Showing papers by "University of Coimbra published in 2006"

Phase III Study of Docetaxel and Cisplatin Plus Fluorouracil Compared With Cisplatin and Fluorouracil As First-Line Therapy for Advanced Gastric Cancer: A Report of the V325 Study Group

Abstract: Purpose In the randomized, multinational phase II/III trial (V325) of untreated advanced gastric cancer patients, the phase II part selected docetaxel, cisplatin, and fluorouracil (DCF) over docetaxel and cisplatin for comparison against cisplatin and fluorouracil (CF; reference regimen) in the phase III part. Patients and Methods Advanced gastric cancer patients were randomly assigned to docetaxel 75 mg/m2 and cisplatin 75 mg/m2 (day 1) plus fluorouracil 750 mg/m2/d (days 1 to 5) every 3 weeks or cisplatin 100 mg/m2 (day 1) plus fluorouracil 1,000 mg/m2/d (days 1 to 5) every 4 weeks. The primary end point was time-to-progression (TTP). Results In 445 randomly assigned and treated patients (DCF = 221; CF = 224), TTP was longer with DCF versus CF (32% risk reduction; log-rank P < .001). Overall survival was longer with DCF versus CF (23% risk reduction; log-rank P = .02). Two-year survival rate was 18% with DCF and 9% with CF. Overall response rate was higher with DCF (χ2 P = .01). Grade 3 to 4 treatment-r...

Octopus: a tool for the application of time-dependent density functional theory

Abstract: We report on the background, current status, and current lines of development of the octopus project. This program materializes the main equations of density-functional theory in the ground state, and of time-dependent density-functional theory for dynamical effects. The focus is nowadays placed on the optical (i.e. electronic) linear response properties of nanostructures and biomolecules, and on the non-linear response to high-intensity fields of finite systems, with particular attention to the coupled ionic-electronic motion (i.e. photo-chemical processes). In addition, we are currently extending the code to the treatment of periodic systems (both to one-dimensional chains, two-dimensional slabs, or fully periodic solids), magnetic properties (ground state properties and excitations), and to the field of quantum-mechanical transport or “molecular electronics.” In this communication, we concentrate on the development of the methodology: we review the essential numerical schemes used in the code, and report on the most recent implementations, with special attention to the introduction of adaptive coordinates, to the extension of our real-space technique to tackle periodic systems, and on large-scale parallelization. More information on the code, as well as the code itself, can be found at http://www.tddft.org/programs/octopus/. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Presynaptic Control of Striatal Glutamatergic Neurotransmission by Adenosine A1–A2A Receptor Heteromers

Abstract: The functional role of heteromers of G-protein-coupled receptors is a matter of debate. In the present study, we demonstrate that heteromerization of adenosine A1 receptors (A1Rs) and A2A receptors (A2ARs) allows adenosine to exert a fine-tuning modulation of glutamatergic neurotransmission. By means of coimmunoprecipitation, bioluminescence and time-resolved fluorescence resonance energy transfer techniques, we showed the existence of A1R–A2AR heteromers in the cell surface of cotransfected cells. Immunogold detection and coimmunoprecipitation experiments indicated that A1R and A2AR are colocalized in the same striatal glutamatergic nerve terminals. Radioligand-binding experiments in cotransfected cells and rat striatum showed that a main biochemical characteristic of the A1R–A2AR heteromer is the ability of A2AR activation to reduce the affinity of the A1R for agonists. This provides a switch mechanism by which low and high concentrations of adenosine inhibit and stimulate, respectively, glutamate release. Furthermore, it is also shown that A1R–A2AR heteromers constitute a unique target for caffeine and that chronic caffeine treatment leads to modifications in the function of the A1R–A2AR heteromer that could underlie the strong tolerance to the psychomotor effects of caffeine.

