MOLES3: implementing an ISO standards driven data catalogue

ISO19156 Observations and Measurements (O&M) provides a standardised framework for organising information about the collection of information about the environment. Here we describe the implementation of a specialisation of O&M for environmental data, the Metadata Objects for Linking Environmental Sciences (MOLES3). MOLES3 provides support for organising information about data, and for user navigation around data holdings. The implementation described here, “CEDA-MOLES”, also supports data management functions for the Centre for Environmental Data Archival, CEDA. The previous iteration of MOLES (MOLES2) saw active use over five years, being replaced by CEDA-MOLES in late 2014. During that period important lessons were learnt both about the information needed, as well as how to design and maintain the necessary information systems. In this paper we review the problems encountered in MOLES2; how and why CEDA-MOLES was developed and engineered; the migration of information holdings from MOLES2 to CEDA-MOLES; and, finally, provide an early assessment of MOLES3 (as implemented in CEDA-MOLES) and its limitations. Key drivers for the MOLES3 development included the necessity for improved data provenance, for further structured information to support ISO19115 discovery metadata export (for EU INSPIRE compliance), and to provide appropriate fixed landing pages for Digital Object Identifiers (DOIs) in the presence of evolving datasets. Key lessons learned included the importance of minimising information structure in free text fields, and the necessity to support as much agility in the information infrastructure as possible without compromising on maintainability both by those using the systems internally and externally (e.g. citing in to the information infrastructure), and those responsible for the systems themselves. The migration itself needed to ensure continuity of service and traceability of archived assets.

A decision framework for considering climate change adaptation in biodiversity conservation planning

General principles of climate change adaptation for biodiversity have been formulated, but do not help prioritize actions. This is inhibiting their integration into conservation planning. We address this need with a decision framework that identifies and prioritizes actions to increase the adaptive capacity of species. The framework classifies species according to their current distribution and projected future climate space, as a basis for selecting appropriate decision trees. Decisions rely primarily on expert opinion, with additional information from quantitative models, where data are available. The framework considers in-situ management, followed by interventions at the landscape scale and finally translocation or ex-situ conservation. Synthesis and applications: From eight case studies, the key interventions identified for integrating climate change adaptation into conservation planning were local management and expansion of sites. We anticipate that, in combination with consideration of socio-economic and local factors, the decision framework will be a useful tool for conservation and natural resource managers to integrate adaptation measures into conservation plans.

HIV/AIDS: use of the ICF in Brazil and South Africa - comparative data from four cross-sectional studies

Introduction Human immunodeficiency virus (HIV) is a serious disease which can be associated with various activity limitations and participation restrictions. The aim of this paper was to describe how HIV affects the functioning and health of people within different environmental contexts, particularly with regard to access to medication. Method Four cross-sectional studies, three in South Africa and one in Brazil, had applied the International Classification of Functioning, Disability and Health (ICF) as a classification instrument to participants living with HIV. Each group was at a different stage of the disease. Only two groups had had continuing access to antiretroviral therapy. The existence of these descriptive sets enabled comparison of the disability experienced by people living with HIV at different stages of the disease and with differing access to antiretroviral therapy. Results Common problems experienced in all groups related to weight maintenance, with two-thirds of the sample reporting problems in this area. Mental functions presented the most problems in all groups, with sleep (50%, 92/185), energy and drive (45%, 83/185), and emotional functions (49%, 90/185) being the most affected. In those on long-term therapy, body image affected 93% (39/42) and was a major problem. The other groups reported pain as a problem, and those with limited access to treatment also reported mobility problems. Cardiopulmonary functions were affected in all groups. Conclusion Functional problems occurred in the areas of impairment and activity limitation in people at advanced stages of HIV, and more limitations occurred in the area of participation for those on antiretroviral treatment. The ICF provided a useful framework within which to describe the functioning of those with HIV and the impact of the environment. Given the wide spectrum of problems found, consideration could be given to a number of ICF core sets that are relevant to the different stages of HIV disease. (C) 2010 Chartered Society of Physiotherapy. Published by Elsevier Ltd. All rights reserved.

