Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda)

An analysis of the relationships of the major arthropod groups Was undertaken using mitochondrial genome data to examine the hypotheses that Hexapoda is polyphyletic and that Collembola is more closely related to branchiopod crustaceans than insects. We sought to examine the sensitivity of this relationship to outgroup choice, data treatment. gene choice and optimality criteria used in the phylogenetic analysis of mitochondrial genome data. Additionally we sequenced the mitochondrial genome of ail archaeognathan, Nesomachilis australica. to improve taxon selection in the apterygote insects, a group poorly represented in previous mitochondrial phylogenies. The sister group of the Collembola was rarely resolved in our analyses with a significant level of support. The use of different outgroups (myriapods, nematodes, or annelids + mollusks) resulted in many different placements of Collembola. The way in which the dataset was coded for analysis (DNA, DNA with the exclusion of third codon position and as amino acids) also had marked affects on tree topology. We found that nodal Support was spread evenly throughout the 13 mitochondrial genes and the exclusion of genes resulted in significantly less resolution in the inferred trees. Optimality criteria had a much lesser effect on topology than the preceding factors; parsimony and Bayesian trees for a given data set and treatment were quite similar. We therefore conclude that the relationships of the extant arthropod groups as inferred by mitochondrial genomes are highly vulnerable to outgroup choice, data treatment and gene choice, and no consistent alternative hypothesis of Collembola's relationships is supported. Pending the resolution of these identified problems with the application of mitogenomic data to basal arthropod relationships, it is difficult to justify the rejection of hexapod monophyly, which is well supported on morphological grounds. (c) The Willi Hennig Society 2004.

Experimental design methodologies for the identification of Michaelis-Menten type kinetics

The main objective of this work was to investigate the application of experimental design techniques for the identification of Michaelis-Menten kinetic parameters. More specifically, this study attempts to elucidate the relative advantages/disadvantages of employing complex experimental design techniques in relation to equidistant sampling when applied to different reactor operation modes. All studies were supported by simulation data of a generic enzymatic process that obeys to the Michaelis-Menten kinetic equation. Different aspects were investigated, such as the influence of the reactor operation mode (batch, fed-batch with pulse wise feeding and fed-batch with continuous feeding) and the experimental design optimality criteria on the effectiveness of kinetic parameters identification. The following experimental design optimality criteria were investigated: 1) minimization of the sum of the diagonal of the Fisher information matrix (FIM) inverse (A-criterion), 2) maximization of the determinant of the FIM (D-criterion), 3) maximization of the smallest eigenvalue of the FIM (E-criterion) and 4) minimization of the quotient between the largest and the smallest eigenvalue (modified E-criterion). The comparison and assessment of the different methodologies was made on the basis of the Cramér-Rao lower bounds (CRLB) error in respect to the parameters vmax and Km of the Michaelis-Menten kinetic equation. In what concerns the reactor operation mode, it was concluded that fed-batch (pulses) is better than batch operation for parameter identification. When the former operation mode is adopted, the vmax CRLB error is lowered by 18.6 % while the Km CRLB error is lowered by 26.4 % when compared to the batch operation mode. Regarding the optimality criteria, the best method was the A-criterion, with an average vmax CRLB of 6.34 % and 5.27 %, for batch and fed-batch (pulses), respectively, while presenting a Km’s CRLB of 25.1 % and 18.1 %, for batch and fed-batch (pulses), respectively. As a general conclusion of the present study, it can be stated that experimental design is justified if the starting parameters CRLB errors are inferior to 19.5 % (vmax) and 45% (Km), for batch processes, and inferior to 42 % and to 50% for fed-batch (pulses) process. Otherwise equidistant sampling is a more rational decision. This conclusion clearly supports that, for fed-batch operation, the use of experimental design is likely to largely improve the identification of Michaelis-Menten kinetic parameters.

Kriging coordinates: what does that mean?

