Renewable power for lean desktops in media applications

An integration of solar microgeneration to supply a low-power IT desktop, using the Power over Ethernet standards IEEE 802.3af/at as a low power distribution network avoiding transformer losses from DC generation to mains power AC and back to low-voltage DC and hence maximising efficiency. The resulting design points to applications in media technology where reducing grid power consumption is critical for improving sustainability, or where there are supply constraints, and indicates new directions in how we manage and consume power for IT devices

Effects of HBV Genetic Variability on RNAi Strategies

RNAi strategies present promising antiviral strategies against HBV. RNAi strategies require base pairing between short RNAi effectors and targets in the HBV pregenome or other RNAs. Natural variation in HBV genotypes, quasispecies variation, or mutations selected by the RNAi strategy could potentially make these strategies less effective. However, current and proposed antiviral strategies against HBV are being, or could be, designed to avoid this. This would involve simultaneous targeting of multiple regions of the genome, or regions in which variation or mutation is not tolerated. RNAi strategies against single genotypes or against variable regions of the genome would need to have significant other advantages to be part of robust therapies

Detecting overlapping coding sequences in virus genomes

BACKGROUND: Detecting new coding sequences (CDSs) in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which can result in unusual patterns of codon usage; conservation between related sequences can be difficult to interpret – especially within overlapping genes; and viruses often employ non-canonical translational mechanisms – e.g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites – which can conceal potentially coding open reading frames (ORFs). RESULTS: In a previous paper we introduced a new statistic – MLOGD (Maximum Likelihood Overlapping Gene Detector) – for detecting and analysing overlapping CDSs. Here we present (a) an improved MLOGD statistic, (b) a greatly extended suite of software using MLOGD, (c) a database of results for 640 virus sequence alignments, and (d) a web-interface to the software and database. Tests show that, from an alignment with just 20 mutations, MLOGD can discriminate non-overlapping CDSs from non-coding ORFs with a typical accuracy of up to 98%, and can detect CDSs overlapping known CDSs with a typical accuracy of 90%. In addition, the software produces a variety of statistics and graphics, useful for analysing an input multiple sequence alignment. CONCLUSION: MLOGD is an easy-to-use tool for virus genome annotation, detecting new CDSs – in particular overlapping or short CDSs – and for analysing overlapping CDSs following frameshift sites. The software, web-server, database and supplementary material are available at

Results of 1/4-Scale Experiments. Vapor Simulant And Liquid Jet A Tests

A quarter-scale engineering model of the center wing tank (CWT) of a 747-100 was constructed. This engineering model replicated the compartmentalization, passageways, and venting to the atmosphere. The model was designed to scale the fluid dynamical and combustion aspects of the explosion, not the structural failure of the beams or spars. The effect of structural failure on combustion was examined by using model beams and spars with deliberately engineered weak connections to the main tank structure. The model was filled with a simulant fuel (a mixture of propane and hydrogen) and ignited with a hot wire. The simulant fuel was chosen on the basis of laboratory testing to model the combustion characteristics (pressure rise and flame speed) of Jet A vapor created by a Jet A liquid layer at 50C at an altitude of 13.8 kft. A series of experiments was carried out in this model in order to: (a) investigate combustion in a CWT geometry; and (b) provide guidance to the TWA 800 crash investigation. The results of the experiments were observed with high-speed film, video, and still cameras, fast and slow pressure sensors, thermocouples, photodetectors, and motion sensors. A special pseudo-schlieren system was used to visualize flame propagation within the tank. This report describes the test program, facility, instrumentation, the first 30 experiments, comparisons between experiments, and performance of the instrumentation; then examines the significance of these results to the TWA 800 crash investigation. The key results of this study are: Flame Motion: The motion of flame was dominated by the effects of turbulence created by jetting through the passageways and vent stringers. A very rapid combustion event (lasting 10 to 20 ms) occurred once the flame traveled outside of the ignition bay and interacted with the turbulent flow. Most of the gas within the tank was burned during this rapid event. Compartments: The combustion time decreased with an increasing number of compartments (bays) within the tank. With six bays, combustion took only 100 to 150 ms to be completed from the time of ignition until the end of the rapid combustion phase. The total combustion event was three to four times shorter with compartments than without. Venting: Venting to the outside of the tank through the model vent stringers had a negligible effect on the combustion progress or on the peak pressure reached at the end of the burn. Ignition Location: Variation of the ignition location produced distinctive pressure loads on the structural components. Liquid Fuel: Lofting of a cold liquid fuel layer was produced by the combustion-induced gas motion. Although this spray of liquid eventually ignited and burned, it did not contribute to the pressure loading. Structural Failure: Structural failure resulted in flame acceleration, decreasing the overall combustion time. TWA 800 Investigation: The pressure loads were sufficiently high, up to 4 bar, and the combustion events were sufficiently short, that the forward portion (spanwise beam 3, front spar) of the CWT structure would fail as a direct consequence of the explosion. A combination of pressure loads was produced in some tests consistent with the TWA 800 wreckage. Replica tests, structural modeling, and sensitivity studies on fuel concentration are needed before any conclusions can be drawn about probable ignition locations. Cargo Bay: Tests with a simplified model of a half-full cargo bay indicated that repeated pressure waves with an amplitude of 1 bar or less are produced when an explosion scenario similar to TWA 800 is tested. Future Testing: Future studies should include replica tests, tests with Jet A vapor and warm liquid Jet A layers, and sensitivity tests to examine ignition location, fuel concentration, and vent area perturbations. Summary: Explosion tests in a 747-100 CWT model reveal that a very complex pattern of combustion occurs due the interaction of the flame and the flow-generated turbulence. A wide range of structural load patterns occur, depending on the location of the ignition source. Some of these load patterns are consistent with damage believed to be associated with the initial explosion event in TWA 800. Sensitivity of the loading to the ignition location indicates that narrowing down the ignition location in TWA 800 may be possible. However, the complexity of the combustion and structural failure processes in the actual center wing tank mandates extremely careful consideration of the uncertainties that enter into this process