Evidence of chromosome fusion in Gymnotus sylvius Albert & Fernandes-Matoli, 1999 (Teleostei: Gymnotiformes) detected by telomeric probes and R-banding

Gymnotus cf. carapo and Gynznotus sylvius are two fish species inhabiting the Upper Parana River Basin, presenting respectively 2n =54 and 2n = 40 chromosomes. In the present cytogenetic analysis, R-banding and telomere-sequence hybridization were carried out in order to determine the possible relationship between the karyotipes of these two species. Incorporation bands (R-bands) obtained for the two species allowed the identification of chromosome similarities, showing to be an usefull alternative to the G-banding methods, which fail in producing satisfying results in most of analyzed fish species. This approach, associated with the hybridization of telomeric sequences, permited to identify chromosomal rearrangements that could be used as indicators of karyotypic evolution within the group. In the present case, telomeric sequences were detected in the centromeric region of two metacentric chromosome pairs of Gymnotus sylvius. The results obtained after hybridization with the telomere sequences, coupled with the chromosome homeologies detected by R-banding, showed that G. cf carapo and G. sylvius should present a common ancestor, and this may also be corroborated by the similarities found in three chromosome pairs, that seem to have been conserved during the evolution of the two species. Based on the data here presented we propose that G. sylvius may have undergone a recent process of chromosome fusion that resulted in the diminution of its chromosome number.

Coding behavioural data for cladistic analysis: using dynamic homology without parsimony

Many of the controversies around the concept of homology rest on the subjectivity inherent to primary homology propositions. Dynamic homology partially solves this problem, but there has been up to now scant application of it outside of the molecular domain. This is probably because morphological and behavioural characters are rich in properties, connections and qualities, so that there is less space for conflicting character delimitations. Here we present a new method for the direct optimization of behavioural data, a method that relies on the richness of this database to delimit the characters, and on dynamic procedures to establish character state identity. We use between-species congruence in the data matrix and topological stability to choose the best cladogram. We test the methodology using sequences of predatory behaviour in a group of spiders that evolved the highly modified predatory technique of spitting glue onto prey. The cladogram recovered is fully compatible with previous analyses in the literature, and thus the method seems consistent. Besides the advantage of enhanced objectivity in character proposition, the new procedure allows the use of complex, context-dependent behavioural characters in an evolutionary framework, an important step towards the practical integration of the evolutionary and ecological perspectives on diversity. (C) The Willi Hennig Society 2010.

A hands-on approach for fitting long-term survival models under the GAMLSS framework

In many data sets from clinical studies there are patients insusceptible to the occurrence of the event of interest. Survival models which ignore this fact are generally inadequate. The main goal of this paper is to describe an application of the generalized additive models for location, scale, and shape (GAMLSS) framework to the fitting of long-term survival models. in this work the number of competing causes of the event of interest follows the negative binomial distribution. In this way, some well known models found in the literature are characterized as particular cases of our proposal. The model is conveniently parameterized in terms of the cured fraction, which is then linked to covariates. We explore the use of the gamlss package in R as a powerful tool for inference in long-term survival models. The procedure is illustrated with a numerical example. (C) 2009 Elsevier Ireland Ltd. All rights reserved.

Recurrence quantification analysis of electrostatic fluctuations in fusion plasmas

We have investigated plasma turbulence at the edge of a tokamak plasma using data from electrostatic potential fluctuations measured in the Brazilian tokamak TCABR. Recurrence quantification analysis has been used to provide diagnostics of the deterministic content of the series. We have focused our analysis on the radial dependence of potential fluctuations and their characterization by recurrence-based diagnostics. Our main result is that the deterministic content of the experimental signals is most pronounced at the external part of the plasma column just before the plasma radius. Since the chaoticity of the signals follows the same trend, we have concluded that the electrostatic plasma turbulence at the tokamak plasma edge can be partially explained by means of a deterministic nonlinear system. (C) 2007 Elsevier B.V. All rights reserved.

Advanced functionality for radio analysis in the Offline software framework of the Pierre Auger Observatory

The advent of the Auger Engineering Radio Array (AERA) necessitates the development of a powerful framework for the analysis of radio measurements of cosmic ray air showers. As AERA performs ""radio-hybrid"" measurements of air shower radio emission in coincidence with the surface particle detectors and fluorescence telescopes of the Pierre Auger Observatory, the radio analysis functionality had to be incorporated in the existing hybrid analysis solutions for fluorescence and surface detector data. This goal has been achieved in a natural way by extending the existing Auger Offline software framework with radio functionality. In this article, we lay out the design, highlights and features of the radio extension implemented in the Auger Offline framework. Its functionality has achieved a high degree of sophistication and offers advanced features such as vectorial reconstruction of the electric field, advanced signal processing algorithms, a transparent and efficient handling of FFTs, a very detailed simulation of detector effects, and the read-in of multiple data formats including data from various radio simulation codes. The source code of this radio functionality can be made available to interested parties on request. (C) 2011 Elsevier B.V. All rights reserved.