Kriging is an interpolation technique whose optimality criteria are based on normality assumptions either for observed or for transformed data. This is the case of normal, lognormal and multigaussian kriging.When kriging is applied to transformed scores, optimality of obtained estimators becomes a cumbersome concept: back-transformed optimal interpolations in transformed scores are not optimal in the original sample space, and vice-versa. This lack of compatible criteria of optimality induces a variety of problems in both point and block estimates. For instance, lognormal kriging, widely used to interpolate positivevariables, has no straightforward way to build consistent and optimal confidence intervals for estimates.These problems are ultimately linked to the assumed space structure of the data support: for instance, positive values, when modelled with lognormal distributions, are assumed to be embedded in the whole real space, with the usual real space structure and Lebesgue measure

Imprecise measurements in quantum mechanics

In this thesis the structure and properties of imprecise quantum measurements are investigated. The starting point for this investigation is the representation of a quantum observable as a normalized positive operator measure. A general framework to describe measurement inaccuracy is presented. Requirements for accurate measurements are discussed, and the relation of inaccuracy to some optimality criteria is studied. A characterization of covariant observables is given in the case when they are imprecise versions of a sharp observable. Also the properties of such observables are studied. The case of position and momentum observables is studied. All position and momentum observables are characterized, and the joint positionmomentum measurements are discussed.

Optimal and Robust Designs of Step-stress Accelerated Life Testing Experiments for Proportional Hazards Models

Accelerated life testing (ALT) is widely used to obtain reliability information about a product within a limited time frame. The Cox s proportional hazards (PH) model is often utilized for reliability prediction. My master thesis research focuses on designing accelerated life testing experiments for reliability estimation. We consider multiple step-stress ALT plans with censoring. The optimal stress levels and times of changing the stress levels are investigated. We discuss the optimal designs under three optimality criteria. They are D-, A- and Q-optimal designs. We note that the classical designs are optimal only if the model assumed is correct. Due to the nature of prediction made from ALT experimental data, attained under the stress levels higher than the normal condition, extrapolation is encountered. In such case, the assumed model cannot be tested. Therefore, for possible imprecision in the assumed PH model, the method of construction for robust designs is also explored.

Systematics and evolution of the genus Deuterocohnia Mez (Bromeliaceae)

