Thu, 24 Jul 2008 23:02:33 BST CiteULike: Author Marques http://www.citeulike.org/author/Marques CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/group/5469/article/3039135 <i>Renewable and Sustainable Energy Reviews, Vol. 9, No. 2. (April 2005), pp. 149-167.</i><br /><br />Traditionally, the decision criteria when analyzing hydropower plants projects, has been based mostly on technical and economical analyses focused on the electric production aspects. Nowadays a broader approach is necessary, which takes into consideration multiple impacts such as:- Energy impacts;- Water resources impacts;- Social-economics development impacts;- Agricultural sector impacts;- Environmental impacts. In order to establish a ranking of the 14 new medium and large (power above 10 MW) hydropower plants identified in the Centre Region of Portugal, a multi-disciplinary team of Coimbra University carried out a study about the impacts associated to each of the hydropower plants. The analysis considered the different aspects associated to the multi-functional character of the hydropower plants. The overall ranking of the hydropower plants was achieved using a methodology that integrates the different aspects using a weighing function [2]. Multi-impact evaluation of new medium and large hydropower plants in Portugal centre region Aníbal de Almeida Pedro Moura Alféu Marques José de Almeida doi:10.1016/j.rser.2004.01.015 Renewable and Sustainable Energy Reviews, Vol. 9, No. 2. (April 2005), pp. 149-167. 2008-07-24T10:42:24-00:00 2005 Renewable and Sustainable Energy Reviews 9 2 149 167 hydropower portugal http://www.citeulike.org/user/djmonstermo/article/3021135 <i>Blood, Vol. 74, No. 1. (July 1989), pp. 326-333.</i><br /><br />The mechanism of effect of high-dose intravenous immunoglobulin (IVIG) therapy in immune cytopenias is incompletely known. One of the leading theories ascribes the short-term effects of IVIG to the competition of infused IVIG for Fc receptors, thereby inhibiting IgG-mediated clearance. Using a system independent of IgG-Fc receptor interactions, we examined another potential mechanism of IVIG action. Guinea pigs were infused with a human IVIG preparation at 600 mg/kg/day for two consecutive days. Parallel groups of animals were treated with the same volume and/or concentration of saline and albumin. Clearance of IgM-sensitized guinea pig erythrocytes, which is wholly complement dependent, was significantly retarded in animals treated with high-dose IVIG. The effect was specific for IVIG, since human albumin (as a second foreign protein) failed to change the clearance of IgM-sensitized guinea pig erythrocytes. Experiments in which IVIG-treated animals were subjected to pre- and posttreatment clearance studies revealed heterogeneity among individual animals in respect to their response to IVIG infusions. Decrease of available plasma complement components did not account for the effect, since both C3 and CH50 values remained unchanged after IVIG treatment, despite rising levels of IVIG in sera of treated animals. The results of in vitro C3 uptake studies and the effect of IVIG on clearance of preopsonized cells suggest that IVIG produces a kinetic depression of C3 uptake and modifies the process of complement fragment deposition on erythrocytes. A generalized effect on mononuclear phagocytes is less likely but cannot be wholly ruled out. These studies establish another potential mechanism of IVIG action and suggest extension of its use to other complement-mediated diseases. High-dose intravenous immunoglobulin modifies complement-mediated in vivo clearance. M Basta PF Langlois M Marques MM Frank LF Fries Blood, Vol. 74, No. 1. (July 1989), pp. 326-333. 2008-07-19T17:30:54-00:00 1989 Blood 0006-4971 74 1 326 333 ivig http://www.citeulike.org/user/JeremyZucker/article/3007783 <i>Applied Physics Letters, Vol. 76, No. 9. (2000), pp. 1197-1199.</i><br /><br />View this record in Web of Science Quantum-dot concentrator and thermodynamic model for the global redshift Keith Barnham Jose Marques John Hassard Paul O'Brien Applied Physics Letters, Vol. 76, No. 9. (2000), pp. 1197-1199. 2008-07-16T07:59:26-00:00 2000 Applied Physics Letters 76 9 1197 1199 AIP solar-power http://www.citeulike.org/user/natstreet/article/2880804 <i>PLoS Biology, Vol. 6, No. 6. (1 June 2008), e140.