Oral squamous cell carcinoma: Review of prognostic and predictive factors

Abstract: Oral squamous cell carcinoma has a remarkable incidence worldwide and a fairly onerous prognosis, encouraging further research on factors that might modify disease outcome. In this review article, the authors approach the factors that may exert influence on the prognosis and eventually guide the selection of patients for more aggressive therapies. Published scientific data was collected, selected, and grouped into 3 main clusters: patient-, tumor-, and treatment-related factors. Well established aspects are discussed, but also those less common or with only supposed usefulness. Disease staging, extracapsular dissemination, resection margin free of disease, and tumor thickness are factors with high influence on the prognosis. There has been an increasing interest in the study of tumor molecular factors, and some have been strongly correlated with the outcome, showing promising pathways for the future development of more effective prognosis systems and anticancer therapies.

Involvement of Oxidative Stress in Alzheimer Disease

Abstract: Genetic and lifestyle-related risk factors for Alzheimer disease (AD) are associated with an increase in oxidative stress, suggesting that oxidative stress is involved at an early stage of the pathologic cascade. Moreover, oxidative stress is mechanistically and chronologically associated with other key features of AD, namely, metabolic, mitochondrial, metal, and cell-cycle abnormalities. Contrary to the commonly held notion that pathologic hallmarks of AD signify etiology, several lines of evidence now indicate that aggregation of amyloid-β and tau is a compensatory response to underlying oxidative stress. Therefore, removal of proteinaceous accumulations may treat the epiphenomenon rather than the disease and may actually enhance oxidative damage. Although some antioxidants have been shown to reduce the incidence of AD, the magnitude of the effect may be modified by individual factors such as genetic predisposition (e.g. apolipoprotein E genotype) and habitual behaviors. Because caloric restriction, exercise, and intellectual activity have been experimentally shown to promote neuronal survival through enhancement of endogenous antioxidant defenses, a combination of dietary regimen of low total calorie and rich antioxidant nutrients and maintaining physical and intellectual activities may ultimately prove to be one of the most efficacious strategies for AD prevention.

New insights on the anticancer properties of dietary polyphenols.

Abstract: Cancer, one of the major causes of death across the world, has shown to be a largely preventable disease, highly susceptible to modulation by dietary factors. Phenolic compounds, abundant in vegetables and fruits ubiquitous in diet, were described to play an important role as chemopreventive agents. Since conventional therapeutic and surgical approaches have not been able to control the incidence of most cancer types, the development of chemopreventive strategies is an urgent priority in public health. The current diet phenolic intake is often insufficient to protect from mutagens (either exogenous or endogenous), which leads to the need for dietary supplementation as an alternative approach. Research efforts are placing increasing emphasis on identifying the biological mechanisms and in particular the signal transduction pathways related to the chemopreventive activities of these compounds. These effects are believed to occur by the regulation of signaling pathways such as nuclear factor-kappaB (NF-kappaB), activator protein-1 (AP-1) or mitogen-activated protein kinases (MAPK). Dietary polyphenols can exert their effects on these pathways separately or sequentially and in addition the occurrence of crosstalk between these pathways cannot be overlooked. By modulating cell signaling pathways, polyphenols activate cell death signals and induce apoptosis in precancerous or malignant cells resulting in the inhibition of cancer development or progression. However, regulation of cell signaling pathways by dietary polyphenols can also lead to cell proliferation/survival or inflammatory responses due to increased expression of several genes. The present review summarizes the most recent advances providing new insights into the molecular mechanisms underlying the promising anticarcinogenic activity of dietary polyphenols.

Safety of low dose glucocorticoid treatment in rheumatoid arthritis: published evidence and prospective trial data

Abstract: Adverse effects of glucocorticoids have been abundantly reported. Published reports on low dose glucocorticoid treatment show that few of the commonly held beliefs about their incidence, prevalence, and impact are supported by clear scientific evidence. Safety data from recent randomised controlled clinical trials of low dose glucocorticoid treatment in RA suggest that adverse effects associated with this drug are modest, and often not statistically different from those of placebo.

