A numerical analysis of generalized Boussinesq-type equation using continuos/discontinuous FEM

An improved class of Boussinesq systems of an arbitrary order using a wave surface elevation and velocity potential formulation is derived. Dissipative effects and wave generation due to a time-dependent varying seabed are included. Thus, high-order source functions are considered. For the reduction of the system order and maintenance of some dispersive characteristics of the higher-order models, an extra O(mu 2n+2) term (n ??? N) is included in the velocity potential expansion. We introduce a nonlocal continuous/discontinuous Galerkin FEM with inner penalty terms to calculate the numerical solutions of the improved fourth-order models. The discretization of the spatial variables is made using continuous P2 Lagrange elements. A predictor-corrector scheme with an initialization given by an explicit RungeKutta method is also used for the time-variable integration. Moreover, a CFL-type condition is deduced for the linear problem with a constant bathymetry. To demonstrate the applicability of the model, we considered several test cases. Improved stability is achieved.

Metop-A generator for single top production via FCNC interactions

We present a generator for single top-quark production via flavour-changing neutral currents. The MEtop event generator allows for Next-to-Leading-Order direct top production pp -> t and Leading-Order production of several other single top processes. A few packages with definite sets of dimension six operators are available. We discuss how to improve the bounds on the effective operators and how well new physics can be probed with each set of independent dimension six operators.

Clustering de dados biomédicos com algoritmos baseados em critérios entrópicos

A procura de padrões nos dados de modo a formar grupos é conhecida como aglomeração de dados ou clustering, sendo uma das tarefas mais realizadas em mineração de dados e reconhecimento de padrões. Nesta dissertação é abordado o conceito de entropia e são usados algoritmos com critérios entrópicos para fazer clustering em dados biomédicos. O uso da entropia para efetuar clustering é relativamente recente e surge numa tentativa da utilização da capacidade que a entropia possui de extrair da distribuição dos dados informação de ordem superior, para usá-la como o critério na formação de grupos (clusters) ou então para complementar/melhorar algoritmos existentes, numa busca de obtenção de melhores resultados. Alguns trabalhos envolvendo o uso de algoritmos baseados em critérios entrópicos demonstraram resultados positivos na análise de dados reais. Neste trabalho, exploraram-se alguns algoritmos baseados em critérios entrópicos e a sua aplicabilidade a dados biomédicos, numa tentativa de avaliar a adequação destes algoritmos a este tipo de dados. Os resultados dos algoritmos testados são comparados com os obtidos por outros algoritmos mais “convencionais" como o k-médias, os algoritmos de spectral clustering e um algoritmo baseado em densidade.

Two distinct arabinofuranosidases contribute to arabino-oligosaccharide degradation in Bacillus subtilis.

Microbiology 154 (2008) 2719-2729

On the requirements of interpolating polynomials for path motion constraints

In the framework of multibody dynamics, the path motion constraint enforces that a body follows a predefined curve being its rotations with respect to the curve moving frame also prescribed. The kinematic constraint formulation requires the evaluation of the fourth derivative of the curve with respect to its arc length. Regardless of the fact that higher order polynomials lead to unwanted curve oscillations, at least a fifth order polynomials is required to formulate this constraint. From the point of view of geometric control lower order polynomials are preferred. This work shows that for multibody dynamic formulations with dependent coordinates the use of cubic polynomials is possible, being the dynamic response similar to that obtained with higher order polynomials. The stabilization of the equations of motion, always required to control the constraint violations during long analysis periods due to the inherent numerical errors of the integration process, is enough to correct the error introduced by using a lower order polynomial interpolation and thus forfeiting the analytical requirement for higher order polynomials.