Inference of transcriptional regulation using gene expression data from the bovine and human genomes

<p>Abstract</p> <p>Background</p> <p>Gene expression is in part regulated by sequences in promoters that bind transcription factors. Thus, co-expressed genes may have shared sequence motifs representing putative transcription factor binding sites (TFBSs). However, for agriculturally important animals the genomic sequence is often incomplete. The more complete human genome may be able to be used for this prediction by taking advantage of the expected evolutionary conservation in TFBSs between the species.</p> <p>Results</p> <p>A method of <it>de novo </it>TFBS prediction based on MEME was implemented, tested, and validated on a muscle-specific dataset.</p> <p>Muscle specific expression data from EST library analysis from cattle was used to predict sets of genes whose expression was enriched in muscle and cardiac tissues. The upstream 1500 bases from calculated orthologous genes were extracted from the human reference set. A set of common motifs were discovered in these promoters. Slightly over one third of these motifs were identified as known TFBSs including known muscle specific binding sites. This analysis also predicted several highly statistically significantly overrepresented sites that may be novel TFBS.</p> <p>An independent analysis of the equivalent bovine genomic sequences was also done, this gave less detailed results than the human analysis due to both the quality of orthologue prediction and assembly in promoter regions. However, the most common motifs could be detected in both sets.</p> <p>Conclusion</p> <p>Using promoter sequences from human genes is a useful approach when studying gene expression in species with limited or non-existing genomic sequence. As the bovine genome becomes better annotated it can in turn serve as the reference genome for other agriculturally important ruminants, such as sheep, goat and deer.</p

Translation of the first upstream ORF in the hepatitis B virus pregenomic RNA modulates translation at the core and polymerase initiation codons

The human hepatitis B virus (HBV) has a compact genome encoding four major overlapping coding regions: the core, polymerase, surface and X. The polymerase initiation codon is preceded by the partially overlapping core and four or more upstream initiation codons. There is evidence that several mechanisms are used to enable the synthesis of the polymerase protein, including leaky scanning and ribosome reinitiation. We have examined the first AUG in the pregenomic RNA, it precedes that of the core. It initiates an uncharacterized short upstream open reading frame (uORF), highly conserved in all HBV subtypes, we designated the C0 ORF. This arrangement suggested that expression of the core and polymerase may be affected by this uORF. Initiation at the C0 ORF was confirmed in reporter constructs in transfected cells. The C0 ORF had an inhibitory role in downstream expression from the core initiation site in HepG2 cells and in vitro, but also stimulated reinitiation at the polymerase start when in an optimal context. Our results indicate that the C0 ORF is a determinant in balancing the synthesis of the core and polymerase proteins

How body mass and lifestyle affect juvenile biomass production in placental mammals

In mammals, the mass-specific rate of biomass production during gestation and lactation, here called maternal productivity, has been shown to vary with body size and lifestyle. Metabolic theory predicts that post-weaning growth of offspring, here termed juvenile productivity, should be higher than maternal productivity, and juveniles of smaller species should be more productive than those of larger species. Furthermore because juveniles generally have similar lifestyles to their mothers, across species juvenile and maternal productivities should be correlated. We evaluated these predictions with data from 270 species of placental mammals in 14 taxonomic/lifestyle groups. All three predictions were supported. Lagomorphs, perissodactyls and artiodactyls were very productive both as juveniles and as mothers as expected from the abundance and reliability of their foods. Primates and bats were unproductive as juveniles and as mothers, as expected as an indirect consequence of their low predation risk and consequent low mortality. Our results point the way to a mechanistic explanation for the suite of correlated life-history traits that has been called the slow–fast continuum

A First Principles Theory of Nuclear Magnetic Resonance J-Coupling in solid-state systems

A method to calculate NMR J-coupling constants from first principles in extended systems is presented. It is based on density functional theory and is formulated within a planewave-pseudopotential framework. The all-electron properties are recovered using the projector augmented wave approach. The method is validated by comparison with existing quantum chemical calculations of solution-state systems and with experimental data. The approach has been applied to verify measured J-coupling in a silicophosphate structure, Si5O(PO4)6Comment: 9 page