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2009
Antunes, R, Coito FV.  2009.  A Cognitive Model for Frequency Signal Classification. International Journal of Mathematical, Physical and Engineering Sciences. 3:240–245(Number 4: Citeseer) Abstract

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Ortigueira, M.  2009.  Comments on ?Modeling fractional stochastic systems as non-random fractional dynamics driven Brownian motions? Applied Mathematical Modelling. 33:2534–2537(Number 5: Elsevier Inc) AbstractWebsite

Some results presented in the paper ?Modeling fractional stochastic systems as non-random fractional dynamics driven Brownian motions? ?I. Podlubny, Fractional Differential Equations, Academic Press, San Diego, 1999? are discussed in this paper. The slightly modified Grünwald-Letnikov derivative proposed there is used to deduce some interesting results that are in contradiction with those proposed in the referred paper. Keywords: Fractional calculus; Grünwald-Letnikov derivative; Fractional Brownian motion

Ribeiro, MP, Espiga A, Silva D, Baptista P, Henriques J, Ferreira C, Silva JC, Borges JP, Pires E, Chaves P, Correia IJ.  2009.  Development of a new chitosan hydrogel for wound dressing. Wound repair and regeneration. 17(6):817–824., Number 6: Blackwell Publishing Inc AbstractWebsite

Wound healing is a complex process involving an integrated response by many different cell types and growth factors in order to achieve rapid restoration of skin architecture and function. The present study evaluated the applicability of a chitosan hydrogel (CH) as a wound dressing. Scanning electron microscopy analysis was used to characterize CH morphology. Fibroblast cells isolated from rat skin were used to assess the cytotoxicity of the hydrogel. CH was able to promote cell adhesion and proliferation. Cell viability studies showed that the hydrogel and its degradation by-products are noncytotoxic. The evaluation of the applicability of CH in the treatment of dermal burns in Wistar rats was performed by induction of full-thickness transcutaneous dermal wounds. Wound healing was monitored through macroscopic and histological analysis. From macroscopic analysis, the wound beds of the animals treated with CH were considerably smaller than those of the controls. Histological analysis revealed lack of a reactive or a granulomatous inflammatory reaction in skin lesions with CH and the absence of pathological abnormalities in the organs obtained by necropsy, which supported the local and systemic histocompatibility of the biomaterial. The present results suggest that this biomaterial may aid the re-establishment of skin architecture.

Almeida, PL, Kundu S, Borges JP, Godinho MH, Figueirinhas JL.  2009.  Electro-optical light scattering shutter using electrospun cellulose-based nano-and microfibers. Applied Physics Letters. 95(4):043501., Number 4: AIP Publishing AbstractWebsite

Electrospun cellulose-based nano and microfibers and a nematic liquid crystal are used to assemble an electro-optical (EO) light-scattering device that shows enhanced characteristics when compared to similar devices. Based on the controlled scattering of light in the composite system, the device can achieve light transmission coefficients tunable from 1% up to around 89%. Simulation of the EO behavior indicates that the roughness of the polymer-liquid crystal interface is crucial for the optical performance of the device.

Rato, R, Ortigueira MD, Batista AG.  2009.  The Empirical Mode Decomposition an Useful Tool for Signal Analysis. New Signal Processing Research.. :455-475.: Nova Science Publishers, Inc Abstract

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Matos, C, Batista AG, Ortigueira MD.  2009.  FILTERS: Fractional vs Integer order. Symposium on Fractional Signals and Systems, Lisbon?09. Abstract

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Ortigueira, MD.  2009.  Fractional Derivatives and Linear Systems. Mobile Computing Research and Applications. :219-269.: Nova Science Publishers, Inc Abstract

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Leal, A, Monteiro J, Secca MF, Jordão C.  2009.  Functional brain mapping of ictal activity in gelastic epilepsy associated with hypothalamic hamartoma: A case report. Epilepsia. 50(6):1624-1631.
Ortigueira, MD, Trujillo JJ.  2009.  Generalized GL Fractional Derivative and its Laplace and Fourier Transform. ASME 2009 International Design Engineering Technical Conferences & Computers and Information in Engineering Conference IDETC?CIE 2009. Abstract