Análise da estrutura e da função da proteína morfogenética RodZ de Bacillus subtilis

Resumo: RodZ é um componente do sistema morfogenético das células bacterianas. É uma proteína transmembranar que localiza em bandas ao longo do eixo longitudinal da célula. Em Bacillus subtilis, RodZ consiste numa porção citoplasmática, RodZn, e em uma parte extra-citoplasmática, RodZc. RodZn contém um domínio em helixturn- helix (HTH), enquanto que RodZc pode ser dividido num domínio coiled-coil e num domínio terminal C, de função desconhecida. Um segmento transmembranar (TM) único separa RodZn de RodZc. A eliminação de rodZ causa alongamento do nucleóide e leva à produção de células polares nucleadas. Aqui, mostramos que RodZn é estruturado, estável e em hélice α. Descobrimos que as substituições Y32A e L33A na suposta hélice de reconhecimento (3) do motivo HTH, bem como as substituições Y49A e F53A, fora do motivo HTH (4), causam divisão assimétrica, mas apenas as últimas levam à deslocalização sub-celular de RodZ. Sugerimos que as hélices 3 e 4 são utilizadas para uma interacção proteína-proteína ou proteína- DNA essencial para divisão celular enquanto que 4 deve contactar um componente do citosqueleto, possivelmente MreB, uma vez que a correcta localização sub-celular de RodZ depende desta proteína. Em todos os mutantes as células polares são anucleadas, pelo que concluímos que o alongamento do nucleóide não é um prérequisito para divisão assimétrica. RodZc é largamente não estruturado mas com conteúdo de folha , sendo estabilizado pelo domínio coiled-coil. Mostramos uma relação homóloga entre RodZc e a bomba de transporte Na+/Ca2+ NCX1 e identificámos dois resíduos no domínio C, G265 e N275, essenciais para a manutenção da forma celular. Estes resíduos fazem parte de um motivo em gancho que pode actuar como um local de interacção com um ligando desconhecido. RodZn e RodZc são monoméricos em solução. Contudo, na membrana, RodZ interage consigo própria num sistema de dois híbridos (Split-Ubiquitin) em levedura, sugerindo que possa formar multímeros in vivo.-----------ABSTRACT: RodZ is a transmembrane component of the bacterial core morphogenic apparatus. RodZ localizes in bands long the longitudinal axis of the cell, and it is though to functionally link the cell wall to the actin cytoskeleton. In Bacillus subtilis, RodZ consists of a cytoplasmic moiety, RodZn, and an extracytoplasmic moiety, RodZc. RodZn contains a predicted helix-turn-helix domain, whereas RodZc is thought to contain a coiled-coil region and a terminal C domain of unknown function. A single transmembrane domain separates RodZn from RodZc. Deletion of rodZ causes elongation of the nucleoid and leads to the production of polar minicells containing DNA. Here, we have studied the structure and function of RodZn and RodZc. We show that RodZn is a stable, folded, -helical domain. We discovered that the Y32A and L33A substitutions within the presumptive recognition helix (3) of the HTH motif, as well as the Y49A and F53A substitutions outside of the HTH motif (in 4) cause asymmetric cell division. However, only the substitutions in 4 cause sub-celular delocalization of RodZ. We suggest that 3 and 4 are used for a protein-protein or protein-DNA interaction important for cell division, whereas 4 is likely to contact a cytoskeletal component, presumably MreB. The polar cells formed by all the mutants are anucleate. We conclude that nucleoid elongation is not a prerequisite for asymmetric division. RodZc appears to be a largely unstructured domain, with some -sheet content, and is stabilized by the coiled-coil region. We show a homology relationship between RodZc and the NCX1 Na+/Ca2+ transporter and we found two residues within the C domain, G265 and N275, that are important for cell shape determination. These residues are predicted to be essential determinants of a claw-like motif, which may act as a binding site for an unknown ligand. Both the isolated RodZn and RodZc proteins are monomeric in solution. However, because full-length RodZ interacts with itself in a split-ubiquitin yeast two-hybrid assay, we suggest that it may dimerize or form higher order multimers in vivo.

The development and implementation of math projects in a HEI: expectations, objectives, experiences and analysis