Sub-barrier fusion of two-neutron halo nuclei

The tunneling of composite systems, where breakup may occur during the barrier penetration process, is considered in connection with the fusion of halo-like radioactive, neutron- and proton-rich nuclei, on heavy targets. The large amount of recent and new data clearly indicates that breakup hinders the fusion at energies near and below the Coulomb barrier. However, clear evidence for enhancement due to halo properties seems to over ride the breakup hindrance at lower energies, owing, to a large extent, to the extended matter density distribution. In particular we report here that at sub-barrier energies the fusion cross section of the Borromean two-neutron halo nucleus (6)He with the actinide nucleus (238)U is significantly enhanced as compared to the fusion of a similar projectile with no halo. This conclusion differs from that of the original work, where it was claimed that no such enhancement ensues. This sub-barrier fusion enhancement is also observed in the (6)He + (209)Bi system. (C) 2010 Elsevier B.V. All rights reserved.

CLUSTER MODEL FOR REACTIONS INDUCED BY WEAKLY BOUND AND/OR EXOTIC HALO NUCLEI WITH MEDIUM-MASS TARGETS

An experimental overview of reactions induced by the stable, but weakly-bound nuclei (6)Li, (7)Li and (9)Be, and by the exotic, halo nuclei (6)He, (8)B, (11)Be and (17)F On medium-mass targets, such as (58)Ni, (59)Co or (64)Zn, is presented. Existing data on elastic scattering, total reaction cross sections, fusion, breakup and transfer channels are discussed in the framework of a CDCC approach taking into account the breakup degree of freedom.

Astrophysical S factors for fusion reactions involving C, O, Ne, and Mg isotopes

Using the Sao Paulo potential and the barrier penetration formalism we have calculated the astrophysical factor S(E) for 946 fusion reactions involving stable and neutron-rich isotopes of C, O, Ne, and Mg for center-of-mass energies E varying from 2 to approximate to 18-30 MeV (covering the range below and above the Coulomb barrier). We have parameterized the energy dependence, S(E), by an accurate universal 9-parameter analytic expression and present tables of fit parameters for all the reactions. We also discuss the reduced 3-parameter version of our fit which is highly accurate at energies below the Coulomb barrier, and outline the procedure for calculating the reaction rates. The results can be easily converted to thermonuclear or pycnonuclear reaction rates to simulate various nuclear burning phenomena, in particular, stellar burning at high temperatures and nucleosynthesis in high density environments. (C) 2010 Elsevier Inc. All rights reserved

Reaction mechanisms for weakly-bound, stable nuclei and unstable, halo nuclei on medium-mass targets

An experimental overview of reactions induced by the stable, but weakly-bound nuclei (6)Li, (7)Li and (9)Be, and by the exotic, halo nuclei (6)He, (8)B, (11)Be and (17)F on medium-mass targets, such as (58)Ni, (59)Co or (64)Zn, is presented. Existing data on elastic scattering, total reaction cross sections, fusion processes, breakup and transfer channels are discussed in the framework of a CDCC approach taking into account the breakup degree of freedom.

Breakup effects in fusion and total reaction cross sections of weakly bound systems

We use a new technique to investigate the systematic behavior of near barrier complete fusion, total fusion and total reaction cross sections of weakly bound systems. A dimensionless fusion excitation function is used as a benchmark to which renormalized fusion data are compared and dynamic breakup effects can be disentangled from static effects. The same reduction procedure is used to study the effect of the direct reaction mechanisms on the total reaction cross section.

Understanding fusion suppression and enhancement in the (18)O+(58,60,64)Ni systems

Realistic coupled-channel calculation results for the (18)[O] + (58,60,64)Ni systems in the bombarding energy range 34.5 <= E(Lab) <= 6-5 MeV are presented. The overall agreement with existing experimental data is quite good. Our calculations predict an unexpected fusion suppression for above-barrier energies, with an important contribution of the two neutron ((18)O, (16)O) transfer channel couplings. The sub-barrier fusion enhancement and the above barrier suppression, predicted by the calculations, are consistent with the nuclear structure of the Ni region. Comparisons with recently reported similar effects in reactions induced by the (6)He projectile are discussed. (C) 2009 Elsevier B.V. All rights reserved.

Dynamic effects of breakup on fusion reactions of weakly bound nuclei

The traditional reduction methods to represent the fusion cross sections of different systems are flawed when attempting to completely eliminate the geometrical aspects, such as the heights and radii of the barriers, and the static effects associated with the excess neutrons or protons in weakly bound nuclei. We remedy this by introducing a new dimensionless universal function, which allows the separation and disentanglement of the static and dynamic aspects of the breakup coupling effects connected with the excess nucleons. Applying this new reduction procedure to fusion data of several weakly bound systems, we find a systematic suppression of complete fusion above the Coulomb barrier and enhancement below it. Different behaviors are found for the total fusion cross sections. They are appreciably suppressed in collisions of neutron-halo nuclei, while they are practically not affected by the breakup coupling in cases of stable weakly bound nuclei. (C) 2009 Elsevier B.V. All rights reserved.