GaSb Inversion-Mode PMOSFETs With Atomic-Layer-Deposited Al2O3 as Gate Dielectric

GaSb inversion-mode PMOSFETs with atomic-layer-deposited (ALD) Al2O3 as gate dielectric are demonstrated. A 0.75-mu m-gate-length device has a maximum drain current of 70 mA/mm, a transconductance of 26 mS/mm, and a hole inversion mobility of 200 cm(2)/V . s. The OFF-state performance is improved by reducing the ALD growth temperature from 300 degrees C to 200 degrees C. The measured interface trap distribution shows a low interface trap density of 2 x 10(12) /cm(2) . eV near the valence band edge. However, it increases to 1 - 4 x 10(13) /cm(2) . eV near the conduction band edge, leading to a drain current on-off ratio of 265 and a subthreshold swing of similar to 600 mV/decade. GaSb, similar to Ge, is a promising channel material for PMOSFETs due to its high bulk hole mobility, high density of states at the valence band edge, and, most importantly, its unique interface trap distribution and trap neutral level alignment

Protocols for creating and distilling multipartite GHZ states with Bell pairs

The distribution of high-quality Greenberger–Horne–Zeilinger (GHZ) states is at the heart of many quantum communication tasks, ranging from extending the baseline of telescopes to secret sharing. They also play an important role in error-correction architectures for distributed quantum computation, where Bell pairs can be leveraged to create an entangled network of quantum computers. We investigate the creation and distillation of GHZ states out of nonperfect Bell pairs over quantum networks. In particular, we introduce a heuristic dynamic programming algorithm to optimize over a large class of protocols that create and purify GHZ states. All protocols considered use a common framework based on measurements of nonlocal stabilizer operators of the target state (i.e., the GHZ state), where each nonlocal measurement consumes another (nonperfect) entangled state as a resource. The new protocols outperform previous proposals for scenarios without decoherence and local gate noise. Furthermore, the algorithms can be applied for finding protocols for any number of parties and any number of entangled pairs involved

Predicting Housekeeping Genes Based on Fourier Analysis

Housekeeping genes (HKGs) generally have fundamental functions in basic biochemical processes in organisms, and usually have relatively steady expression levels across various tissues. They play an important role in the normalization of microarray technology. Using Fourier analysis we transformed gene expression time-series from a Hela cell cycle gene expression dataset into Fourier spectra, and designed an effective computational method for discriminating between HKGs and non-HKGs using the support vector machine (SVM) supervised learning algorithm which can extract significant features of the spectra, providing a basis for identifying specific gene expression patterns. Using our method we identified 510 human HKGs, and then validated them by comparison with two independent sets of tissue expression profiles. Results showed that our predicted HKG set is more reliable than three previously identified sets of HKGs

Prostate Cancer-Specific and Potent Antitumor Effect of a DD3-Controlled Oncolytic Virus Harboring the PTEN Gene

Prostate cancer is a major health problem for men in Western societies. Here we report a Prostate Cancer-Specific Targeting Gene-Viro-Therapy (CTGVT-PCa), in which PTEN was inserted into a DD3-controlled oncolytic viral vector (OV) to form Ad.DD3.E1A.E1B(Δ55)-(PTEN) or, briefly, Ad.DD3.D55-PTEN. The woodchuck post-transcriptional element (WPRE) was also introduced at the downstream of the E1A coding sequence, resulting in much higher expression of the E1A gene. DD3 is one of the most prostate cancer-specific genes and has been used as a clinical bio-diagnostic marker. PTEN is frequently inactivated in primary prostate cancers, which is crucial for prostate cancer progression. Therefore, the Ad.DD3.D55-PTEN has prostate cancer specific and potent antitumor effect. The tumor growth rate was almost completely inhibited with the final tumor volume after Ad.DD3.D55-PTEN treatment less than the initial volume at the beginning of Ad.DD3.D55-PTEN treatment, which shows the powerful antitumor effect of Ad.DD3.D55-PTEN on prostate cancer tumor growth. The CTGVT-PCa construct reported here killed all of the prostate cancer cell lines tested, such as DU145, 22RV1 and CL1, but had a reduced or no killing effect on all the non-prostate cancer cell lines tested. The mechanism of action of Ad.DD3.D55-PTEN was due to the induction of apoptosis, as detected by TUNEL assays and flow cytometry. The apoptosis was mediated by mitochondria-dependent and -independent pathways, as determined by caspase assays and mitochondrial membrane potential

RNAcentral : a hub of information for non-coding RNA sequences

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org

Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes

Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) has also brought about a large variety of assemblers. Although these have been extensively tested on model species such as Homo sapiens and Drosophila melanogaster, such benchmarking has not been done in Mollusca, which lacks widely adopted model species. Molluscan genomes are notoriously rich in repeats and are often highly heterozygous, making their assembly challenging. Here, we benchmarked 10 assemblers based on ONT raw reads from two published molluscan genomes of differing properties, the gastropod Chrysomallon squamiferum (356.6 Mb, 1.59% heterozygosity) and the bivalve Mytilus coruscus (1593 Mb, 1.94% heterozygosity). By optimizing the assembly pipeline, we greatly improved both genomes from previously published versions. Our results suggested that 40–50X of ONT reads are sufficient for high-quality genomes, with Flye being the recommended assembler for compact and less heterozygous genomes exemplified by C. squamiferum, while NextDenovo excelled for more repetitive and heterozygous molluscan genomes exemplified by M. coruscus. A phylogenomic analysis using the two updated genomes with 32 other published high-quality lophotrochozoan genomes resulted in maximum support across all nodes, and we show that improved genome quality also leads to more complete matrices for phylogenomic inferences. Our benchmarking will ensure efficiency in future assemblies for molluscs and perhaps also for other marine phyla with few genomes available. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’

Isotopic signatures of mercury contamination in latest Permian oceans

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155765/1/Grasby_et_al_2017_isotopic_signatures.pd

Mercury stable isotopes for monitoring the effectiveness of the Minamata Convention on Mercury

The Minamata Convention on Mercury (MC) includes provisions for a global monitoring program (GMP) and effectiveness evaluation (EE) to provide information on changes in mercury sources in various environmental media. While conventional measurement and modeling techniques have limitations in explaining the changes in mercury concentrations, the measurements of natural abundances of mercury stable isotopes have become powerful tracers for distinguishing between mercury sources and for understanding biogeochemical processes in the environment. Unfortunately, it is uncertain whether mercury isotope ratios can provide globally comparable results on specific mercury sources for the GMP and trend analyses for the EE. We have compiled a dataset from the literature to evaluate large-scale patterns of mercury isotope ratios in various environmental samples and to summarize sample types that can be used for the GMP. Total gaseous mercury, precipitation, foliage, and litter can provide comparable source information regarding atmospheric mercury across a large spatial scale. Interpretation of spatially relevant information using sediment and fish mercury isotope ratios are challenging because they represent multiple mercury sources and contain mercury that has been subject to biogeochemical transformation leading to isotope fractionation. In regards to the EE, data that provides evidence of changes due to source regulation needs to be gathered from local point source regions to assess health impacts. We recommend that the measurements of particulate-bound mercury in the atmosphere and sediment mercury isotope ratios near mercury hotspots and in fish, are needed to identify ecosystems sensitive to atmospheric deposition and to evaluate the effectiveness of the MC.11Nsciescopu