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Correia, DV, D'Orey F, Cardoso BA, Lança T, Grosso AR, DeBarros A, Martins LR, Barata JT, Silva-santos B.  2009.  Highly active microbial phosphoantigen induces rapid yet sustained MEK/Erk- and PI-3K/Akt-mediated signal transduction in anti-tumor human gammadelta T-cells. PloS one. 4:e5657., Number 5 AbstractWebsite

BACKGROUND:
The unique responsiveness of Vgamma9Vdelta2 T-cells, the major gammadelta subset of human peripheral blood, to non-peptidic prenyl pyrophosphate antigens constitutes the basis of current gammadelta T-cell-based cancer immunotherapy strategies. However, the molecular mechanisms responsible for phosphoantigen-mediated activation of human gammadelta T-cells remain unclear. In particular, previous reports have described a very slow kinetics of activation of T-cell receptor (TCR)-associated signal transduction pathways by isopentenyl pyrophosphate and bromohydrin pyrophosphate, seemingly incompatible with direct binding of these antigens to the Vgamma9Vdelta2 TCR. Here we have studied the most potent natural phosphoantigen yet identified, (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), produced by Eubacteria and Protozoa, and examined its gammadelta T-cell activation and anti-tumor properties.
METHODOLOGY/PRINCIPAL FINDINGS:
We have performed a comparative study between HMB-PP and the anti-CD3epsilon monoclonal antibody OKT3, used as a reference inducer of bona fide TCR signaling, and followed multiple cellular and molecular gammadelta T-cell activation events. We show that HMB-PP activates MEK/Erk and PI-3K/Akt pathways as rapidly as OKT3, and induces an almost identical transcriptional profile in Vgamma9(+) T-cells. Moreover, MEK/Erk and PI-3K/Akt activities are indispensable for the cellular effects of HMB-PP, including gammadelta T-cell activation, proliferation and anti-tumor cytotoxicity, which are also abolished upon antibody blockade of the Vgamma9(+) TCR Surprisingly, HMB-PP treatment does not induce down-modulation of surface TCR levels, and thereby sustains gammadelta T-cell activation upon re-stimulation. This ultimately translates in potent human gammadelta T-cell anti-tumor function both in vitro and in vivo upon transplantation of human leukemia cells into lymphopenic mice,
CONCLUSIONS/SIGNIFICANCE:
The development of efficient cancer immunotherapy strategies critically depends on our capacity to maximize anti-tumor effector T-cell responses. By characterizing the intracellular mechanisms of HMB-PP-mediated activation of the highly cytotoxic Vgamma9(+) T-cell subset, our data strongly support the usage of this microbial antigen in novel cancer clinical trials.

Pina, AS, Hussain A, Roque ACA.  2009.  An historical overview of drug discovery. Ligand-Macromolecule Interactions in Drug Discovery. (Roque, A. C. A., Ed.).:3-12., USA: Humana Press Inc. Abstract

Drug Discovery in modern times straddles three main periods. The first notable period can be traced to the nineteenth century where the basis of drug discovery relied on the serendipity of the medicinal chemists. The second period commenced around the early twentieth century when new drug structures were found, which contributed for a new era of antibiotics discovery. Based on these known structures, and with the development of powerful new techniques such as molecular modelling, combinatorial chemistry, and automated high-throughput screening, rapid advances occurred in drug discovery towards the end of the century. The period also was revolutionized by the emergence of recombinant DNA technology, where it became possible to develop potential drugs target candidates. With all the expansion of new technologies and the onset of the "Omics" revolution in the twenty-first century, the third period has kick-started with an increase in biopharmaceutical drugs approved by FDA/EMEA for therapeutic use.

