Goal-refinement appraisal of soft projects (GRASP)

Industrial projects are often complex and burdened with time pressures and a lack of information. The term 'soft-project' used here stands for projects where the ‘what’ and/or the ‘how’ is uncertain, which is often the experience in projects involving software intensive systems developments. This thesis intertwines the disciplines of project management and requirements engineering in a goal-oriented application of the maxim ‘keep all objectives satisfied’. It thus proposes a method for appraising projects. In this method, a goal-oriented analysis establishes a framework with which expert judgements are collected so as to construct a confidence profile in regard to the feasibility and adequacy of the project's planned outputs. It is hoped that this appraisal method will contribute to the activities of project ‘shaping’ and aligning stakeholders’ expectations whilst helping project managers appreciate what parts of their project can be progressed and what parts should be held pending further analysis. This thesis offers the following original contribution: an appreciation of appraisal in the project context; a goal-oriented confidence profiling technique; and: a technique to produce goal-refinement diagrams – referred to as Goal Sketching. Collectively these amount to a method for the ‘Goal Refinement Appraisal of Soft-Projects’ (GRASP). The validity of the GRASP method is shown for two projects. In the first it is used for shaping a business investigation project. This is done in real-time in the project. The second case is a retrospective study of an enterprise IT project. This case tests the effectiveness of forecasting project difficulty from an initial confidence profile.

Anisotropic refinement of the structure of Thermoascus aurantiacusxylanase I

The isotropic crystallographic model of the structure of xylanase I from Thermoascus aurantiacus (TAXI) has now been refined anisotropically at 1.14 Å resolution to a standard residual of R = 11.1% for all data. TAXI is amongst the five largest proteins deposited in the Protein Data Bank to have been refined with anisotropic displacement parameters (ADPs) at this level of resolution. The anisotropy analysis revealed a more isotropic distribution of anisotropy than usually observed previously. Adding ADPs resulted in high-quality electron-density maps which revealed discrepancies from the previously suggested primary sequences for this enzyme. Side-chain conformational disorder was modelled for 16 residues, including Trp275, a bulky residue at the active site. An unrestrained refinement was consistent with the protonation of the catalytic acid/base glutamate and the deprotonation of the nucleophile glutamate, as required for catalysis. The thermal stability of TAXI is reinterpreted in the light of the new refined model.

Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5-BrU)]2 at 1.46 Å and 100 K

A four-wavelength MAD experiment on a new brominated octanucleotide is reported here. d[ACGTACG(5-BrU)], C77H81BrN30O32P7, (DNA) = 2235, tetragonal, P43212 (No. 96), a = 43.597, c = 26.268 Å, V = 49927.5 Å3, Z = 8, T = 100 K, R = 10.91% for 4312 reflections between 15.0 and 1.46 Å resolution. The self-complementary brominated octanucleotide d[ACGTACG(5-BrU)]2 has been crystallized and data measured to 1.45 Å at both 293 K and a second crystal flash frozen at 100 K. The latter data collection was carried out to the same resolution at the four wavelengths 0.9344, 0.9216, 0.9208 and 0.9003 Å, around the Br K edge at 0.92 Å and the structure determined from a map derived from a MAD data analysis using pseudo-MIR methodology, as implemented in the program MLPHARE. This is one of the first successful MAD phasing experiments carried out at Sincrotrone Elettra in Trieste, Italy. The structure was refined using the data measured at 0.9003 Å, anisotropic temperature factors and the restrained least-squares refinement implemented in the program SHELX96, and the helical parameters are compared with those previously determined for the isomorphous d(ACGTACGT)2 analogue. The asymmetric unit consists of a single strand of octamer with 96 water molecules. No countercations were located. The A-DNA helix geometry obtained has been analysed using the CURVES program.

Spectroscopic properties of alkenylferrocenes; crystal and molecular structure of (Z)-(1,2-diphenylethenyl)ferrocene

Studies of the 1H n.m.r. and electronic spectra of a series of alkenylferrocenes including (E) and (Z) stereoisomers of various styrylferrocenes, have provided methods of structure elucidation. Crystals of the title compound are monoclinic, space group P21/c with Z= 4 in a unit cell of dimensions a= 17.603(2), b= 10.218(2), c= 10.072 Å, β= 103.27(2)°. The structure has been determined by the heavy-atom method from diffractometer data and refind by full-matrix least-squares techniques to R= 0.043 for 2 219 unique reflections.