The present study investigates the systematics and evolution of the Neotropical genus Deuterocohnia Mez (Bromeliaceae). It provides a comprehensive taxonomic revision as well as phylogenetic analyses based on chloroplast and nuclear DNA sequences and presents a hypothesis on the evolution of the genus. A broad morphological, anatomical, biogeographical and ecological overview of the genus is given in the first part of the study. For morphological character assessment more than 700 herbarium specimens from 39 herbaria as well as living plant material in the field and in the living collections of botanical gardens were carefully examined. The arid habitats, in which the species of Deuterocohnia grow, are reflected by the morphological and anatomical characters of the species. Important characters for species delimitation were identified, like the length of the inflorescence, the branching order, the density of flowers on partial inflorescences, the relation of the length of the primary bracts to that of the partial inflorescence, the sizes of floral bracts, sepals and petals, flower colour, the presence or absence of a pedicel, the curvature of the stamina and the petals during anthesis. After scrutinizing the nomenclatural history of the taxa belonging to Deuterocohnia – including the 1992 syonymized genus Abromeitiella – 17 species, 4 subspecies and 4 varieties are accepted in the present revision. Taxonomic changes were made in the following cases: (I) New combinations: A. abstrusa (A. Cast.) N. Schütz is re-established – as defined by Castellanos (1931) – and transfered to D. abstrusa; D. brevifolia (Griseb.) M.A. Spencer & L.B. Sm. includes accessions of the former D. lorentziana (Mez) M.A. Spencer & L.B. Sm., which are not assigned to D. abstrusa; D. bracteosa W. Till is synonymized to D. strobilifera Mez; D. meziana Kuntze ex Mez var. carmineo-viridiflora Rauh is classified as a subspecies of D. meziana (ssp. carmineo-viridiflora (Rauh) N. Schütz); D. pedicellata W. Till is classified as a subspecies of D. meziana (ssp. pedicellata (W. Till) N. Schütz); D. scapigera (Rauh & L. Hrom.) M.A. Spencer & L.B. Sm ssp. sanctae-crucis R. Vásquez & Ibisch is classified as a species (D. sanctae-crucis (R. Vásquez & Ibisch) N. Schütz); (II) New taxa: a new subspecies of D. meziana Kuntze ex Mez is established; a new variety of D. scapigera is established; (the new taxa will be validly published elsewhere); (III) New type: an epitype for D. longipetala was chosen. All other species were kept according to Spencer and Smith (1992) or – in the case of more recently described species – according to the protologue. Beside the nomenclatural notes and the detailed descriptions, information on distribution, habitat and ecology, etymology and taxonomic delimitation is provided for the genus and for each of its species. An key was constructed for the identification of currently accepted species, subspecies and varieties. The key is based on easily detectable morphological characters. The former synonymization of the genus Abromeitiella into Deuterocohnia (Spencer and Smith 1992) is re-evalutated in the present study. Morphological as well as molecular investigations revealed Deuterocohnia incl. Abromeitiella as being monophyletic, with some indications that a monophyletic Abromeitiella lineage arose from within Deuterocohnia. Thus the union of both genera is confirmed. The second part of the present thesis describes and discusses the molecular phylogenies and networks. Molecular analyses of three chloroplast intergenic spacers (rpl32-trnL, rps16-trnK, trnS-ycf3) were conducted with a sample set of 119 taxa. This set included 103 Deuterocohnia accessions from all 17 described species of the genus and 16 outgroup taxa from the remainder of Pitcairnioideae s.str. (Dyckia (8 sp.), Encholirium (2 sp.), Fosterella (4 sp.) and Pitcairnia (2 sp.)). With its high sampling density, the present investigation by far represents the most comprehensive molecular study of Deuterocohnia up till now. All data sets were analyzed separately as well as in combination, and various optimality criteria for phylogenetic tree construction were applied (Maximum Parsimony, Maximum Likelihood, Bayesian inferences and the distance method Neighbour Joining). Congruent topologies were generally obtained with different algorithms and optimality criteria, but individual clades received different degrees of statistical support in some analyses. The rps16-trnK locus was the most informative among the three spacer regions examined. The results of the chloroplast DNA analyses revealed a highly supported paraphyly of Deuterocohnia. Thus, the cpDNA trees divide the genus into two subclades (A and B), of which Deuterocohnia subclade B is sister to the included Dyckia and Encholirium accessions, and both together are sister to Deuterocohnia subclade A. To further examine the relationship between Deuterocohnia and Dyckia/Encholirium at the generic level, two nuclear low copy markers (PRK exon2-5 and PHYC exon1) were analysed with a reduced taxon set. This set included 22 Deuterocohnia accessions (including members of both cpDNA subclades), 2 Dyckia, 2 Encholirium and 2 Fosterella species. Phylogenetic trees were constructed as described above, and for comparison the same reduced taxon set was also analysed at the three cpDNA data loci. In contrast to the cpDNA results, the nuclear DNA data strongly supported the monophyly of Deuterocohnia, which takes a sister position to a clade of Dyckia and Encholirium samples. As morphology as well as nuclear DNA data generated in the present study and in a former AFLP analysis (Horres 2003) all corroborate the monophyly of Deuterocohnia, the apparent paraphyly displayed in cpDNA analyses is interpreted to be the consequence of a chloroplast capture event. This involves the introgression of the chloroplast genome from the common ancestor of the Dyckia/ Encholirium lineage into the ancestor of Deuterocohnia subclade B species. The chloroplast haplotypes are not species-specific in Deuterocohnia. Thus, one haplotype was sometimes shared by several species, where the same species may harbour different haplotypes. The arrangement of haplotypes followed geographical patterns rather than taxonomic boundaries, which may indicate some residual gene flow among populations from different Deuteroccohnia species. Phenotypic species coherence on the background of ongoing gene flow may then be maintained by sets of co-adapted alleles, as was suggested by the porous genome concept (Wu 2001, Palma-Silva et al. 2011). The results of the present study suggest the following scenario for the evolution of Deuterocohnia and its species. Deuterocohnia longipetala may be envisaged as a representative of the ancestral state within the genus. This is supported by (1) the wide distribution of this species; (2) the overlap in distribution area with species of Dyckia; (3) the laxly flowered inflorescences, which are also typical for Dyckia; (4) the yellow petals with a greenish tip, present in most other Deuterocohnia species. The following six extant lineages within Deuterocohnia might have independently been derived from this ancestral state with a few changes each: (I) D. meziana, D. brevispicata and D. seramisiana (Bolivia, lowland to montane areas, mostly reddish-greenish coloured, very laxly to very densely flowered); (II) D. strobilifera (Bolivia, high Andean mountains, yellow flowers, densely flowered); (III) D. glandulosa (Bolivia, montane areas, yellow-greenish flowers, densely flowered); (IV) D. haumanii, D. schreiteri, D. digitata, and D. chrysantha (Argentina, Chile, E Andean mountains and Atacama desert, yellow-greenish flowers, densely flowered); (V) D. recurvipetala (Argentina, foothills of the Andes, recurved yellow flowers, laxly flowered); (VI) D. gableana, D. scapigera, D. sanctae-crucis, D. abstrusa, D. brevifolia, D. lotteae (former Abromeitiella species, Bolivia, Argentina, higher Andean mountains, greenish-yellow flowers, inflorescence usually simple). Originating from the lower montane Andean regions, at least four lineages of the genus (I, II, IV, VI) adapted in part to higher altitudes by developing densely flowered partial inflorescences, shorter flowers and – in at least three lineages (II, IV, VI) – smaller rosettes, whereas species spreading into the lowlands (I, V) developed larger plants, laxly flowered, amply branched inflorescences and in part larger flowers (I).

