Exercise sheet 2

Exercises and solutions in LaTex

System Design: UML Activity and Sequence Diagrams

In this session we look at how to model flow of control and interactions between components using UML Activity and Sequence Diagrams. This is an introductory session and so for Activity Diagrams we only cover branching, forks and joins and swim lanes, and for Sequence we cover lifelines, messages and returns, and alt, par and opt frames.

Caracterización de las variantes anatómicas de las venas pulmonares en pacientes candidatos a aislamiento de venas pulmonares en Colombia

Introducción y objetivos: El conocimiento de la anatomía de las venas pulmonares y de la aurícula izquierda es fundamental para la planeación y prevención de posibles complicaciones durante la ablación de las venas pulmonares, procedimiento realizado para el manejo de la fibrilación auricular. Este estudio pretende caracterizar la anatomía (tamaño y forma) de las venas pulmonares y determinar las variantes anatómicas más comunes de las mismas. Métodos: Se analizaron 277 estudios de angioresonancia tridimensional y tomografía computarizada realizados previo al procedimiento de aislamiento de venas pulmonares. Se evaluaron los diámetros de la aurícula izquierda, de los ostia de las venas pulmonares y se determinaron la presencia de venas pulmonares comunes, accesorias y ramificaciones tempranas. Resultados: 75% de nuestros pacientes presentaron la anatomía normal de dos venas pulmonares derechas y dos izquierdas. En un 10,1% de los casos se encontraron venas supernumerarias y en un 11,2% se encontró un tronco común. En un 61% de los pacientes se encontraron ramas ostiales, las cuales en un 39,4% de los casos se presentaron en la vena pulmonar inferior derecha. Conclusiones: La evaluación de la morfología de la aurícula derecha y las venas pulmonares por medio de angioresonancia o tomografía computarizada, es necesaria para la realización de ablación por radiofrecuencia dada la alta frecuencia de variantes anatómicas y presencia de ramas ostiales.

The curvature of the conical intersection seam: an approximate second-order analysis

We present a method for analyzing the curvature (second derivatives) of the conical intersection hyperline at an optimized critical point. Our method uses the projected Hessians of the degenerate states after elimination of the two branching space coordinates, and is equivalent to a frequency calculation on a single Born-Oppenheimer potential-energy surface. Based on the projected Hessians, we develop an equation for the energy as a function of a set of curvilinear coordinates where the degeneracy is preserved to second order (i.e., the conical intersection hyperline). The curvature of the potential-energy surface in these coordinates is the curvature of the conical intersection hyperline itself, and thus determines whether one has a minimum or saddle point on the hyperline. The equation used to classify optimized conical intersection points depends in a simple way on the first- and second-order degeneracy splittings calculated at these points. As an example, for fulvene, we show that the two optimized conical intersection points of C2v symmetry are saddle points on the intersection hyperline. Accordingly, there are further intersection points of lower energy, and one of C2 symmetry - presented here for the first time - is found to be the global minimum in the intersection space

Morfogénesis del valle de Sant Miquel de Campmajor

A series of circumstances which converge in a little valley in the province of Girona, result in a peculiar type of morphogenetic evolution and a quite singular mechanical instability of its buttons. Very recent tectonic movements as well as dissolution phenomena of its subsoil due to pressurized underground water have played an important role in the morphogenesis. Such conditions have resulted in a fast morphological evolution which a progressive lowering of the valley floor as well as peculiar morphological features which favour the existence of numerous pits caused by sudden collapses distributed in altitude and time

Podmiotowość a zmiana społeczna w pismach teoretycznych Margaret S. Archer. Analiza, porównania, rekonceptualizacja pojęć

Wydział Nauk Społecznych: Instytut Socjologii

Controls on development and diversity of Early Archean stromatolites

The ≈3,450-million-year-old Strelley Pool Formation in Western Australia contains a reef-like assembly of laminated sedimentary accretion structures (stromatolites) that have macroscale characteristics suggestive of biological influence. However, direct microscale evidence of biology—namely, organic microbial remains or biosedimentary fabrics—has to date eluded discovery in the extensively-recrystallized rocks. Recently-identified outcrops with relatively good textural preservation record microscale evidence of primary sedimentary processes, including some that indicate probable microbial mat formation. Furthermore, we find relict fabrics and organic layers that covary with stromatolite morphology, linking morphologic diversity to changes in sedimentation, seafloor mineral precipitation, and inferred microbial mat development. Thus, the most direct and compelling signatures of life in the Strelley Pool Formation are those observed at the microscopic scale. By examining spatiotemporal changes in microscale characteristics it is possible not only to recognize the presence of probable microbial mats during stromatolite development, but also to infer aspects of the biological inputs to stromatolite morphogenesis. The persistence of an inferred biological signal through changing environmental circumstances and stromatolite types indicates that benthic microbial populations adapted to shifting environmental conditions in early oceans.