</i><br /><br />Gene duplication was prevalent during hominoid evolution, yet little is known about the functional fate of new ape gene copies. We characterized the CDC14B cell cycle gene and the functional evolution of its hominoid-specific daughter gene, CDC14Bretro. We found that CDC14B encodes four different splice isoforms that show different subcellular localizations (nucleus or microtubule-associated) and functional properties. A microtubular CDC14B variant spawned CDC14Bretro through retroposition in the hominoid ancestor 18–25 million years ago (Mya). CDC14Bretro evolved brain-/testis-specific expression after the duplication event and experienced a short period of intense positive selection in the African ape ancestor 7–12 Mya. Using resurrected ancestral protein variants, we demonstrate that by virtue of amino acid substitutions in distinct protein regions during this time, the subcellular localization of CDC14Bretro progressively shifted from the association with microtubules (stabilizing them) to an association with the endoplasmic reticulum. CDC14Bretro evolution represents a paradigm example of rapid, selectively driven subcellular relocalization, thus revealing a novel mode for the emergence of new gene function. Birth and Rapid Subcellular Adaptation of a Hominoid-Specific CDC14 Protein Lia Rosso Ana Marques Manuela Weier Nelle Lambert Marie-Alexandra Lambot Pierre Vanderhaeghen Henrik Kaessmann doi:10.1371/journal.pbio.0060140 PLoS Biology, Vol. 6, No. 6. (1 June 2008), e140. 2008-06-10T19:41:00-00:00 2008 PLoS Biology 6 6 e140 no-tag http://www.citeulike.org/group/1906/article/2985375 <i>J. Biol. Chem., Vol. 281, No. 17. (28 April 2006), pp. 11981-11991.</i><br /><br />When Pseudomonas putida KT2440 cells encounter toluene in the growth medium, they perceive it simultaneously as a potential nutrient to be metabolized, as a membrane-damaging toxic drug to be extruded, and as a macromolecule-disrupting agent from which to protect proteins. Each of these inputs requires a dedicated transcriptional response that involves a large number of genes. We used DNA array technology to decipher the interplay between these responses in P. putida KT2440 subjected to a short challenge (15 min) with toluene. We then compared the results with those in cells exposed to o-xylene (a non-biodegradable toluene counterpart) and 3-methylbenzoate (a specific substrate of the lower TOL pathway of the P. putida pWW0 plasmid). The resulting expression profiles suggest that the bulk of the available transcriptional machinery is reassigned to endure general stress, whereas only a small share of the available machinery is redirected to the degradation of the aromatic compounds. Specifically, both toluene and o-xylene induce the TOL pathways and a dedicated but not always productive metabolic program. Similarly, 3-methylbenzoate induces the expression not only of the lower meta pathway but also of the non-productive and potentially deleterious genes for the metabolism of (nonsubstituted) benzoate. In addition, toluene (and to a lesser extent o-xylene) inhibit motility functions as an unequivocal response to aromatic toxicity. We argue that toluene is sensed by P. putida KT2440 as a stressor rather than as a nutrient and that the inhibition by the aromatic compounds of many functions we tested is the tradeoff for activating stress tolerance genes at a minimal cost in terms of energy. 10.1074/jbc.M509848200 Transcriptional Tradeoff between Metabolic and Stress-response Programs in Pseudomonas putida KT2440 Cells Exposed to Toluene Patricia Dominguez-Cuevas Jose-Eduardo Gonzalez-Pastor Silvia Marques Juan-Luis Ramos Victor de Lorenzo doi:10.1074/jbc.M509848200 J. Biol. Chem., Vol. 281, No. 17. (28 April 2006), pp. 11981-11991. 2008-07-10T14:49:44-00:00 2006 J. Biol. Chem. 281 17 11981 11991 for-the-review integration regulation stress transcription http://www.citeulike.org/group/3565/article/2959252 <i>BMC Genomics, Vol. 9 (03 July 2008), 318.</i> A genome-wide 20K citrus microarray for gene expression analysis Angeles Martinez-Godoy Nuria Mauri Jose Juarez Carmen Marques Julia Santiago Javier Forment Jose Gadea doi:10.1186/1471-2164-9-318 BMC Genomics, Vol. 9 (03 July 2008), 318. 2008-07-03T13:47:00-00:00 2008 BMC Genomics 1471-2164 9 318 citrus microarray plant http://www.citeulike.org/user/bakakaj/article/2933185 <i>J. Antimicrob. Chemother., Vol. 56, No. 4. (1 October 2005), pp. 665-671.