A detailed single chain model for molten poly(tetrafluoroethylene) from a novel structure refinement technique on neutron scattering data

We present a new methodology that couples neutron diffraction experiments over a wide Q range with single chain modelling in order to explore, in a quantitative manner, the intrachain organization of non-crystalline polymers. The technique is based on the assignment of parameters describing the chemical, geometric and conformational characteristics of the polymeric chain, and on the variation of these parameters to minimize the difference between the predicted and experimental diffraction patterns. The method is successfully applied to the study of molten poly(tetrafluoroethylene) at two different temperatures, and provides unambiguous information on the configuration of the chain and its degree of flexibility. From analysis of the experimental data a model is derived with CC and CF bond lengths of 1.58 and 1.36 Å, respectively, a backbone valence angle of 110° and a torsional angle distribution which is characterized by four isometric states, namely a split trans state at ± 18°, giving rise to a helical chain conformation, and two gauche states at ± 112°. The probability of trans conformers is 0.86 at T = 350°C, which decreases slightly to 0.84 at T = 400°C. Correspondingly, the chain segments are characterized by long all-trans sequences with random changes in sign, rather anisotropic in nature, which give rise to a rather stiff chain. We compare the results of this quantitative analysis of the experimental scattering data with the theoretical predictions of both force fields and molecular orbital conformation energy calculations.

Sea ice–ocean coupling using a rescaled vertical coordinate z*

Realistic representation of sea ice in ocean models involves the use of a non-linear free-surface, a real freshwater flux and observance of requisite conservation laws. We show here that these properties can be achieved in practice through use of a rescaled vertical coordinate ‘‘z*” in z-coordinate models that allows one to follow undulations in the free-surface under sea ice loading. In particular, the adoption of "z*" avoids the difficult issue of vanishing levels under thick ice. Details of the implementation within MITgcm are provided. A high resolution global ocean sea ice simulation illustrates the robustness of the z* formulation and reveals a source of oceanic variability associated with sea ice dynamics and ice-loading effects. The use of the z* coordinate allows one to achieve perfect conservation of fresh water, heat and salt, as shown in extended integration of coupled ocean sea ice atmospheric model.

Using E-Z Reader to examine the concurrent development of eye-movement control and reading skill

Compared to skilled adult readers, children typically make more fixations that are longer in duration, shorter saccades, and more regressions, thus reading more slowly (Blythe & Joseph, 2011). Recent attempts to understand the reasons for these differences have discovered some similarities (e.g., children and adults target their saccades similarly; Joseph, Liversedge, Blythe, White, & Rayner, 2009) and some differences (e.g., children’s fixation durations are more affected by lexical variables; Blythe, Liversedge, Joseph, White, & Rayner, 2009) that have yet to be explained. In this article, the E-Z Reader model of eye-movement control in reading (Reichle, 2011; Reichle, Pollatsek, Fisher, & Rayner, 1998) is used to simulate various eye-movement phenomena in adults versus children in order to evaluate hypotheses about the concurrent development of reading skill and eye-movement behavior. These simulations suggest that the primary difference between children and adults is their rate of lexical processing, and that different rates of (post-lexical) language processing may also contribute to some phenomena (e.g., children’s slower detection of semantic anomalies; Joseph et al., 2008). The theoretical implications of this hypothesis are discussed, including possible alternative accounts of these developmental changes, how reading skill and eye movements change across the entire lifespan (e.g., college-aged vs. elderly readers), and individual differences in reading ability.

On the Relationship between Zaprionus spinipilus Chassagnard & McEvey and Z. vittiger Coquillett, the Type Species of the Genus Zaprionus (Diptera: Drosophilidae)

Zaprionus vittiger Coquillett is the type species of the genus Zaprionus Coquillett. However, the species is only known from five old museum specimens collected from South Africa and Malawi. It has often been confused with many other Zaprionus species, especially with Z. spinipilus Chassagnard & McEvey, a widespread species in Africa known from Madagascar, Malawi, Ethiopia and Cameroon. We have recently collected flies from the type localities of both species (South Africa and Madagascar, respectively). This has prompted us to test the taxonomic boundaries of these two nominal species using molecular (the mitochondrial COII and the nuclear Amyrel genes), chromosomal, morphological (internal and external genitalia), and reproductive isolation analyses. The results suggest Z. spinipilus to be a junior synonym to Z. vittiger.

