Where Fail-Safe Default Logics Fail

Reiter's original definition of default logic allows for the application of a default that contradicts a previously applied one. We call failure this condition. The possibility of generating failures has been in the past considered as a semantical problem, and variants have been proposed to solve it. We show that it is instead a computational feature that is needed to encode some domains into default logic

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

BACKGROUND: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. METHODOLOGY/PRINCIPAL FINDINGS: A set of approximately 30K unique sequences (UniSeqs) representing approximately 19K clusters were generated from approximately 98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66% of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases. CONCLUSIONS/SIGNIFICANCE: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics

Terahertz Response of Field-Effect Transistors in Saturation Regime

We report on the broadband THz response of InGaAs/GaAs HEMTs operating at 1.63 THz and room temperature deep in the saturation regime. We demonstrate that responses show linear increase with drain-to-source voltage (or drain bias current) and reach very high values up to 170V/W. We also develop a phenomenological theory valid both in the ohmic and in the saturation regimes.Comment: 11 pages, 3 figure

The origin recognition complex in silencing, cell cycle progression, and DNA replication

This report describes the isolation of ORC5, the gene encoding the fifth largest subunit of the origin recognition complex, and the properties of mutants with a defective allele of ORC5. The orc5-1 mutation caused temperature-sensitive growth and, at the restrictive temperature, caused cell cycle arrest. At the permissive temperature, the orc5-1 mutation caused an elevated plasmid loss rate that could be suppressed by additional tandem origins of DNA replication. The sequence of ORC5 revealed a potential ATP binding site, making Orc5p a candidate for a subunit that mediates the ATP-dependent binding of ORC to origins. Genetic interactions among orc2-1 and orc5-1 and other cell cycle genes provided further evidence for a role for the origin recognition complex (ORC) in DNA replication. The silencing defect caused by orc5-1 strengthened previous connections between ORC and silencing, and combined with the phenotypes caused by orc2 mutations, suggested that the complex itself functions in both processes

Epigenetic Chromatin Silencing: Bistability and Front Propagation

The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. We formulate a coarse-grained model of chromatin silencing in yeast and study the conditions under which the system becomes bistable, allowing for different epigenetic states. We also study the dynamics of the boundary between the two locally stable states of chromatin: silenced and unsilenced. The model could be of use in guiding the discussion on chromatin silencing in general. In the context of silencing in budding yeast, it helps us understand the phenotype of various mutants, some of which may be non-trivial to see without the help of a mathematical model. One such example is a mutation that reduces the rate of background acetylation of particular histone side-chains that competes with the deacetylation by Sir2p. The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. Our mathematical analysis brings forth the different dynamical behaviors possible within the same molecular model and guides the formulation of more refined hypotheses that could be addressed experimentally.Comment: 19 pages, 5 figure

Excess noise in GaAs and AlGaAs avalanche photodiodes with GaSb absorption regions—composite structures grown using interfacial misfit arrays

Interfacial misfit arrays were embedded within two avalanche photodiode (APD) structures. This allowed GaSb absorption layers to be combined with wide-bandgap multiplication regions, consisting of GaAs and Al0.8Ga0.2As, respectively. The GaAs APD represents the simplest case. The Al0.8Ga0.2As APD shows reduced dark currents of 5.07 μAcm−2 at 90% of the breakdown voltage, and values for effective below 0.2. Random-path-length modeled excess noise is compared with experimental data, for both samples. The designs could be developed further, allowing operation to be extended to longer wavelengths, using other established absorber materials which are lattice matched to GaSb

Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2-7 (minichromosome maintenance proteins 2-7) double hexamer. During S phase, each Mcm2-7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC-Cdc6 function to recruit a single Cdt1-Mcm2-7 heptamer to replication origins prior to Cdt1 release and ORC-Cdc6-Mcm2-7 complex formation, but how the second Mcm2-7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC-Cdc6-Mcm2-7 complex and an ORC-Cdc6-Mcm2-7-Mcm2-7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2-7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2-7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability

Kleptoparasitic melees--modelling food stealing featuring contests with multiple individuals

Kleptoparasitism is the stealing of food by one animal from another. This has been modelled in various ways before, but all previous models have only allowed contests between two individuals. We investigate a model of kleptoparasitism where individuals are allowed to fight in groups of more than two, as often occurs in real populations. We find the equilibrium distribution of the population amongst various behavioural states, conditional upon the strategies played and environmental parameters, and then find evolutionarily stable challenging strategies. We find that there is always at least one ESS, but sometimes there are two or more, and discuss the circumstances when particular ESSs occur, and when there are likely to be multiple ESSs

Cryo-EM structure of a helicase loading intermediate containing ORC-Cdc6-Cdt1-MCM2-7 bound to DNA

In eukaryotes, the Cdt1-bound replicative helicase core MCM2-7 is loaded onto DNA by the ORC-Cdc6 ATPase to form a prereplicative complex (pre-RC) with an MCM2-7 double hexamer encircling DNA. Using purified components in the presence of ATP-γS, we have captured in vitro an intermediate in pre-RC assembly that contains a complex between the ORC-Cdc6 and Cdt1-MCM2-7 heteroheptamers called the OCCM. Cryo-EM studies of this 14-subunit complex reveal that the two separate heptameric complexes are engaged extensively, with the ORC-Cdc6 N-terminal AAA+ domains latching onto the C-terminal AAA+ motor domains of the MCM2-7 hexamer. The conformation of ORC-Cdc6 undergoes a concerted change into a right-handed spiral with helical symmetry that is identical to that of the DNA double helix. The resulting ORC-Cdc6 helicase loader shows a notable structural similarity to the replication factor C clamp loader, suggesting a conserved mechanism of action

Curricular orientations to real-world contexts in mathematics

A common claim about mathematics education is that it should equip students to use mathematics in the ‘real world’. In this paper, we examine how relationships between mathematics education and the real world are materialised in the curriculum across a sample of eleven jurisdictions. In particular, we address the orientation of the curriculum towards application of mathematics, the ways that real-world contexts are positioned within the curriculum content, the ways in which different groups of students are expected to engage with real-world contexts, and the extent to which high-stakes assessments include real-world problem solving. The analysis reveals variation across jurisdictions and some lack of coherence between official orientations towards use of mathematics in the real world and the ways that this is materialised in the organisation of the content for students