</i><br /><br />Objectives: To utilize bioluminescence to follow the effect of ciprofloxacin challenge on Pseudomonas aeruginosa biofilms. Methods: The Sorbarod continuous perfusion culture system was used for the cultivation of biofilms of a self-bioluminescent strain of P. aeruginosa PAO1. Biofilms were challenged with ciprofloxacin (5 mg/L) in the perfusing medium for 3 h and allowed to recover to pre-challenge population levels before initiation of a second 3 h challenge. In addition to determining eluate and biofilm cell survival by conventional viable plate counts, light output was monitored via a luminometer and a low-light-level ICCD camera, to give an indication of metabolism. The effect of drug challenge on biofilm structure was investigated using an environmental scanning electron microscope, which allowed discernment of changes to the three-dimensional biofilm architecture. Results: On challenge with ciprofloxacin, eluate light output measurements declined to a lesser extent than viable counts for the same samples and also indicated that post-challenge recovery of the biofilm metabolism did not occur as rapidly as suggested by viable count data. Photon detection by ICCD camera allowed real-time, non-invasive imaging of metabolic activity within intact biofilms. Conclusions: The application of a bioluminescent reporter strain to biofilm research provides valuable real-time positional data on the efficacy of anti-biofilm treatment strategies. 10.1093/jac/dki285 Discrepancy between viable counts and light output as viability measurements, following ciprofloxacin challenge of self-bioluminescent Pseudomonas aeruginosa biofilms Claudia Marques Vyvyan Salisbury John Greenman Karen Bowker Shona Nelson doi:10.1093/jac/dki285 J. Antimicrob. Chemother., Vol. 56, No. 4. (1 October 2005), pp. 665-671. 2008-06-27T09:42:53-00:00 2005 J. Antimicrob. Chemother. 56 4 665 671 aeruginosa bioluminescence http://www.citeulike.org/user/whitew0a/article/2925700 <i>The Journal of investigative dermatology, Vol. 126, No. 1. (January 2006), pp. 69-73.</i><br /><br />Mice lacking the desmosome protein Perp exhibit blistering in their stratified epithelia and display postnatal lethality. However, it is unclear if these phenotypes are strictly related to Perp function in stratified epithelia, as Perp expression is not restricted to these tissues during embryogenesis, and certain desmosomal blistering diseases such as pemphigus vulgaris and pemphigus foliaceus have non-cell-intrinsic bases. Furthermore, we show here that Perp is expressed in the heart, raising the possibility that defects in heart function could account for lethality in the Perp-deficient mice. To determine conclusively if Perp function in stratified epithelia is crucial for postnatal survival and epithelial adhesion, we specifically ablated Perp in stratified epithelia by breeding conditional Perp knockout mice to keratin 5 (K5)-Cre transgenic mice. We found that the majority of mice lacking Perp in stratified epithelia die within 10 days after birth, accompanied by blistering and hyperproliferation in the epithelia, similar to the constitutive Perp null mice. Together, these findings indicate that Perp's requirement for both viability and epithelial integrity reflects a role in the stratified epithelial compartment. The requirement for perp in postnatal viability and epithelial integrity reflects an intrinsic role in stratified epithelia. MR Marques RA Ihrie JS Horner LD Attardi doi:10.1038/sj.jid.5700032 The Journal of investigative dermatology, Vol. 126, No. 1. (January 2006), pp. 69-73. 2008-06-25T11:17:24-00:00 2006 The Journal of investigative dermatology 0022-202X 126 1 69 73 desmosome epithelium p63 perp http://www.citeulike.org/user/whitew0a/article/2925698 <i>Cell, Vol. 120, No. 6. (25 March 2005), pp. 843-856.