Kriging coordinates: what does that mean?

Kriging is an interpolation technique whose optimality criteria are based on normality assumptions either for observed or for transformed data. This is the case of normal, lognormal and multigaussian kriging. When kriging is applied to transformed scores, optimality of obtained estimators becomes a cumbersome concept: back-transformed optimal interpolations in transformed scores are not optimal in the original sample space, and vice-versa. This lack of compatible criteria of optimality induces a variety of problems in both point and block estimates. For instance, lognormal kriging, widely used to interpolate positive variables, has no straightforward way to build consistent and optimal confidence intervals for estimates. These problems are ultimately linked to the assumed space structure of the data support: for instance, positive values, when modelled with lognormal distributions, are assumed to be embedded in the whole real space, with the usual real space structure and Lebesgue measure

Phylogenetic relationships within the moss family Bryaceae based on chloroplast DNA evidence

The Bryaceae are a large cosmopolitan family of mosses containing genera of considerable taxonomic difficulty. Phylogenetic relationships within the family were inferred using data from chloroplast DNA sequences (rps4 and trnL-trnF region). Parsimony and maximum likelihood optimality criteria, and Bayesian phylogenetic inference procedures were employed to reconstruct relationships. The genera Bryum and Brachymenium are not monophyletic groups. A clade comprising Plagiobryum, Acidodontium, Mielichhoferia macrocarpa, Bryum sects. Bryum, Apalodictyon, Limbata, Leucodontium, Caespiticia, Capillaria (in part: sect. Capillaria), and Brachymenium sect. Dicranobryum, is well supported in all analyses and represents a major lineage within the family. Section Dicranobryum of Brachymenium is more closely related to section Bryum than to the other sections of Brachymenium, as are Mielichhoferia macrocarpa and M. himalayana. Species of Acidodontium form a clade with Anomobryum julaceum. The grouping of species with a rosulate gametophytic growth form suggests the presence of a 'rosulate' clade similar in circumscription to the genus Rosulabryum. Mielichhoferia macrocarpa and M. himalayana are transferred to Bryum as B. porsildii and B. caucasicum, respectively.

Optimal power management strategy for energy storage with stochastic loads

In this paper, a power management strategy (PMS) has been developed for the control of energy storage in a system subjected to loads of random duration. The PMS minimises the costs associated with the energy consumption of specific systems powered by a primary energy source and equipped with energy storage, under the assumption that the statistical distribution of load durations is known. By including the variability of the load in the cost function, it was possible to define the optimality criteria for the power flow of the storage. Numerical calculations have been performed obtaining the control strategies associated with the global minimum in energy costs, for a wide range of initial conditions of the system. The results of the calculations have been tested on a MATLAB/Simulink model of a rubber tyre gantry (RTG) crane equipped with a flywheel energy storage system (FESS) and subjected to a test cycle, which corresponds to the real operation of a crane in the Port of Felixstowe. The results of the model show increased energy savings and reduced peak power demand with respect to existing control strategies, indicating considerable potential savings for port operators in terms of energy and maintenance costs.