Effects of metal pollution on soil macroinvertebrate burrow systems

A reduction in the numbers of macroinvertebrates present in soil may have a negative effect on soil structure, infiltration rates, and gas exchanges. Soil pollution by metal is known to have a detrimental effect on soil macrofauna. The aim of the present study was to evaluate (1) direct and indirect effects of soil pollution on soil macroinvertebrate bioturbation and (2) effects of the two macroinvertebrate communities found in a polluted and a nonpolluted area (one supposed sensitive, the other tolerant to metals) on burrow systems parameters. Macroinvertebrate porosity was studied using X-ray tomography. Three-dimensional reconstructions and characterisation of the burrow system were obtained using image analysis. Results showed that metal pollution principally affected the spatial distribution of macropores (more macropores were found near the soil surface) and the shape of the burrow system (branching rate was higher in the polluted soil), whereas soil macroinvertebrate composition principally affects burrow density parameters (the number of burrows was higher for the sensitive macroinvertebrate community).

Evolutionary relationships of "candidatus riesia spp.," endosymbiotic enterobacteriaceae living within hematophagous primate lice

The primary endosymbiotic bacteria from three species of parasitic primate lice were characterized molecularly. We have confirmed the characterization of the primary endosymbiont (P-endosymbiont) of the human head/body louse Pediculus humanus and provide new characterizations of the P-endosymbionts from Pediculus schaeffi from chimpanzees and Pthirus pubis, the pubic louse of humans. The endosymbionts show an average percent sequence divergence of 11 to 15% from the most closely related known bacterium "Candidatus Arsenophonus insecticola." We propose that two additional species be added to the genus "Candidatus Riesia." The new species proposed within "Candidatus Riesia" have sequence divergences of 3.4% and 10 to 12% based on uncorrected pairwise differences. Our Bayesian analysis shows that the branching pattern for the primary endosymbionts was the same as that for their louse hosts, suggesting a long coevolutionary history between primate lice and their primary endosymbionts. We used a calibration of 5.6 million years to date the divergence between endosymbionts from human and chimpanzee lice and estimated an evolutionary rate of nucleotide substitution of 0.67% per million years, which is 15 to 30 times faster than previous estimates calculated for Buchnera, the primary endosymbiont in aphids. Given the evidence for cospeciation with primate lice and the evidence for fast evolutionary rates, this lineage of endosymbiotic bacteria can be evaluated as a fast-evolving marker of both louse and primate evolutionary histories.

Development of the mammalian urethra is controlled by Fgfr2-IIIb

Development of external genitalia in mammalian embryos requires tight coordination of a complex series of morphogenetic events involving outgrowth, proximodistal and dorsoventral patterning, and epithelial tubulogenesis. Hypospadias is a congenital defect of the external genitalia that results from failure of urethral tube closure. Although this is the second most common birth defect in humans, affecting one in every 250 children, the molecular mechanisms that regulate morphogenesis of the mammalian urethra are poorly understood. We report that mice lacking the IIIb isoform of fibroblast growth factor receptor 2 (Fgfr2) exhibit severe hypospadias. Urethral signaling regions, as indicated by Shh and Fgf8 expression, are established in Fgfr2-IIIb null mice; however, cell proliferation arrests prematurely and maturation of the urethral epithelium is disrupted. Fgfr2-IIIb(-/-) mutants fail to maintain the progenitor cell population required for uroepithelial renewal during tubular morphogenesis. In addition, we show that antagonism of the androgen receptor (AR) leads to loss of Fgfr2-IIIb and Fgf10 expression in the urethra, and an associated hypospadias phenotype, suggesting that these genes are downstream targets of AR during external genital development. Genitourinary defects resulting from disruption of AR activity, by either genetic or environmental factors, may therefore involve negative regulation of the Fgfr2 pathway. This represents the first example of how the developing genitourinary system integrates cues from systemically circulating steroid hormones with a locally expressed growth factor pathway.

Monitoring growth of hard corals as performance indicators for coral reefs

Digital videophotography, computer image analysis and physical measurements have been used to monitor sedimentation rates, coral cover, genera richness, rugosity and estimated recruitment dates of massive corals at three different sites in the Wakatobi Marine National Park, Indonesia, and on the reefs around Discovery Bay, Jamaica. Semi-structured interviews with key stakeholders in the Wakatobi Marine National Park indicated that coral mining was extensively practised, and is responsible for the absence of large non-branching corals on the Sampela reef Blast fishing is also practised in the Wakatobi Marine Park, and the authors, together with students, showed that blast fishing resulted in coral bleaching and not mortality of two Porites lutea colonies. In addition, we showed that monitoring of bleaching in Porites colonies induced by blast fishing could be a useful way of monitoring blast fishing practices in susceptible areas in the Indo-Pacific. The techniques used in this study are appropriate for use by volunteers with sufficient training, and provide excellent projects for dissertation students reading undergraduate degrees.

