Redefinition and Statistical Analysis of Measures for Evaluating the Quality of Ontologies

OntoQualitas is a framework to evaluate an ontology whose purpose is the interchange of information between different contexts. However, the framework does not propose acceptance thresholds of the measure values. In this paper, measures proposed in this framework are redefined in order to improve their usefulness in assessing the quality of such ontologies. These measures were calculated semi-automatically on a set of ontologies and its results were described by means of a statistical analysis as a first step to the definition of their acceptance thresholds.Sociedad Argentina de Informática e Investigación Operativa (SADIO

Redefinition and Statistical Analysis of Measures for Evaluating the Quality of Ontologies

OntoQualitas is a framework to evaluate an ontology whose purpose is the interchange of information between different contexts. However, the framework does not propose acceptance thresholds of the measure values. In this paper, measures proposed in this framework are redefined in order to improve their usefulness in assessing the quality of such ontologies. These measures were calculated semi-automatically on a set of ontologies and its results were described by means of a statistical analysis as a first step to the definition of their acceptance thresholds.Sociedad Argentina de Informática e Investigación Operativa (SADIO

From insect to man: Photorhabdus sheds light on the emergence of human pathogenicity

Photorhabdus are highly effective insect pathogenic bacteria that exist in a mutualistic relationship with Heterorhabditid nematodes. Unlike other members of the genus, Photorhabdus asymbiotica can also infect humans. Most Photorhabdus cannot replicate above 34°C, limiting their host-range to poikilothermic invertebrates. In contrast, P. asymbiotica must necessarily be able to replicate at 37°C or above. Many well-studied mammalian pathogens use the elevated temperature of their host as a signal to regulate the necessary changes in gene expression required for infection. Here we use RNA-seq, proteomics and phenotype microarrays to examine temperature dependent differences in transcription, translation and phenotype of P. asymbiotica at 28°C versus 37°C, relevant to the insect or human hosts respectively. Our findings reveal relatively few temperature dependant differences in gene expression. There is however a striking difference in metabolism at 37°C, with a significant reduction in the range of carbon and nitrogen sources that otherwise support respiration at 28°C. We propose that the key adaptation that enables P. asymbiotica to infect humans is to aggressively acquire amino acids, peptides and other nutrients from the human host, employing a so called “nutritional virulence” strategy. This would simultaneously cripple the host immune response while providing nutrients sufficient for reproduction. This might explain the severity of ulcerated lesions observed in clinical cases of Photorhabdosis. Furthermore, while P. asymbiotica can invade mammalian cells they must also resist immediate killing by humoral immunity components in serum. We observed an increase in the production of the insect Phenol-oxidase inhibitor Rhabduscin normally deployed to inhibit the melanisation immune cascade. Crucially we demonstrated this molecule also facilitates protection against killing by the alternative human complement pathway

The chalcolithic of the Near East and south-eastern Europe: Discoveries and new perspectives from the cave complex Areni-1, Armenia

The archaeological exploration of a cave in the southern Caucasus revealed evidence for early social complexity, ritual burial and wine-making in the early fourth millennium. The marvellous preservation of wood, leather and plants offers a valuable contrast to the poorer assemblages on contemporary tell sites. The authors make the case that the Areni-1 cave complex indicates connections between the urbanisation of early Mesopotamia and the Maikop culture of south Russia.</jats:p

The chalcolithic of the Near East and south-eastern Europe: Discoveries and new perspectives from the cave complex Areni-1, Armenia

APPEAL FROM THIRD DISTRICT COURT HONORABLE LESLIE A. LEWIS, PRESIDIN

A left-hand superiority for the implicit detection of a rule

We set out to test the hypothesis of right-hemisphere superiority for the implicit detection of a rule. Forty healthy men provided speeded manual responses to randomly presented digits from 1 to 6 (left hand to 1-3, right hand to 4-6). Red digits on trial n signaled that the response on trial n+1 should be made with one hand, blue digits with the other hand. White digits gave no signal (control trials). Half the participants were told that the stimulus color conveyed a rule that could be exploited to improve performance, the other half were not. After completing the first run, participants' awareness of the presence and nature of the rule was assessed and all were debriefed. Participants then performed a second run with identical stimulus conditions. In Run 1, none of the participants reported being aware of the nature of the rule. Reaction times (RTs) were longer after signal than no-signal trials, but only for the left hand. Participants informed about the presence of a rule tended to have longer RTs, irrespective of hand. In Run 2, RTs were shorter after signal than no-signal trials, and there were no differences between hands. The observed RT effect for the left-hand points to a right-hemisphere superiority for the detection and application of a rule in the absence of verbal awareness. Longer (instead of shorter) RTs in the signal trials are discussed in the framework of interhemispheric inhibition

The genus <i>Photorhabdus</i> contains three predominant species.

<p>A stylized representation of a previous six gene MLST phylogeny (<i>adk</i>, <i>ghd</i>, <i>mdk</i>, <i>ndh</i>, <i>pgm</i> and <i>recA</i>) of <i>Photorhabdus</i> (adapted from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144937#pone.0144937.ref005" target="_blank">5</a>]) is shown. The grey areas indicate species that consist of multiple strains, the majority of which are unable to grow above 34°C, with only a few <i>P</i>. <i>luminescens</i> strains capable of growth at temperatures up to 37°C. Example strains are <i>P</i>. <i>luminescens</i>^TT01 and <i>P</i>. <i>temperata</i>^K122. The clinical strains adapted to 37°C are boxed. The stars and circles indicate the potential historical timing of temperature adaptation, which could have occurred ancestrally (star) or independently (circles) in different geographical isolates.</p

A schematic summarising some key differences in metabolism at 37°C compared to 28°C, centred on glutamate/asparagine metabolism and the TCA cycle.

<p>This model is predicted by integrating data from the RNA-seq, proteomics and phenotype microarray studies. Intermediates (boxes) and pathways (arrows) predicted to be down regulated at 37°C are in red while those up regulated are in green. Data suggests TCA cycle intermediates (back boxes) would be relatively isolated from glutamate/asparagine metabolism and could be maintained via the conversion of L-serine into citrate via pyruvate. Black arrows indicate certain potential enzyme pathways that are present and predicted to be unchanged at 37°C. The data suggests a central role for imported peptides and amino acids in metabolism at 37°C. Opp/Dpp represent oligo- and di-peptide importers, TCT represents tricarboxylic acid and PEP is Phosphoenolpyruvate.</p

Clinical <i>Photorhabdus</i> isolates are able to survive exposure to higher temperatures than most non-clinical isolates.

<p>The optical density achieved by representative strains after overnight growth in static conditions (at 28°C in LB medium) after prior 18 h exposure to a range of temperatures. A range of clinical (N. American and Australian) and non-clinical (European) strains of <i>P</i>. <i>asymbiotica (Pa)</i> were tested, and the well-studied <i>P</i>. <i>luminescens</i> strain (<i>Pl</i>^TT01) was included for comparison. Green stars and red diamonds indicate thermal tolerance and intolerance respectively. <i>Pa</i> strain designations are indicated as superscripts.</p