Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines.

BackgroundTo reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results.ResultsLog::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution. It can also be used to compare the environments of two executions to determine whether there were any differences that might affect (or explain) their operation.AvailabilityThe source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).ConclusionUsing Log::ProgramInfo in programs creating result data for publishable research, and including the Log::ProgramInfo output log as part of the publication of that research is a valuable method to assist others to duplicate the programming environment as a precursor to validating and/or extending that research

A qualitative study in rural and urban areas on whether - and how - to consult during routine and out of hours

Peer reviewedPublisher PD

Volcanic Mound Fields on the East Pacific Rise, 16˚-19˚S: Low Effusion Rate Eruptions at Overlapping Spreading Centers for the Past 1 Myr

Volcanic mound fields identified on SeaMARC II and HMR1 12 kHz side-scan data from the southern East Pacific Rise (SEPR) occur near overlapping spreading centers (OSCs) and migration traces of OSCs. The volcanic mound fields appear as a distinctive hummocky seafloor fabric due to side-scan backscatter reflections from clusters of moundshaped reflectors. The lack of growth of the mound fields away from the ridge axis, and their occurrence in association with OSC traces, suggests that mound fields form along the ridge crest near OSCs. Volcanic mound fields are found where 120 kHz side-scan and visual observations find fields of pillow mounds. Since pillow mounds are constructed by low effusion rate eruptions, the volcanic mound fields found near the OSCs and in their migration traces indicate that volcanic effusion rates tend to be lower near ridge discontinuities than midsegment regions. This tendency for low effusion rate eruptions at OSCs is documented for the past _1 Myr. Three independent measurements of ridge segmentation, (1) volcanic segment boundaries marked by the low effusion rate eruptions, (2) tectonic segments defined by OSCs, and (3) magmatic segment boundaries based on continuity of parental magma composition, all coincide in the study area. High backscatter off-axis lava fields not associated with seamounts are found on seafloor younger than _0.2 Ma. The _0.2 Ma corridor corroborates previous results from the distribution of small isolated volcanoes that indicates randomly distributed off-axis eruptions mainly occur on crust younger than _0.2 Ma

Peralkaline Silicic Extrusive Rocks: Magma Genesis, Evolution, Plumbing Systems, and Eruption.

Peralkaline silicic extrusive rocks are an important component of the volcanological record. Here we review several aspects of their formation and evolution, including the tectonic settings in which they occur, their main petrological and geochemical features, the magmatic lineages along which they evolve, and the parameters (T, P, fO2, melt water contents) that control the lineages. Particular attention is paid to the composition of the extraordinary melts formed at the lowest temperatures. Various lines of evidence are presented to explain the silica-gaps in some lineages. The partial melting of continental crust and the role of crustal contamination are considered to be of relatively minor importance in their genesis. High P-T experiments aimed at quantifying the lineages are assessed. Geophysical and petrological evidence for the depth and nature of the plumbing systems is presented. Differentiation mechanisms within reservoirs and the ubiquity of the formation of compositional zonation are discussed, as are the timescales involved. Volcanic hazards and the environmental impact of eruptions are described and a brief assessment of the ore potential of the extrusives is given

Bilayer Quantum Hall Systems at Filling Factor \nu=2: An Exact Diagonalisation Study

We present an exact diagonalisation study of bilayer quantum Hall systems at a filling factor of two in the spherical geometry. We find the high-Zeeman-coupling phase boundary of the broken symmetry canted antiferromagnet is given exactly by previous Hartree-Fock mean-field theories, but that the state's stability at weak Zeeman coupling has been qualitatively overestimated. In the absence of interlayer tunneling, degeneracies occur between total spin multiplets due to the Hamiltonian's invariance under independent spin-rotations in top and bottom two-dimensional electron layers.Comment: Some remarks added in the discussion of the phase diagram, and some typos corrected. Version to be published in Phys. Rev. Let

Extreme Differentiation along Multiple Liquid Lines of Descent in Strongly Peralkaline Magma Series at Pantelleria (Italy)