Using Queueing Theory to Increase the Effectiveness of Emergency Department Provider Staffing

Abstract: Objectives: Significant variation in emergency department (ED) patient arrival rates necessitates the adjustment of staffing patterns to optimize the timely care of patients. This study evaluated the effectiveness of a queueing model in identifying provider staffing patterns to reduce the fraction of patients who leave without being seen. Methods: The authors collected detailed ED arrival data from an urban hospital and used a Lag SIPP queueing analysis to gain insights on how to change provider staffing to decrease the proportion of patients who leave without being seen. The authors then compared this proportion for the same 39-week period before and after the resulting changes. Results: Despite an increase in arrival volume of 1,078 patients (6.3%), an average increase in provider hours of 12 hours per week (3.1%) resulted in 258 fewer patients who left without being seen. This represents a decrease in the proportion of patients who left without being seen by 22.9%. Restricting attention to a four-day subset of the week during which there was no increase in total provider hours, a reallocation of providers based on the queueing model resulted in 161 fewer patients who left without being seen (21.7%), despite an additional 548 patients (5.5%) arriving in the second half of the study. Conclusions: Timely access to a provider is a critical dimension of ED quality performance. In an environment in which EDs are often understaffed, analyses of arrival patterns and the use of queueing models can be extremely useful in identifying the most effective allocation of staff.

An energy-efficient ant-based routing algorithm for wireless sensor networks

Abstract: Wireless Sensor Networks are characterized by having specific requirements such as limited energy availability, low memory and reduced processing power. On the other hand, these networks have enormous potential applicability, e.g., habitat monitoring, medical care, military surveillance or traffic control. Many protocols have been developed for Wireless Sensor Networks that try to overcome the constraints that characterize this type of networks. Ant-based routing protocols can add a significant contribution to assist in the maximisation of the network lifetime, but this is only possible by means of an adaptable and balanced algorithm that takes into account the Wireless Sensor Networks main restrictions. This paper presents a new Wireless Sensor Network routing protocol, which is based on the Ant Colony Optimization metaheuristic. The protocol was studied by simulation for several Wireless Sensor Network scenarios and the results clearly show that it minimises communication load and maximises energy savings.

Antifungal activity of the essential oil of Thymus pulegioides on Candida, Aspergillus and dermatophyte species.

Abstract: The composition of the essential oil of Thymus pulegioides and its antifungal activity on Candida, Aspergillus and dermatophyte fungal strains were studied. Essential oil from the aerial parts of the plant was obtained by hydrodistillation and analysed by GC and GC-MS. The oil showed high contents of carvacrol and thymol. The MIC and minimal lethal concentration were used to evaluate the antifungal activity against Candida (seven clinical isolates and four ATCC type strains), Aspergillus [five clinical isolates, and two Coleccion Espanola de Cultivos Tipo (CECT) and two ATCC type strains] and five clinical dermatophyte strains. Antifungal activity was evaluated for the essential oil and for its main components. To clarify its mechanism of action on yeasts and filamentous fungi, flow-cytometric studies of cytoplasmic membrane integrity were performed, and the effect on the amount of ergosterol was investigated. Results showed that T. pulegioides essential oil exhibited a significant activity against clinically relevant fungi, mainly due to lesion formation in the cytoplasmic membrane and a considerable reduction of the ergosterol content. The present study indicates that T. pulegioides essential oil has considerable antifungal activity, deserving further investigation for clinical applications.

Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies

Abstract: The genome-wide distribution of linkage disequilibrium (LD) determines the strategy for selecting markers for association studies, but it varies between populations. We assayed LD in large samples (200 individuals) from each of 11 well-described population isolates and an outbred European-derived sample, using SNP markers spaced across chromosome 22. Most isolates show substantially higher levels of LD than the outbred sample and many fewer regions of very low LD (termed 'holes'). Young isolates known to have had relatively few founders show particularly extensive LD with very few holes; these populations offer substantial advantages for genome-wide association mapping.