Plumatella geimermassardi, a newly recognized freshwater bryozoan from Britain, Ireland, and continental Europe (Bryozoa : Phylactolaemata)

Plumatella geimermassardi is a newly recognized species of phylactolaemate bryozoan. Its known range extends from Ireland east through southern Norway and south into Italy. Colonies grow close to the substrate with little free branching; the body wall is mostly transparent and without an obvious raphe. Floatoblasts are broadly oval and relatively small, with distinctively large dorsal fenestra and uniformly narrow ventral annulus. The sessoblast basal valve is low and dish-shaped; the annulus bears tubercles which vary in their prominence. This species brings to 14 the number of phylactolaemate bryozoans known in the region.

Oestrogenic activity of benzylparaben

Previous work has demonstrated that the alkyl esters of p-hydroxybenzoic acid (parabens) possess oestrogenic activity, which increases with length of alkyl chain from methylparaben to n-butylparaben and with branching in the alkyl chain from n-butylparaben to isobutylparaben. This study reports on the oestrogenic activity of benzylparaben in a variety of assays in vitro and in vivo. Benzylparaben was able to displace [H-3]oestradiol from cytosolic oestrogen receptor (ER) of MCF7 human breast cancer cells by 22% at 1000-fold molar excess, by 40% at 10000-fold molar excess, by 57% at 100000-fold molar excess and by 100% at 1000000-fold molar excess. It was able to increase expression of a stably transfected oestrogen responsive reporter gene (ERE-CAT) in MCF7 cells after 24 h at 10(-5)M/10(-4)M and after 7 days at 10(-6)M/10(-5)M/10(-4)M. Proliferation of MCF7 cells could be increased by 10(-6)M/10(-5)M benzylparaben and this could be inhibited by 10(-7)M pure anti-oestrogen ICI 182,780, indicating that growth effects were ER mediated. Further evidence for ER-mediation was provided from the ability of benzylparaben to increase the growth of a second oestrogen-dependent human breast cancer cell line ZR-75-1, but not the oestrogen-insensitive NIDA-MB-231 cell line. When tested in the presence of 10(-10)M 17beta-oestradiol, benzylparaben gave no antagonist response on the growth of either MCF7 or ZR-75-1 cells. Finally, benzylparaben could increase uterine weight in the immature mouse following topical application of three daily doses of 33 mg to dorsal skin. These results demonstrate that the oestrogenicity of methylparaben can be increased by the addition of an aryl group as well as by lengthening or branching the alkyl grouping. Copyright (C) 2003 John Wiley Sons, Ltd.

Fragrance release from the surface of branched poly(amide)s

Enzymes are powerful tools in organic synthesis that are able to catalyse a wide variety of selective chemical transformations under mild and environmentally friendly conditions. Enzymes such as the lipases have also found applications in the synthesis and degradation of polymeric materials. However, the use of these natural catalysts in the synthesis and the post-synthetic modification of dendrimers and hyperbranched molecules is an application of chemistry yet to be explored extensively. In this study the use of two hydrolytic enzymes, a lipase from Candida cylindracea and a cutinase from Fusarium solani pisii, were investigated in the selective cleavage of ester groups situated on the peripheral layer of two families of branched polyamides. These branched polyamides were conjugated to simple fragrances citronellol and L-menthol via ester linkages. Hydrolysis of the ester linkage between the fragrances and the branched polyamide support was carried out in aqueous buffered systems at slightly basic pH values under the optimum operative conditions for the enzymes used. These preliminary qualitative investigations revealed that partial cleavage of the ester functionalities from the branched polyamide support had occurred. However, the ability of the enzymes to interact with the substrates decreased considerably as the branching density, the rigidity of the structure and the bulkiness of the polyamide-fragrance conjugates increased.

Synthesis and characterization of hyperbranched polyesters incorporating the AB(2) monomer 3,5-bis(3-hydroxylprop-1-ynyl)benzoic acid

The AB, monomer, 3,5-bis(3-hydroxylprop-1-ynyl)benzoic acid 1, has been synthesized using a Sonogashira cross-coupling with a palladium catalyst system developed for use with deactivated aryl halides. Numerous condensation methods have then been assessed in the homopolymerization of the acid-diol monomer 1 to afford hyperbranched polyesters. However, as a result of the thermal instability of the monomer, direct thermal polymerizations could not be employed. Alternative approaches using carbodiimide-coupling reagents enabled the production of soluble polyesters possessing molecular weights and degrees of branching ranging from 2500 to 11,000 and 0.22 to 0.33, respectively. (C) 2003 Elsevier Ltd. All rights reserved.