An overwhelming problem in Math Curriculums in Higher Education Institutions (HEI), we are daily facing in the last decade, is the substantial differences in Math background of our students. When you try to transmit, engage and teach subjects/contents that your “audience” is unable to respond to and/or even understand what we are trying to convey, it is somehow frustrating. In this sense, the Math projects and other didactic strategies, developed through Learning Management System Moodle, which include an array of activities that combine higher order thinking skills with math subjects and technology, for students of HE, appear as remedial but important, proactive and innovative measures in order to face and try to overcome these considerable problems. In this paper we will present some of these strategies, developed in some organic units of the Polytechnic Institute of Porto (IPP). But, how “fruitful” are the endless number of hours teachers spent in developing and implementing these platforms? Do students react to them as we would expect? Do they embrace this opportunity to overcome their difficulties? How do they use/interact individually with LMS platforms? Can this environment that provides the teacher with many interesting tools to improve the teaching – learning process, encourages students to reinforce their abilities and knowledge? In what way do they use each available material – videos, interactive tasks, texts, among others? What is the best way to assess student’s performance in these online learning environments? Learning Analytics tools provides us a huge amount of data, but how can we extract “good” and helpful information from them? These and many other questions still remain unanswered but we look forward to get some help in, at least, “get some drafts” for them because we feel that this “learning analysis”, that tackles the path from the objectives to the actual results, is perhaps the only way we have to move forward in the “best” learning and teaching direction.

Spatial point pattern analysis of gorilla nest sites in the Kagwene Sanctuary, Cameroon: Towards understanding the nesting behavior of a critically endangered subspecies

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Automatic Small Bowel Tumor Diagnosis by Using Multi-Scale Wavelet-Based Analysis in Wireless Capsule Endoscopy Images

BACKGROUND: Wireless capsule endoscopy has been introduced as an innovative, non-invasive diagnostic technique for evaluation of the gastrointestinal tract, reaching places where conventional endoscopy is unable to. However, the output of this technique is an 8 hours video, whose analysis by the expert physician is very time consuming. Thus, a computer assisted diagnosis tool to help the physicians to evaluate CE exams faster and more accurately is an important technical challenge and an excellent economical opportunity. METHOD: The set of features proposed in this paper to code textural information is based on statistical modeling of second order textural measures extracted from co-occurrence matrices. To cope with both joint and marginal non-Gaussianity of second order textural measures, higher order moments are used. These statistical moments are taken from the two-dimensional color-scale feature space, where two different scales are considered. Second and higher order moments of textural measures are computed from the co-occurrence matrices computed from images synthesized by the inverse wavelet transform of the wavelet transform containing only the selected scales for the three color channels. The dimensionality of the data is reduced by using Principal Component Analysis. RESULTS: The proposed textural features are then used as the input of a classifier based on artificial neural networks. Classification performances of 93.1% specificity and 93.9% sensitivity are achieved on real data. These promising results open the path towards a deeper study regarding the applicability of this algorithm in computer aided diagnosis systems to assist physicians in their clinical practice.

A logical foundation for session-based concurrent computation

Linear logic has long been heralded for its potential of providing a logical basis for concurrency. While over the years many research attempts were made in this regard, a Curry-Howard correspondence between linear logic and concurrent computation was only found recently, bridging the proof theory of linear logic and session-typed process calculus. Building upon this work, we have developed a theory of intuitionistic linear logic as a logical foundation for session-based concurrent computation, exploring several concurrency related phenomena such as value-dependent session types and polymorphic sessions within our logical framework in an arguably clean and elegant way, establishing with relative ease strong typing guarantees due to the logical basis, which ensure the fundamental properties of type preservation and global progress, entailing the absence of deadlocks in communication. We develop a general purpose concurrent programming language based on the logical interpretation, combining functional programming with a concurrent, session-based process layer through the form of a contextual monad, preserving our strong typing guarantees of type preservation and deadlock-freedom in the presence of general recursion and higher-order process communication. We introduce a notion of linear logical relations for session typed concurrent processes, developing an arguably uniform technique for reasoning about sophisticated properties of session-based concurrent computation such as termination or equivalence based on our logical approach, further supporting our goal of establishing intuitionistic linear logic as a logical foundation for sessionbased concurrency.

