Profiling for run-time checking of computational properties and performance debugging in logic programs

Although several profiling techniques for identifying performance bottlenecks in logic programs have been developed, they are generally not automatic and in most cases they do not provide enough information for identifying the root causes of such bottlenecks. This complicates using their results for guiding performance improvement. We present a profiling method and tool that provides such explanations. Our profiler associates cost centers to certain program elements and can measure different types of resource-related properties that affect performance, preserving the precedence of cost centers in the cali graph. It includes an automatic method for detecting procedures that are performance bottlenecks. The profiling tool has been integrated in a previously developed run-time checking framework to allow verification of certain properties when they cannot be verified statically. The approach allows checking global computational properties which require complex instrumentation tracking information about previous execution states, such as, e.g., that the execution time accumulated by a given procedure is not greater than a given bound. We have built a prototype implementation, integrated it in the Ciao/CiaoPP system and successfully applied it to performance improvement, automatic optimization (e.g., resource-aware specialization of programs), run-time checking, and debugging of global computational properties (e.g., resource usage) in Prolog programs

Galaxy and Mass Assembly (GAMA): Variation in galaxy structure across the green valley

Using a sample of 472 local Universe (z \u3c 0.06) galaxies in the stellar mass range 10.25 \u3c logM*/M⊙ \u3c 10.75, we explore the variation in galaxy structure as a function of morphology and galaxy colour. Our sample of galaxies is subdivided into red, green, and blue colour groups and into elliptical and non-elliptical (disk-type) morphologies. Using Kilo- Degree Survey (KiDS) and Visible and Infrared Survey Telescope for Astronomy (VISTA) Kilo-Degree Infrared Galaxy Survey (VIKING) derived postage stamp images, a group of eight volunteers visually classified bars, rings, morphological lenses, tidal streams, shells, and signs of merger activity for all systems. We find a significant surplus of rings (2.3s) and lenses (2.9s) in disk-type galaxies as they transition across the green valley. Combined, this implies a joint ring/lens green valley surplus significance of 3.3s relative to equivalent disk-types within either the blue cloud or the red sequence. We recover a bar fraction of ~44 per cent which remains flat with colour, however, we find that the presence of a bar acts to modulate the incidence of rings and (to a lesser extent) lenses, with rings in barred disk-type galaxies more common by ~20-30 percentage points relative to their unbarred counterparts, regardless of colour. Additionally, green valley disk-type galaxies with a bar exhibit a significant 3.0s surplus of lenses relative to their blue/red analogues. The existence of such structures rules out violent transformative events as the primary end-of-life evolutionary mechanism, with a more passive scenario the favoured candidate for the majority of galaxies rapidly transitioning across the green valley

ALMA <sup>13</sup>CO(J = 1 − 0) Observations of NGC 604 in M33: Physical properties of molecular clouds

We present Atacama Large Millimeter/submillimeter Array (ALMA) observations of 13CO(J=1−0) line and 104 GHz continuum emission from NGC 604, a giant HII region (GHR) in the nearby spiral galaxy M33. Our high spatial resolution images ( 3.2"× 2.4", corresponding to 13×10 pc physical scale) allow us to detect fifteen molecular clouds. We find spatial offsets between the 13CO and 104 GHz continuum emission and also detect continuum emission near the centre of the GHR. The identified molecular clouds have sizes ranging from 5-21 pc, linewidths of 0.3-3.0 kms−1 and luminosity-derived masses of (0.4-80.5) ×103 M⨀. These molecular clouds are in near virial equilibrium, with a spearman correlation coefficient of 0.98. The linewidth-size relationship for these clouds is offset from the corresponding relations for the Milky Way and for NGC 300, although this may be an artefact of the dendrogram process

PPARδ status and mismatch repair mediated neoplasia in the mouse intestine

Background:Therapeutic regulation of PPARδ activity using selective agonists has been proposed for various disorders. However, the consequences of altered peroxisome proliferator-activated receptor delta (PPARδ) activity in the context of intestinal tumourigenesis remain somewhat unclear. Contradictory evidence suggesting PPARδ either attenuates or potentiates intestinal neoplasia. To further investigate the PPARδ dependency of intestinal tumourigenesis, we have analysed the consequences of PPARδ deficiency upon intestinal neoplasia occurring in mice with impaired mismatch DNA repair. Methods:Mice deficient for both PPARδ and the mismatch repair gene Mlh1 were produced and the incidence and severity of intestinal neoplasia recorded. Results:No significant differences between the control genotypes and the double mutant genotypes were recorded indicating that deficiency of PPARδ does not modify impaired mismatch repair induced neoplasia. Conclusion:In contrast with the previously observed acceleration of intestinal neoplasia in the context of the Apc[superscript Min/+]mouse, PPARδ deficiency does not alter the phenotype of mismatch repair deficiency. This data supports the notion that PPARδ is not required for adenoma formation and indicate that any pro-tumourigenic effect of PPARδ inactivation may be highly context dependent

Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS)

Trushar Shah, Etienne de Villiers, Evans Taracha, Roger Pelle and Richard Bishop are ILRI authorsTranscriptome analysis can provide useful data for refining genome sequence annotation. Application of massively parallel signature sequencing (MPSS) revealed reproducible transcription, in multiple MPSS cycles, from 73% of computationally predicted genes in the Theileria parva schizont lifecycle stage. Signatures spanning consecutive exons confirmed 142 predicted introns. MPSS identified 83 putative genes, > 100 codons overlooked by annotation software, and 139 potentially incorrect gene models (with either truncated ORFs or overlooked exons) by interfacing signature locations with stop codon maps. Twenty representative models were confirmed as likely to be incorrect using reverse transcription PCR amplification from independent schizont cDNA preparations. More than 50% of the 60 putative single copy genes in T. parva that were absent from the genome of the closely related T. annulata had MPSS signatures. This study illustrates the utility of MPSS for improving annotation of small, gene-rich microbial eukaryotic genomes

Mineralogy, petrology, geochemistry, and chronology of the Murrili (H5) meteorite fall: The third recovered fall from the Desert Fireball Network

Murrili, the third meteorite recovered by the Desert Fireball Network, is analyzed using mineralogy, oxygen isotopes, bulk chemistry, physical properties, noble gases, and cosmogenic radionuclides. The modal mineralogy, bulk chemistry, magnetic susceptibility, physical properties, and oxygen isotopes of Murrili point to it being an H5 ordinary chondrite. It is heterogeneously shocked (S2–S5), depending on the method used to determine it, although Murrili is not obviously brecciated in texture. Cosmogenic radionuclides yield a cosmic ray exposure age of 6–8 Ma, and a pre-atmospheric meteoroid size of 15–20 cm in radius. Murrili’s fall and subsequent month-long embedment into the salt lake Kati Thanda significantly altered the whole rock, evident in its Mössbauer spectra, and visual inspection of cut sections. Murrili may have experienced minor, but subsequent, impacts after its formation 4475.3 ± 2.3 Ma, which left it heterogeneously shocked