</i><br /><br />p63 is a master regulator of stratified epithelial development that is both necessary and sufficient for specifying this multifaceted program. We show here that Perp, a tetraspan membrane protein originally identified as an apoptosis-associated target of the p53 tumor suppressor, is the first direct target of p63 clearly involved in mediating this developmental program in vivo. During embryogenesis, Perp is expressed in an epithelial pattern, and its expression depends on p63. Perp-/- mice die postnatally, with dramatic blistering in stratified epithelia symptomatic of compromised adhesion. Perp localizes specifically to desmosomes, adhesion junctions important for tissue integrity, and numerous structural defects in desmosomes are observed in Perp-deficient skin, suggesting a role for Perp in promoting the stable assembly of desmosomal adhesive complexes. These findings demonstrate that Perp is a key effector in the p63 developmental program, playing an essential role in an adhesion subprogram central to epithelial integrity and homeostasis. Perp is a p63-regulated gene essential for epithelial integrity. RA Ihrie MR Marques BT Nguyen JS Horner C Papazoglu RT Bronson AA Mills LD Attardi doi:10.1016/j.cell.2005.01.008 Cell, Vol. 120, No. 6. (25 March 2005), pp. 843-856. 2008-06-25T11:16:20-00:00 2005 Cell 0092-8674 120 6 843 856 desmosome epithelium p63 perp http://www.citeulike.org/user/fhsantanna/article/2919527 <i>Nature, Vol. 406, No. 6792. (13 July 2000), pp. 151-159.</i><br /><br />Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. AJ Simpson FC Reinach P Arruda FA Abreu M Acencio R Alvarenga LM Alves JE Araya GS Baia CS Baptista MH Barros ED Bonaccorsi S Bordin JM Bové MR Briones MR Bueno AA Camargo LE Camargo DM Carraro H Carrer NB Colauto C Colombo FF Costa MC Costa CM Costa-Neto LL Coutinho M Cristofani E Dias-Neto C Docena H El-Dorry AP Facincani AJ Ferreira VC Ferreira JA Ferro JS Fraga SC França MC Franco M Frohme LR Furlan M Garnier GH Goldman MH Goldman SL Gomes A Gruber PL Ho JD Hoheisel ML Junqueira EL Kemper JP Kitajima JE Krieger EE Kuramae F Laigret MR Lambais LC Leite EG Lemos MV Lemos SA Lopes CR Lopes JA Machado MA Machado AM Madeira HM Madeira CL Marino MV Marques EA Martins EM Martins AY Matsukuma CF Menck EC Miracca CY Miyaki CB Monteriro-Vitorello DH Moon MA Nagai AL Nascimento LE Netto A Nhani FG Nobrega LR Nunes MA Oliveira MC de Oliveira RC de Oliveira DA Palmieri A Paris BR Peixoto GA Pereira HA Pereira JB Pesquero RB Quaggio PG Roberto V Rodrigues AJ de M Rosa VE de Rosa RG de Sá RV Santelli HE Sawasaki AC da Silva AM da Silva FR da Silva WA da Silva JF da Silveira ML Silvestri WJ Siqueira AA de Souza AP de Souza MF Terenzi D Truffi SM Tsai MH Tsuhako H Vallada MA Van Sluys S Verjovski-Almeida AL Vettore MA Zago M Zatz J Meidanis JC Setubal doi:10.1038/35018003 Nature, Vol. 406, No. 6792. (13 July 2000), pp. 151-159. 2008-06-23T18:08:58-00:00 2000 Nature 0028-0836 406 6792 151 159 genome pathogen vegetal xyllella http://www.citeulike.org/user/shoshin/article/347392 <i>PLoS Biol, Vol. 3, No. 11. (11 October 2005)</i><br /><br />The origin of new genes through gene duplication is fundamental to the evolution of lineage- or species-specific phenotypic traits. In this report, we estimate the number of functional retrogenes on the lineage leading to humans generated by the high rate of retroposition (retroduplication) in primates. Extensive comparative sequencing and expression studies coupled with evolutionary analyses and simulations suggest that a significant proportion of recent retrocopies represent bona fide human genes. We estimate that at least one new retrogene per million years emerged on the human lineage during the past approximately 63 million years of primate evolution. Detailed analysis of a subset of the data shows that the majority of retrogenes are specifically expressed in testis, whereas their parental genes show broad expression patterns. Consistently, most retrogenes evolved functional roles in spermatogenesis. Proteins encoded by X chromosome-derived retrogenes were strongly preserved by purifying selection following the duplication event, supporting the view that they may act as functional autosomal substitutes during X-inactivation of late spermatogenesis genes. Also, some retrogenes acquired a new or more adapted function driven by positive selection. We conclude that retroduplication significantly contributed to the formation of recent human genes and that most new retrogenes were progressively recruited during primate evolution by natural and/or sexual selection to enhance male germline function. Emergence of Young Human Genes after a Burst of Retroposition in Primates. Ana Claudia Marques Isabelle Dupanloup Nicolas Vinckenbosch Alexandre Reymond Henrik Kaessmann doi:10.1371/journal.pbio.0030357 PLoS Biol, Vol. 3, No. 11. (11 October 2005) 2005-10-11T04:57:16-00:00 2005 PLoS Biol 1545-7885 3 11 gene_duplication genomics human_evolution selfish_dna http://www.citeulike.org/user/cbeltran/article/2862781 <i>Multimedia, IEEE Transactions on, Vol. 8, No. 4. (2006), pp. 761-774.