The liquid line of descent from trachyte to pantellerite is controlled primarily by fractional crystallization of alkali feldspar, with whole rock compositions following a fractionation path along the ‘thermal valley’ in the peralkaline haplogranite system Qz-Ab-Or-Ac-Ns and terminating at a minimum on the feldspar-quartz cotectic. Although whole-rock compositions for different pantelleritic suites follow nearly identical paths in a Qz-Ab-Or projection that terminate near the experimental minimum (Qz40.5Or34.5Ab25 at 100 MPa, projected from Ac-Ns), matrix glass from samples with near-minimum compositions record extreme differentiation and form a ‘cotectic delta’ beyond the terminus of the ‘thermal valley’. Although each glass trend shows a continuing increase in Zr to \u3e3000 μg/g, the most evolved compositions in each suite differ in peralkalinity (mol [Na+K] / Al) and in the proportions of FeOT, Qz, Ab, Or, and other components, which are related to subtle variations in the mafic phases controlled mainly by differences in oxygen fugacity (fO2)and pressure (P). To determine the controls over mafic mineral crystallization in pantelleritic magmas and the various paths these suites take beyond the apparent (whole-rock) minimum, amphibole-phyric suites from the ∼159 ka Cala dell’Altura and Cala Gadir volcanic centres and the ∼8–10 ka Cuddia Mida volcanic centre on Pantelleria have been analyzed and compared with each other and with the well-characterized and amphibole-free, compositionally zoned Green Tuff, the ∼46 ka caldera-forming ignimbrite of the Cinque Denti caldera. Differences between the extended fractionation trends may be ultimately attributed to variations in oxygen fugacity, depth of emplacement, and water saturation. Shallower (lower pressure) magma reservoirs such as the one for the Green Tuff are water saturated and undergo degassing, which leads to an increase in relative oxygen fugacity. Deeper (higher pressure) magma reservoirs remain water-undersaturated and retain water in the melt, which both maintains lower relative oxygen fugacities and enables the crystallization of amphibole. Amphibole formation appears to require melt water contents \u3e4 wt%, low oxygen fugacity

Evolution of the magma system of Pantelleria (Italy) from 190 ka to present

The eruptive history of Pantelleria has been marked by the eruption of nine peralkaline ignimbrites, with inter-ignimbrite episodes from small, local volcanic centres. New whole-rock geochemical data are presented for seven ignimbrites and used with published data for younger units to track compositional changes with time. From»190 ka, silicicmagmatismwas dominated by comenditic trachyte to comendite compositions, evolving along generally similar liquid lines of descent (LLOD). The final ignimbrite, the Green Tuff (»46 ka), was tapped from a compositionally zoned pantelleritic upper reservoir to a trachytic mush zone. Younger (20–7 ka) silicic magmatism has been relatively small scale, with compositions similar to the earliest pre-Green Tuff pantelleritic ignimbrite (Zinedi). These data suggest that the comenditic reservoirs may have been emplaced at deeper levels than the pantelleritic reservoirs. While both types of series evolved along similar LLOD dominated by fractionation of alkali feldspar, it is the fractionation of iron that determines whether comendite or pantellerite is produced. The deeper reservoirs were more oxidizing and wetter, thus leading to the crystallization of magnetite and therefore the fractionation of iron

Differences in radionuclide and heavy metal concentrations found in the kidneys of barren-ground caribou from the western Northwest Territories 1994/95 to 2000/01

Aluminum, nickel, cadmium, mercury, and lead concentrations were measured in the kidney tissue of known aged barren-ground caribou wintering in the western Northwest Territories harvested during winter 1994/1995 and during winters 2000/2001 and 2001/2002. 40K, 137Cs, and 210Pb concentrations were measured in the kidney tissue of known aged barren-ground caribou during winter 2000/2001 and compared to concentrations in winter 1993/1994 reported in Macdonald et al. (1996). Renal concentrations of aluminum were higher (P<0.001)in winter 2000/2001 than winter 1994/1995. Contrastingly renal concentrations of mercury were lower (P<0.001) in winter 2000/2001 than 1994/1995. 137Cs (P<0.02), 40K (P=0.01), 210Pb (P<0.01) had lower renal concentrations in winter 2000/2001 than 1993/1994. Renal concentrations of cadmium (P<0.001) and 137Cs (P<0.04) had a positive relationship with caribou age. We also document renal concentrations of arsenic, copper, selenium, zinc, 232Th, 226Ra, and 235U in the kidneys of caribou harvested in winters 2000/2001 and 2001/2002. Renal zinc concentrations were positively correlated with the age of caribou