G-quadruplex ligands for cancer therapy

DNA may fold into a diversity of structures and topologies such as duplexes and triplexes. Some specific guanine-rich DNA sequences may even fold into a higher order structures denominated guanine G-quadruplexes (G4). These G-quadruplex forming sequences have shown biological interest since were found in telomeres and in promoter region of oncogenes. Thus, these G4 forming sequences have been explored as therapeutic targets for cancer therapy, since G4 formation was demonstrated to inhibit RNA-polymerase and telomerase activity. However, the G4 structures are transient and are only formed under specific conditions. Hence the main objective of this work is to develop new G4-specific ligands which may potentially find applications in the therapeutic area. Several potential G4-binding ligands were synthesized and characterized. The synthesis of these compounds consisted on a procedure based on van Leusen chemistry and a cross-coupling reaction through C-H activation, affording phenanthroline compounds (Phen-1, 50%; Phen-2, 20%), phenyl (Iso-1, 61%; Iso-2, 21%; Ter-1, 85%; Ter-2, 35%), and quinolyl (Quin-1, 85%; Quin-2, 45%) compounds. Screening assays for selecting the potential G4 compounds were performed by FRET-melting, G4-FID, CD-melting and DSF. Qualitative biophysical studies were performed by fluorescence and CD spectroscopy. Two high-specific G-quadruplex ligands, Phen-1 and Phen-2, were found to effectively bind telomeric and c-myc G4 structures. Phen-1 was found to stabilize parallel telomeric 22AG and c-myc sequence by 4.1 and 4.3 ˚C, respectively. Phen-2 also displayed high affinity towards 22AG (

Short-term corneal changes with gas-permeable contact lens wear in keratoconus subjects: a comparison of two fitting approaches

Purpose: To evaluate changes in anterior corneal topography and higher-order aberrations (HOA) after 14-days of rigid gas-permeable (RGP) contact lens (CL) wear in keratoconus subjects comparing two different fitting approaches. Methods: Thirty-one keratoconus subjects (50 eyes) without previous history of CL wear were recruited for the study. Subjects were randomly fitted to either an apical-touch or three-pointtouch fitting approach. The lens’ back optic zone radius (BOZR) was 0.4 mm and 0.1 mm flatter than the first definite apical clearance lens, respectively. Differences between the baseline and post-CL wear for steepest, flattest and average corneal power (ACP) readings, central corneal astigmatism (CCA), maximum tangential curvature (KTag), anterior corneal surface asphericity, anterior corneal surface HOA and thinnest corneal thickness measured with Pentacam were compared. Results: A statistically significant flattening was found over time on the flattest and steepest simulated keratometry and ACP in apical-touch group (all p < 0.01). A statistically significant reduction in KTag was found in both groups after contact lens wear (all p < 0.05). Significant reduction was found over time in CCA (p = 0.001) and anterior corneal asphericity in both groups (p < 0.001). Thickness at the thinnest corneal point increased significantly after CL wear (p < 0.0001). Coma-like and total HOA root mean square (RMS) error were significantly reduced following CL wearing in both fitting approaches (all p < 0.05). Conclusion: Short-term rigid gas-permeable CL wear flattens the anterior cornea, increases the thinnest corneal thickness and reduces anterior surface HOA in keratoconus subjects. Apicaltouch was associated with greater corneal flattening in comparison to three-point-touch lens wear.

Abnormalities in the processing of emotional prosody from single words in schizophrenia

Background: Abnormalities in emotional prosody processing have been consistently reported in schizophrenia and are related to poor social outcomes. However, the role of stimulus complexity in abnormal emotional prosody processing is still unclear. Method: We recorded event-related potentials in 16 patients with chronic schizophrenia and 16 healthy controls to investigate: 1) the temporal course of emotional prosody processing; and 2) the relative contribution of prosodic and semantic cues in emotional prosody processing. Stimuli were prosodic single words presented in two conditions: with intelligible (semantic content condition—SCC) and unintelligible semantic content (pure prosody condition—PPC). Results: Relative to healthy controls, schizophrenia patients showed reduced P50 for happy PPC words, and reduced N100 for both neutral and emotional SCC words and for neutral PPC stimuli. Also, increased P200 was observed in schizophrenia for happy prosody in SCC only. Behavioral results revealed higher error rates in schizophrenia for angry prosody in SCC and for happy prosody in PPC. Conclusions: Together, these data further demonstrate the interactions between abnormal sensory processes and higher-order processes in bringing about emotional prosody processing dysfunction in schizophrenia. They further suggest that impaired emotional prosody processing is dependent on stimulus complexity.