</i><br /><br />In this paper, we propose novel methods to evaluate the performance of object detection algorithms in video sequences. This procedure allows us to highlight characteristics (e.g., region splitting or merging) which are specific of the method being used. The proposed framework compares the output of the algorithm with the ground truth and measures the differences according to objective metrics. In this way it is possible to perform a fair comparison among different methods, evaluating their strengths and weaknesses and allowing the user to perform a reliable choice of the best method for a specific application. We apply this methodology to segmentation algorithms recently proposed and describe their performance. These methods were evaluated in order to assess how well they can detect moving regions in an outdoor scene in fixed-camera situations. Performance evaluation of object detection algorithms for video surveillance JC Nascimento JS Marques doi:10.1109/TMM.2006.876287 Multimedia, IEEE Transactions on, Vol. 8, No. 4. (2006), pp. 761-774. 2008-06-04T22:11:41-00:00 2006 Multimedia, IEEE Transactions on 8 4 761 774 no-tag http://www.citeulike.org/user/Quarem/article/2902932 <i>Journal of Applied Physics, Vol. 96, No. 3. (2004), pp. 1398-1408.</i><br /><br />View This Record in Scopus Zinc oxide as an ozone sensor R Martins E Fortunato P Nunes I Ferreira A Marques M Bender N Katsarakis V Cimalla G Kiriakidis Journal of Applied Physics, Vol. 96, No. 3. (2004), pp. 1398-1408. 2008-06-17T18:01:44-00:00 2004 Journal of Applied Physics 96 3 1398 1408 AIP sensor sputter zno http://www.citeulike.org/user/dchen/article/1175923 <i>Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 75, No. 2. (2007)</i><br /><br />The shapes of flat pebbles may be characterized in terms of the statistical distribution of curvatures measured along their contours. We illustrate this method for clay pebbles eroded in a controlled laboratory apparatus, and also for naturally occurring rip-up clasts formed and eroded in the Mont St.-Michel bay. We find that the curvature distribution allows finer discrimination than traditional measures of aspect ratios. Furthermore, it connects to the microscopic action of erosion processes that are typically faster at protruding regions of high curvature. We discuss in detail how the curvature may be reliably deduced from digital photographs. Shape and erosion of pebbles DJ Durian H Bideaud P Duringer AP Schroder CM Marques doi:10.1103/PhysRevE.75.021301 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 75, No. 2. (2007) 2007-03-19T13:52:50-00:00 2007 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 75 2 APS 2007 cool durian grains pre qualif2 shape http://www.citeulike.org/user/deves/article/2847458 <i>Cerebellum (London, England), Vol. 1, No. 4. (December 2002), pp. 259-263.</i><br /><br />Cell proliferation is an essential force to build up the size, shape, and function of an organ. This force is particularly prominent in the production of the cerebellar granule neurons, which represent 80% of all brain neurons. Extensive cell biological and tissue transplantation studies have uncovered both long-range diffusible and local cell-cell, contact-dependent growth cues for the granular neurons. The assignment of specific gene products to their contributions to the genesis of the granular neurons is greatly facilitated by in vitro culture assays and knock-out mouse analyses. Among them, the Growth arrest specific gene 1 (Gas1), a known negative regulator of the cell cycle, was shown to have profound influence on the production of the granule cells. Our aim here is to review the contributions of Gas1 and a few other selected genes and put them into a more comprehensive framework, though it may be speculative at times, of granule cell proliferation regulation. Growth arrest specific gene 1: a fuel for driving growth in the cerebellum. G Marques CM Fan Cerebellum (London, England), Vol. 1, No. 4. (December 2002), pp. 259-263. 