Phylogenetic relationships within anuran clade Terrarana, with emphasis on the placement of Brazilian Atlantic rainforest frogs genus Ischnocnema (Anura: Brachycephalidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Optimum design of experiments for statistical inference

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Public debt sustainability in the Caribbean

This paper analyses public debt in the most indebted Caribbean countries – i.e. Barbados, Belize, Guyana, Jamaica, Antigua and Barbuda, Dominica, Grenada, and St. Kitts and Nevis – from the standpoint of its sustainability. A level of debt is deemed to be sustainable when the debt-to-GDP ratio remains constant or declines. The concept of sustainability is closely linked to that of solvency. A government is solvent if the net present value of its future primary balances (i.e. that excludes interest payments) is equal to or greater than the present value of public debt stock. It can be demonstrated that if the debt-to-GDP ratio is not on an explosive path, that it either stable or decreasing, the solvency condition holds. It is worth noting that the concept of fiscal sustainability addressed in this paper differs from that of optimality of public debt. The analysis that follows is intended to determine whether the service of the current debt levels is consistent with the fiscal stance. Therefore, it does not set out to identify the target debt level based on any optimality criteria. The next section presents the main features of different theoretical approaches to analyse public debt sustainability.1 Section II discusses the situation of public debt in the Caribbean countries showing different indicators; Section III analyses debt sustainability in countries with access to market financing; Section IV does the same in Guyana – a country dependent on concessional financing and, as such, included in the Highly Indebted Poor Countries (HIPC) Initiative – and the countries of the Eastern Caribbean Currency Union (ECCU). Sections V and VI go beyond debt levels as determinants of fiscal sustainability, highlighting the importance of the currency composition of debt and the variability of fiscal revenue. The last section concludes.

Enumerating constrained elementary flux vectors of metabolic networks

The concept of elementary vector is generalised to the case where the steady-state space of the metabolic network is not a flux cone but is a general polyhedron due to further inhomogeneous constraints on the flows through some of the reactions. On one hand, this allows to selectively enumerate elementary modes which satisfy certain optimality criteria and this can yield a large computational gain compared with full enumeration. On the other hand, in contrast to the single optimum found by executing a linear program, this enables a comprehensive description of the set of alternate optima often encountered in flux balance analysis. The concepts are illustrated on a metabolic network model of human cardiac mitochondria.

Some results on the design of field experiments for comparing unreplicated treatments

In early generation variety trials, large numbers of new breeders' lines need to be compared, and usually there is little seed available for each new line. A so-called unreplicated trial has each new line on just one plot at a site, but includes several (often around five) replicated check or control (or standard) varieties. The total proportion of check plots is usually between 10% and 20%. The aim of the trial is to choose some good performing lines (usually around 1/3 of those tested) to go on for further testing, rather than precise estimation of their mean yield. Now that spatial analyses of data from field experiments are becoming more common, there is interest in an efficient layout of an experiment given a proposed spatial analysis. Some possible design criteria are discussed, and efficient layouts under spatial dependence are considered.

Efficient experimental designs when most treatments are unreplicated

In early generation variety trials, large numbers of new breeders' lines (varieties) may be compared, with each having little seed available. A so-called unreplicated trial has each new variety on just one plot at a site, but includes several replicated control varieties, making up around 10% and 20% of the trial. The aim of the trial is to choose some (usually around one third) good performing new varieties to go on for further testing, rather than precise estimation of their mean yields. Now that spatial analyses of data from field experiments are becoming more common, there is interest in an efficient layout of an experiment given a proposed spatial analysis and an efficiency criterion. Common optimal design criteria values depend on the usual C-matrix, which is very large, and hence it is time consuming to calculate its inverse. Since most varieties are unreplicated, the variety incidence matrix has a simple form, and some matrix manipulations can dramatically reduce the computation needed. However, there are many designs to compare, and numerical optimisation lacks insight into good design features. Some possible design criteria are discussed, and approximations to their values considered. These allow the features of efficient layouts under spatial dependence to be given and compared. (c) 2006 Elsevier Inc. All rights reserved.