Spastic Paraplegia, Optic Atrophy, and Neuropathy: New Observations, Locus Refinement, and Exclusion of Candidate Genes

SPOAN is an autosomal recessive neurodegenerative disorder which was recently characterized by our group in a large inbred Brazilian family with 25 affected individuals. This condition is clinically defined by: 1. congenital optic atrophy; 2. progressive spastic paraplegia with onset in infancy; and 3. progressive motor and sensory axonal neuropathy. Overall, we are now aware of 68 SPOAN patients (45 females and 23 males, with age ranging from 5 to 72 years), 44 of which are presented here for the first time. They were all born in the same geographic micro region. Those 68 patients belong to 43 sibships, 40 of which exhibit parental consanguinity. Sixty-one patients were fully clinically evaluated and 64 were included in the genetic investigation. All molecularly studied patients are homozygotes for D11S1889 at 11q13. This enabled us to reduce the critical region for the SPOAN gene from 4.8 to 2.3 Mb, with a maximum two point lod score of 33.2 (with marker D11S987) and of 27.0 (with marker D11S1889). Three genes located in this newly defined critical region were sequenced, but no pathogenic mutation was detected. The gene responsible for SPOAN remains elusive.

Formal validation of automated policy refinement in the management of network security systems

Policy hierarchies and automated policy refinement are powerful approaches to simplify administration of security services in complex network environments. A crucial issue for the practical use of these approaches is to ensure the validity of the policy hierarchy, i.e. since the policy sets for the lower levels are automatically derived from the abstract policies (defined by the modeller), we must be sure that the derived policies uphold the high-level ones. This paper builds upon previous work on Model-based Management, particularly on the Diagram of Abstract Subsystems approach, and goes further to propose a formal validation approach for the policy hierarchies yielded by the automated policy refinement process. We establish general validation conditions for a multi-layered policy model, i.e. necessary and sufficient conditions that a policy hierarchy must satisfy so that the lower-level policy sets are valid refinements of the higher-level policies according to the criteria of consistency and completeness. Relying upon the validation conditions and upon axioms about the model representativeness, two theorems are proved to ensure compliance between the resulting system behaviour and the abstract policies that are modelled.

The meson Z(+) (4430) as a tetraquark state

We test the validity of the QCD sum rules applied to the meson Z(+)(4430). by considering a diquark-antidiquark type of current with J(P) = 0(-) and with J(P) = 1(-). We find that, with the studied currents, it is possible to find an acceptable Borel window. In such a Borel window we have simultaneously a good OPE convergence and a pole contribution which is bigger than the continuum contribution. We get m(z) = (4.52 +/- 0.09) GeV and m(Z) = (4.84 +/- 0.14) GeV for the currents with J(P) = 0(-) and J(P) = 1(-), respectively. We conclude that the QCD sum rules results favors J(P) = 0(-) quantum numbers for the Z(+) (4430) meson. (C) 2008 Elsevier B.V. All rights reserved.

QCD sum rules study of the meson Z(+)(4430)

We use QCD sum rules to study the recently observed meson Z(+)(4430), considered as a D*D-1 molecule with J(P) = 0(-). We consider the contributions of condensates up to dimension eight and work at leading order in alpha(s). We get m(Z) = (4.40 +/- 0.10) GeV in a very good agreement with the experimental value. We also make predictions for the analogous mesons Z(s) and Z(bb) considered as D-s*D-1 and B*B-1 molecules, respectively. For Z(s) we predict mZ(s) = (4.70 +/- 0.06) GeV, which is above the D-s* D-1 threshold, indicating that it is probably a very broad state and, therefore, difficult to observe experimentally. For Z(bb) we predict m(Zbb) = (10.74 +/- 0.12) GeV, in agreement with quark model predictions. (c) 2008 Elsevier B.V. All rights reserved.