The role of a transcrustal shear zone in orogenic gold mineralization at the Aijanahalli Mine, Dharwar Craton, South India

The Ajjanahalli gold mine is spatially associated with a Late Archean craton-scale shear zone in the eastern Chitradurga greenstone belt of the Dharwar craton, India. Gold mineralization is hosted by an similar to100-m-wide antiform in a banded iron formation. Original magnetite and siderite are replaced by a peak metamorphic alteration assemblage of chlorite, stilpnomelane, minnesotaite, sericite, ankerite, arsenopyrite, pyrite, pyrrhotite, and gold at ca. 300degrees to 350degreesC. Elements enriched in the banded iron formation include Ca, Mg, C, S, An, As, Bi. Cu, Sb, Zn, Pb, Se, Ag, and Te, whereas in the wall rocks As, Cu, Zn, Bi, Ag, and An are only slightly enriched. Strontium correlates with CaO, MgO, CO2, and As, which indicates cogenetic formation of arsenopyrite and Mg-Ca carbonates. The greater extent of alteration in the Fe-rich banded iron formation layers than in the wall rock reflects the greater reactivity of the banded iron formation layers. The ore fluids, as interpreted from their isotopic composition (delta(18)O = 6.5-8.5parts per thousand; initial Sr-87/Sr-86 = 0.7068-0.7078), formed by metamorphic devolatilization of deeper levels of the Chitradurga greenstone belt. Arsenopyrite, chalcopyrite, and pyrrhotite have delta(34)S values within a narrow range between 2.1 and 2.7 per mil, consistent with a sulfur source in Chitradurga greenstone belt lithologies. Based on spatial and temporal relationships between mineralization, local structure development, and sinistral strike-slip deformation in the shear zone at the eastern contact of the Chitradurga greenstone belt, we suggest that the Ajjanahalli gold mineralization formed by fluid infiltration into a low strain area within the first-order structure. The ore fluids were transported along this shear zone into relatively shallow crustal levels during lateral terrane accretion and a change from thrust to transcurrent tectonics. Based on this model of fluid flow, exploration should focus on similar low strain areas or potentially connected higher order splays of the first-order shear zone.

Modularity of auditory spatial representations

Abstract : Auditory spatial functions are of crucial importance in everyday life. Determining the origin of sound sources in space plays a key role in a variety of tasks including orientation of attention, disentangling of complex acoustic patterns reaching our ears in noisy environments. Following brain damage, auditory spatial processing can be disrupted, resulting in severe handicaps. Complaints of patients with sound localization deficits include the inability to locate their crying child or being over-loaded by sounds in crowded public places. Yet, the brain bears a large capacity for reorganization following damage and/or learning. This phenomenon is referred as plasticity and is believed to underlie post-lesional functional recovery as well as learning-induced improvement. The aim of this thesis was to investigate the organization and plasticity of different aspects of auditory spatial functions. Overall, we report the outcomes of three studies: In the study entitled "Learning-induced plasticity in auditory spatial representations" (Spierer et al., 2007b), we focused on the neurophysiological and behavioral changes induced by auditory spatial training in healthy subjects. We found that relatively brief auditory spatial discrimination training improves performance and modifies the cortical representation of the trained sound locations, suggesting that cortical auditory representations of space are dynamic and subject to rapid reorganization. In the same study, we tested the generalization and persistence of training effects over time, as these are two determining factors in the development of neurorehabilitative intervention. In "The path to success in auditory spatial discrimination" (Spierer et al., 2007c), we investigated the neurophysiological correlates of successful spatial discrimination and contribute to the modeling of the anatomo-functional organization of auditory spatial processing in healthy subjects. We showed that discrimination accuracy depends on superior temporal plane (STP) activity in response to the first sound of a pair of stimuli. Our data support a model wherein refinement of spatial representations occurs within the STP and that interactions with parietal structures allow for transformations into coordinate frames that are required for higher-order computations including absolute localization of sound sources. In "Extinction of auditory stimuli in hemineglect: space versus ear" (Spierer et al., 2007a), we investigated auditory attentional deficits in brain-damaged patients. This work provides insight into the auditory neglect syndrome and its relation with neglect symptoms within the visual modality. Apart from contributing to a basic understanding of the cortical mechanisms underlying auditory spatial functions, the outcomes of the studies also contribute to develop neurorehabilitation strategies, which are currently being tested in clinical populations.