Albuquerque, SS, Carret C, Grosso AR, Tarun AS, Peng X, Kappe SHII, Prudêncio M, Mota MM.  2009.  Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events. BMC Genomics. 10:270., Number 1 AbstractWebsite

BACKGROUND:
Plasmodium sporozoites migrate to the liver where they traverse several hepatocytes before invading the one inside which they will develop and multiply into thousands of merozoites. Although this constitutes an essential step of malaria infection, the requirements of Plasmodium parasites in liver cells and how they use the host cell for their own survival and development are poorly understood.
RESULTS:
To gain new insights into the molecular host-parasite interactions that take place during malaria liver infection, we have used high-throughput microarray technology to determine the transcriptional profile of P. berghei-infected hepatoma cells. The data analysis shows differential expression patterns for 1064 host genes starting at 6 h and up to 24 h post infection, with the largest proportion correlating specifically with the early stages of the infection process. A considerable proportion of those genes were also found to be modulated in liver cells collected from P. yoelii-infected mice 24 and 40 h after infection, strengthening the data obtained with the in vitro model and highlighting genes and pathways involved in the host response to rodent Plasmodium parasites.
CONCLUSION:
Our data reveal that host cell infection by Plasmodium sporozoites leads to a coordinated and sequential set of biological events, ranging from the initial stage of stress response up to the engagement of host metabolic processes and the maintenance of cell viability throughout infection.

Godinho, MH, Canejo JP, Pinto LFV, Borges JP, Teixeira PIC.  2009.  How to mimic the shapes of plant tendrils on the nano and microscale: spirals and helices of electrospun liquid crystalline cellulose derivatives. Soft Matter. 5(14):2772–2776., Number 14: Royal Society of Chemistry AbstractWebsite

We show that suspended nano and microfibres electrospun from liquid crystalline cellulosic solutions will curl into spirals if they are supported at just one end, or, if they are supported at both ends, will twist into a helix of one handedness over half of its length and of the opposite handedness over the other half, the two halves being connected by a short straight section. This latter phenomenon, known as perversion, is a consequence of the intrinsic curvature of the fibres and of a topological conservation law. Furthermore, agreement between theory and experiment can only be achieved if account is taken of the intrinsic torsion of the fibres. Precisely the same behaviour is known to be exhibited by the tendrils of climbing plants such as Passiflora edulis, albeit on a lengthscale of millimetres, i.e., three to four orders of magnitude larger than in our fibres. This suggests that the same basic, coarse-grained physical model is applicable across a range of lengthscales.

Roque, ACA.  2009.  Ligand-Macromolecule Interactions in Drug Discovery. , U.S.A.: Methods in Molecular Biology, Humana Press Inc.Website
Viciosa, MT, Correia NT, Sánchez SM, Ribelles GJL, Dionísio M.  2009.  Molecular Dynamics of Ethylene Glycol Dimethacrylate Glass Former: Influence of Different Crystallization Pathways. Journal of Phyiscal Chemsitry B. 113:14196-14208.Website
Ortigueira, MD.  2009.  On the Linear Scale Fractional Systems: An Application of the Fractional Quantum Derivative. On the Linear Scale Fractional Systems: An Application of the Fractional Quantum Derivative. Abstract

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Compagna, D, Derpmann S, Mauz K.  2009.  The Operation of Autonomous Mobile Robot Assistants in the Environment of Care Facilities Adopting a User-Centered Development Design. Enterprise and Work Innovation Studies. 5:11-24. AbstractWebsite

The successful development of autonomous mobile robot assistants depends significantly on the well-balanced reconcilements of the technically possible and the socially desirable. Based on empirical research 2 substantiated conclusions can be established for the suitability of "scenario-based design" (Rosson/Carroll 2003) for the successful development of mobile robot assistants and automated guided vehicles to be applied for service functions in stationary care facilities for seniors.

Pokkuluri, PR, Londer YY, Wood SJ, Duke NEC, Morgado L, Salgueiro CA, Schiffer M.  2009.  Outer membrane cytochrome c, OmcF, from Geobacter sulfurreducens: High structural similarity to an algal cytochrome c6. Proteins: Structure, Function, and Bioinformatics. 74(1):266-270. AbstractWebsite

No abstract included.