2008-05-30T14:47:21-00:00 2002 Cerebellum (London, England) 1473-4222 1 4 259 263 gas1 http://www.citeulike.org/user/psique/article/2838060 <i>Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Vol. 1782, No. 6. (June 2008), pp. 363-369.</i><br /><br />The sirtuins are a family of enzymes which control diverse and vital cellular functions, including metabolism and aging. Manipulations of sirtuin activities cause activation of anti-apoptotic, anti-inflammatory, anti-stress responses, and the modulation of an aggregation of proteins involved in neurodegenerative disorders. Recently, sirtuins were found to be disease-modifiers in various models of neurodegeneration. However, almost in all instances, the exact mechanisms of neuroprotection remain elusive. Nevertheless, the manipulation of sirtuin activities is appealing as a novel therapeutic strategy for the treatment of currently fatal human disorders such as Alzheimer's and Parkinson's diseases. Here, we review current data which support the putative therapeutic roles of sirtuin in aging and in neurodegenerative diseases and the feasibility of the development of sirtuin-based therapies. Therapeutic role of sirtuins in neurodegenerative disease Tiago Outeiro Oldriska Marques Aleksey Kazantsev doi:10.1016/j.bbadis.2008.02.010 Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Vol. 1782, No. 6. (June 2008), pp. 363-369. 2008-05-27T18:48:02-00:00 2008 Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease 1782 6 363 369 neurodegeneration sirtuins http://www.citeulike.org/user/dcastro/article/2822768 <i>Antennas and Propagation, IEEE Transactions on, Vol. 51, No. 10. (2003), pp. 2572-2581.</i><br /><br />This paper develops a quasi-analytical and self-consistent model to compute the polarizabilities of split ring resonators (SRRs). An experimental setup is also proposed for measuring the magnetic polarizability of these structures. Experimental data are provided and compared with theoretical results computed following the proposed model. By using a local field approach, the model is applied to the obtaining of the dispersion characteristics of discrete negative magnetic permeability and left-handed metamaterials. Two types of SRRs, namely, the so-called edge coupled- and broadside coupled- SRRs, have been considered. A comparative analysis of these two structures has been carried out in connection with their suitability for the design of metamaterials. Advantages and disadvantages of both structures are discussed. Comparative analysis of edge- and broadside- coupled split ring resonators for metamaterial design - theory and experiments R Marques F Mesa J Martel F Medina doi:10.1109/TAP.2003.817562 Antennas and Propagation, IEEE Transactions on, Vol. 51, No. 10. (2003), pp. 2572-2581. 2008-05-22T10:36:11-00:00 2003 Antennas and Propagation, IEEE Transactions on 51 10 2572 2581 metamaterial srr http://www.citeulike.org/user/dchen/article/2767637 <i>Physical Review Letters, Vol. 100, No. 10. (2008)</i><br /><br />We introduce a general methodology based on magnetic colloids to study the recognition kinetics of tethered biomolecules. Access to the full kinetics of the reaction is provided by an explicit measure of the time evolution of the reactant densities. Binding between a single ligand and its complementary receptor is here limited by the colloidal rotational diffusion. It occurs within a binding distance that can be extracted by a reaction-diffusion theory that properly accounts for the rotational Brownian dynamics. Our reaction geometry allows us to probe a large diversity of bioadhesive molecules and tethers, thus providing a quantitative guidance for designing more efficient reactive biomimetic surfaces, as required for diagnostic, therapeutic, and tissue engineering techniques. Measuring the Kinetics of Biomolecular Recognition with Magnetic Colloids Cohen Tannoudji E Bertrand J Baudry C Robic C Goubault M Pellissier A Johner F Thalmann Lee CM Marques J Bibette doi:10.1103/PhysRevLett.100.108301 Physical Review Letters, Vol. 100, No. 10. (2008) 2008-05-07T23:01:32-00:00 2008 Physical Review Letters 100 10 APS 2008 colloids magnetic http://www.citeulike.org/user/rice/article/2764035 <i>Applied Physics Letters, Vol. 85, No. 13. (2004), pp. 2541-2543.