C → T transitions, as observed in existing work [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167047#pone.0167047.ref017" target="_blank">17</a>].</p

Overview of mutation and sequencing model generation.

<p>Overview of mutation and sequencing model generation.</p

SNP substitution frequency matrices for Leukemia model.

<p>SNP substitution frequency matrices for Leukemia model.</p

SNP substitution frequency matrices for breast cancer model.

<p>The label for each 4 × 4 matrix specifies the nucleotide immediately preceding and following the SNP position. For example, row 3 column 2 of the “A_A” matrix specifies the frequency of AGA mutating into ACA, as observed in the breast cancer SSM dataset.</p

Empirical GC% coverage bias from an example BAM file.

<p>Empirical GC% coverage bias from an example BAM file.</p

Comparison of mutation statistics between CDS (blue) and nonCDS (cyan) regions.

<p>Comparison of mutation statistics between CDS (blue) and nonCDS (cyan) regions.</p

Example false negative variant call diagnosis for a toy dataset: Several hundred variants were introduced into a 10M subset of human chromosome 21. The false negative variants were those that were inserted into the data by NEAT, but were not recovered by a particular variant calling workflow (Novoalign → Haplotype Caller, following GATK best practices).

<p>In this example we see that a majority of the false negatives were due to variants having been inserted into regions that were not uniquely mappable with the simulated read lengths. A lower number of false negatives were due to inadequate coverage (DP).</p

Trinucleotide mutation frequencies for NA12878 high confidence variants in CDS (blue) and nonCDS (cyan) regions.

<p>Trinucleotide mutation frequencies for NA12878 high confidence variants in CDS (blue) and nonCDS (cyan) regions.</p