Firm Growth and Liquidity Constraints: A Dynamic Analysis

Abstract: Using a large unbalanced panel data set of Portuguese manufacturing firms surviving over the period from 1990 to 2001, the purpose of this paper is to examine whether liquidity constraints faced by business firms affect firm growth. We use a GMM-system to estimate a dynamic panel data model of firm growth that incorporates cash flow as a measure of liquidity constraints and persistence of growth. The model is estimated for all size classes, including micro firms. Our findings reveal that smaller and younger firms have higher growth-cash flow sensitivities than larger and more mature firms. This is consistent with the suggestion that financial constraints on firm growth may be relatively more severe for small and young firms. Nevertheless, the same finding can be interpreted in a different way if we consider the more recent literature which interpret the higher investment/cash flow sensitivity of younger and smaller firm in absence of financial market imperfection as the outcome of these firms reaction to the fact that realisation of their cash flows reveals them the direction to go in presence of uncertainty of their growth prospect. Besides, firms that were small and young at the beginning of the sample period exhibited more persistent growth than those that were large and old. Finally, these results have significant policy implications.

Stimulation of leaf litter decomposition and associated fungi and invertebrates by moderate eutrophication : implications for stream assessment

Abstract: Summary 1. We investigated the effect of moderate eutrophication on leaf litter decomposition and associated invertebrates in five reference and five eutrophied streams in central Portugal. Fungal parameters and litter N and P dynamics were followed in one pair of streams. Benthic invertebrate parameters that are considered useful in bioassessment were estimated in all streams. Finally, we evaluated the utility of decomposition as a tool to assess stream ecosystem functional integrity. 2. Decomposition of alder and oak leaves in coarse mesh bags was on average 2.3–2.7× faster in eutrophied than in reference streams. This was attributed to stimulation of fungal activity (fungal biomass accrual and sporulation of aquatic hyphomycetes) by dissolved nutrients. These effects were more pronounced for oak litter (lower quality substrate) than alder. N content of leaf litter did not differ between stream types, while P accrual was higher in the eutrophied than in the reference stream. Total invertebrate abundances and richness associated with oak litter, but not with alder, were higher in eutrophied streams. 3. We found only positive correlations between stream nutrients (DIN and SRP) and leaf litter decomposition rates in both fine and coarse mesh bags, associated sporulation rates of aquatic hyphomycetes and, in some cases, total invertebrate abundances and richness. 4. Some metrics based on benthic invertebrate community data (e.g. % shredders, % shredder taxa) were significantly lower in eutrophied than in reference streams, whereas the IBMWP index that is specifically designed for the Iberian peninsula classified all 10 streams in the highest possible class as having ‘very good’ ecological conditions. 5. Leaf litter decomposition was sufficiently sensitive to respond to low levels of eutrophication and could be a useful functional measure to complement assessment programmes based on structural parameters.

Whole-stream nitrate addition affects litter decomposition and associated fungi but not invertebrates

Abstract: We assessed the effect of whole-stream nitrate enrichment on decomposition of three substrates differing in nutrient quality (alder and oak leaves and balsa veneers) and associated fungi and invertebrates. During the 3-month nitrate enrichment of a headwater stream in central Portugal, litter was incubated in the reference site (mean NO3-N 82 μg l−1) and four enriched sites along the nitrate gradient (214–983 μg NO3-N l−1). A similar decomposition experiment was also carried out in the same sites at ambient nutrient conditions the following year (33–104 μg NO3-N l−1). Decomposition rates and sporulation of aquatic hyphomycetes associated with litter were determined in both experiments, whereas N and P content of litter, associated fungal biomass and invertebrates were followed only during the nitrate addition experiment. Nitrate enrichment stimulated decomposition of oak leaves and balsa veneers, fungal biomass accrual on alder leaves and balsa veneers and sporulation of aquatic hyphomycetes on all substrates. Nitrate concentration in stream water showed a strong asymptotic relationship (Michaelis–Menten-type saturation model) with temperature-adjusted decomposition rates and percentage initial litter mass converted into aquatic hyphomycete conidia for all substrates. Fungal communities did not differ significantly among sites but some species showed substrate preferences. Nevertheless, certain species were sensitive to nitrogen concentration in water by increasing or decreasing their sporulation rate accordingly. N and P content of litter and abundances or richness of litter-associated invertebrates were not affected by nitrate addition. It appears that microbial nitrogen demands can be met at relatively low levels of dissolved nitrate, suggesting that even minor increases in nitrogen in streams due to, e.g., anthropogenic eutrophication may lead to significant shifts in microbial dynamics and ecosystem functioning.