Boscolo, B, Leal SS, Salgueiro CA, Ghibaudi EM, Gomes CM.  2009.  The prominent conformational plasticity of lactoperoxidase: A chemical and pH stability analysis. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1794(7):1041-1048. AbstractWebsite

Lactoperoxidase (LPO) is a structurally complex and stable mammalian redox enzyme. Here we aim at evaluating the influence of ionic interactions and how these intertwine with the structural dynamics, stability and activity of LPO. In this respect, we have compared LPO guanidinium hydrochloride (GdmCl) and urea denaturation pathways and performed a detailed investigation on the effects of pH on the LPO conformational dynamics and stability. Our experimental findings using far-UV CD, Trp fluorescence emission and ESR spectroscopies clearly indicate that LPO charged-denaturation with GdmCl induced a sharp two-step process versus a three-step unfolding mechanism induced by urea. This differential effect between GdmCl and urea suggests that ionic interactions must play a rather prominent role in the stabilization of LPO. With both denaturants, the protein core was shown to retain activity up to near the respective Cm values. Moreover, a pH titration of LPO evidenced no significant conformational alterations or perturbation of heme activity within the 4 to 11 pH interval. In contrast, alterations of ionic interactions by poising LPO at pH 3, 2 and 12 resulted in a loss of secondary structure, loosening of tertiary contacts and loss of activity, which appear to be associated with the perturbation of the hydrophobic core, as evidenced by ANS binding, as well as disruption of the heme pocket demonstrated by optical and EPR spectroscopies. Overall, LPO is characterised by a high degree of peripheral structural plasticity without perturbation of the core heme moiety. The possible physiological meaning of such features is discussed.

Viciosa, MT, Correia N, Sánchez SM, Ribelles GJL, Carvalho AL, Romão MJ, Dionísio M.  2009.  Real-Time Monitoring of Molecular Dynamics of Ethylene Glycol Dimethacrylate Glass Former. journal of Physical Chemistry B. 113:14209-14217.Website
Moniz, AB.  2009.  Synthesis about a collaborative project on “Technology Assessment of Autonomous Systems”. Enterprise and Work Innovation Studies. 5:83-91. AbstractWebsite

The project started in 2009 with the support of DAAD in Germany and CRUP in Portugal under the “Collaborative German-Portuguese University Actions” programme. One central goal is the further development of a theory of technology assessment applied to robotics and autonomous systems in general that reflects in its methodology the changing conditions of knowledge production in modern societies and the emergence of new robotic technologies and of associated disruptive changes. Relevant topics here are handling broadened future horizons and new clusters of science and technology (medicine, engineering, interfaces, industrial automation, micro-devices, security and safety), as well as new governance structures in policy decision making concerning research and development (R&D).

Moniz, AB.  2009.  Synthesis about a collaborative project on “Technology Assessment of Autonomous Systems”. Enterprise and Work Innovation Studies. 5:83-91. AbstractWebsite

The project started in 2009 with the support of DAAD in Germany and CRUP in Portugal under the “Collaborative German-Portuguese University Actions” programme. One central goal is the further development of a theory of technology assessment applied to robotics and autonomous systems in general that reflects in its methodology the changing conditions of knowledge production in modern societies and the emergence of new robotic technologies and of associated disruptive changes. Relevant topics here are handling broadened future horizons and new clusters of science and technology (medicine, engineering, interfaces, industrial automation, micro-devices, security and safety), as well as new governance structures in policy decision making concerning research and development (R&D).

Henriques, C, Vidinha R, Botequim D, Borges JP, Silva JC.  2009.  A systematic study of solution and processing parameters on nanofiber morphology using a new electrospinning apparatus. Journal of nanoscience and nanotechnology. 9(6):3535–3545., Number 6: American Scientific Publishers AbstractWebsite

We assembled a new electrospinning apparatus and used poly(ethylene oxide) as a model polymer to perform a systematic study on the influence of solution and processing parameters on the morphology of electrospun nanofibers. Solution parameters studied were polymer concentration and molecular mass. The solvent used, 60 wt% water,40 wt% ethanol, was the same throughout the study. Processing parameters analyzed were: solution feed rate, needle tip-collector distance and electrostatic potential difference between the needle and collector. Solution viscosity increased both with polymer concentration and molecular mass. Polymer concentration plays a decisive role on the outcome of the electrospinning process: a low concentration led to the formation of beaded fibers; an intermediate concentration yielded good quality fibers; a high concentration resulted in a bimodal size distribution and at even higher concentration a distributed deposition. Fiber diameter increased with polymer molecular mass and higher molecular masses are associated with a higher frequency of splaying events. Fiber diameter increased linearly with solution feed rate. While an increase in needle-collector distance represents a weaker electric field, a greater distance to be covered by the fibers and a longer flight time, presumably favoring the formation of thinner fibers, as solvent evaporation leads to a local increase of concentration and viscosity, viscoelastic forces opposing stretching caused an increase of fiber diameter with needle-collector distance. A higher voltage applied at the needle is associated with a higher charging of the polymer and a higher electrical current through it ultimately leading to incomplete solvent evaporation and merged fibers being produced. Controlling the charging of the polymer independently of the electric field strength was achieved by applying a voltage to the collector while distance and potential difference were kept constant. The increased electrostatic repulsion associated with an increase of the high voltage applied to the needle led to the disappearance of merged fibers.

Fonseca, BM, Saraiva IH, Paquete CM, Soares CM, Pacheco I, Salgueiro CA, Louro RO.  2009.  The tetraheme cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the hemes. Journal of Biological Inorganic Chemistry. 14(3):375-385. AbstractWebsite

Bacteria of the genus Shewanella contain an abundant small tetraheme cytochrome in their periplasm when growing anaerobically. Data collected for the protein isolated from S. oneidensis MR-1 and S. frigidimarina indicate differences in the order of oxidation of the hemes. A detailed thermodynamic characterization of the cytochrome from S. oneidensis MR-1 in the physiological pH range was performed, with data collected in the pH range 5.5-9.0 from NMR experiments using partially oxidized samples and from redox titrations followed by visible spectroscopy. These data allow the parsing of the redox and redox-protonation interactions that occur during the titration of hemes. The results show that electrostatic effects dominate the heme-heme interactions, in agreement with modest redox-linked structural modifications, and protonation has a considerable influence on the redox properties of the hemes in the physiological pH range. Theoretical calculations using the oxidized and reduced structures of this protein reveal that the bulk redox-Bohr effect arises from the aggregate fractional titration of several of the heme propionates. This detailed characterization of the thermodynamic properties of the cytochrome shows that only a few of the multiple microscopic redox states that the protein can access are significantly populated at physiological pH. On this basis a functional pathway for the redox activity of the small tetraheme cytochrome from S. oneidensis MR-1 is proposed, where reduction and protonation are thermodynamically coupled in the physiological range. The differences between the small tetraheme cytochromes from the two organisms are discussed in the context of their biological role.

Morgado, L, Fernandes AP, Londer YY, Pokkuluri PR, Schiffer M, Salgueiro CA.  2009.  Thermodynamic characterization of the redox centres in a representative domain of a novel c-type multihaem cytochrome. Biochemical Journal. 420(3):485-492. AbstractWebsite

Multihaem cytochromes that could form protein “nanowires” were identified in the Geobacter sulfurreducens genome, and represent a new type of multihaem cytochrome. The sequences of these proteins, two with 12 haems (GSU1996, GSU0592) and one with 27 haems (GSU2210), suggest that they are formed with domains homologous to the trihaem cytochrome c7. Although all three haems have bis-His co-ordination in cytochromes c7, in each domain of the above polymers, the haem equivalent to haem IV has His-Met co-ordination. We previously determined the structure and measured the macroscopic redox potential of one representative domain (domain C) of a dodecahaem cytochrome (GSU1996). In the present study, the microscopic redox properties of the individual haem groups of domain C were determined using NMR and UV–visible spectroscopies. The reduction potentials of the haems for the fully reduced and protonated protein are different from each other (haem I, −106 mV; haem III, −136 mV; and haem IV, −125 mV) and are strongly modulated by redox interactions. This result is rather surprising since the His-Met co-ordinated haem IV does not have the highest potential as was expected. The polypeptide environment of each haem group and the strong haem pairwise redox interactions must play a dominant role in controlling the individual haem potentials. The strong redox interactions between the haems extend the range of their operating potentials at physiological pH (haem I, −71 mV, haem III, −146 mV and haem IV, −110 mV). Such a modulation in haem potentials is likely to have a functional significance in the metabolism of G. sulfurreducens.