Dysfunctional Sexual Beliefs as Vulnerability Factors for Sexual Dysfunction

Abstract: The differences on sexual beliefs presented by men and women with sexual dysfunction and their sexually functional counterparts were investigated. A total of 488 participants (160 females and 232 males without sexual problems and 47 females and 49 males with a DSM-IV diagnosis of sexual dysfunction) answered the Sexual Dysfunctional Beliefs Questionnaire. Findings showed that, although effects have only reached statistical significance for the female group, both dysfunctional men and women endorsed more sexual dysfunctional beliefs than functional. Women presented significantly more age related beliefs (after menopause women loose their sexual desire, as women age, the pleasure they get from sex decreases) and body image beliefs (women who are not physically attractive cannot be sexually satisfied). Additionally, sexually dysfunctional males presented higher scores (not statistically significant) on 'macho' belief (a real man has sexual intercourse very often) and the beliefs about women satisfaction (the quality of the erection is what most satisfies women). Overall, findings support the idea that sexual beliefs may play a role as vulnerability factors for sexual dysfunction.

Review and current status of emulsion/dispersion technology using an internal gelation process for the design of alginate particles

Abstract: Emulsification/internal gelation has been suggested as an alternative to extrusion/external gelation in the encapsulation of several compounds including sensitive biologicals such as protein drugs. Protein-loaded microparticles offer an inert environment within the matrix and encapsulation is conducted at room temperature in a media free of organic solvents. Recently, the concept of internal gelation has been applied to formulating nanoparticles as drug delivery systems. Emulsification/internal gelation technologies available for microparticles preparation, particularly that involving alginate polymer, are described as well as recent advances towards applications in nanotechnology. Those methods show great promise as a tool for the development of encapsulation processes, especially for the new field of nanotechnology using natural polymers.

Particle swarm-based olfactory guided search

Abstract: This article presents a new algorithm for searching odour sources across large search spaces with groups of mobile robots. The proposed algorithm is inspired in the particle swarm optimization (PSO) method. In this method, the search space is sampled by dynamic particles that use their knowledge about the previous sampled space and share this knowledge with other neighbour searching particles allowing the emergence of efficient local searching behaviours. In this case, chemical searching cues about the potential existence of upwind odour sources are exchanged. By default, the agents tend to avoid each other, leading to the emergence of exploration behaviours when no chemical cue exists in the neighbourhood. This behaviour improves the global searching performance. The article explains the relevance of searching odour sources with autonomous agents and identifies the main difficulties for solving this problem. A major difficulty is related with the chaotic nature of the odour transport in the atmosphere due to turbulent phenomena. The characteristics of this problem are described in detail and a simulation framework for testing and analysing different odour searching algorithms was constructed. The proposed PSO-based searching algorithm and modified versions of gradient-based searching and biased random walk-based searching strategies were tested in different environmental conditions and the results, showing the effectiveness of the proposed strategy, were analysed and discussed.

Tools for kinetic modeling of biochemical networks.

Abstract: The number of software packages for kinetic modeling of biochemical networks continues to grow. Although most packages share a common core of functionality, the specific capabilities and user interfaces of different packages mean that choosing the best package for a given task is not trivial. We compare 12 software packages with respect to their functionality, reliability, efficiency, user-friendliness and compatibility. Although most programs performed reliably in all numerical tasks tested, SBML compatibility and the set-up of multicompartmentalization are problematic in many packages. For simple models, GEPASI seems the best choice for non-expert users. For large-scale models, environments such as Jarnac/JDesigner are preferable, because they allow modular implementation of models. Virtual Cell is the most versatile program and provides the simplest and clearest functionality for setting up multicompartmentalization.