</i> Wide-bandgap high-mobility ZnO thin-film transistors produced at room temperature Elvira Fortunato Pedro Barquinha Ana Pimentel Alexandra Gon\ccalves António Marques Rodrigo Martins Luis Pereira Applied Physics Letters, Vol. 85, No. 13. (2004), pp. 2541-2543. 2008-05-07T06:52:34-00:00 2004 Applied Physics Letters 85 13 2541 2543 AIP apl http://www.citeulike.org/user/rice/article/2711525 <i>Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Vol. 180, No. 1-4. (June 2001), pp. 12-16.</i> Atomistic modeling of the effects of dose and implant temperature on dopant diffusion and amorphization in Si Lourdes Pelaz Luis Marques George Gilmer Martin Jaraiz Juan Barbolla doi:10.1016/S0168-583X(01)00390-1 Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Vol. 180, No. 1-4. (June 2001), pp. 12-16. 2008-04-24T04:53:03-00:00 2001 Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 180 1-4 12 16 ion-implanted http://www.citeulike.org/user/pverstra/article/2694782 <i>(1999)</i><br /><br />. A recent adaptive algorithm, named Ant System, is introduced and used to solve the problem of job shop scheduling. The algorithm was first introduced by Dorigo, Maniezzo and Colorni in 1991 and is derived from the foraging and recruiting behaviour observed in an ant colony. It can be applied to combinatorial optimisation problems. This paper outlines the algorithm's implementation and performance when applied to job shop scheduling. The algorithm parameter settings seem to play a crucial role ... Ant Colony Optimisation for Job Shop Scheduling S van der Zwaan C Marques (1999) 2008-04-21T09:36:48-00:00 1999 aco scheduling http://www.citeulike.org/user/aec187/article/2678415 <i>Neurobiology of Learning and Memory, Vol. 88, No. 3. (October 2007), pp. 381-385.</i><br /><br />Transthyretin (TTR) is a plasma and cerebrospinal fluid carrier for thyroxine and retinol, described also to sequester the amyloid beta peptide. TTR levels have been described as decreased in the cerebrospinal fluid of patients with Alzheimer's disease. In order to investigate the role of TTR in learning and memory, we studied young adult and old TTR-null 129/Sv mice for cognitive performance. In the absence of TTR, 5-month-old mice display spatial reference memory impairment when compared to age-matched wild-type mice. Interestingly, while aging in wild-type mice is associated with a worsening reference memory performance, TTR-null mice show no further impairment with increasing age. As a result, no significant differences were found in this spatial reference task in old mice. Our data show that the absence of TTR seems to accelerate the poorer cognitive performance normally associated with aging. Transthyretin influences spatial reference memory João Sousa Fernanda Marques Eduardo Dias-Ferreira João Cerqueira Nuno Sousa Joana Palha doi:10.1016/j.nlm.2007.07.006 Neurobiology of Learning and Memory, Vol. 88, No. 3. (October 2007), pp. 381-385. 2008-04-16T15:58:51-00:00 2007 Neurobiology of Learning and Memory 88 3 381 385 alzheimers animal learning memory spatial http://www.citeulike.org/user/jyuh/article/2673393 <i>Clin J Am Soc Nephrol, Vol. 3, No. 2. (1 March 2008), pp. 348-354.</i><br /><br />Background and objectives: For addressing the influence of muscle mass on serum and urinary creatinine and serum cystatin C, body composition was assessed by skinfold thickness measurement and bioelectrical impedance analyses. Design, setting, participants, & measurements: A total of 170 healthy individuals (92 women, 78 men) were classified as sedentary or with mild or moderate/intense physical activity. Blood, 24-h urine samples, and 24-h food recall were obtained from all individuals. Results: Serum and urinary creatinine correlated significantly with body weight, but the level of correlation with lean mass was even greater. There was no significant correlation between body weight and lean mass with cystatin C. Individuals with moderate/intense physical activity presented significantly lower mean body mass index (23.1 +/- 2.5 versus 25.7 +/- 3.9 kg/m2) and higher lean mass (55.3 +/- 10.0 versus 48.5 +/- 10.4%), serum creatinine (1.04 +/- 0.12 versus 0.95 +/- 0.17 mg/dl), urinary creatinine (1437 +/- 471 versus 1231 +/- 430 mg/24 h), protein intake (1.4 +/- 0.6 versus 1.1 +/- 0.6 g/kg per d), and meat intake (0.7 +/- 0.3 versus 0.5 +/- 0.4 g/kg per d) than the sedentary individuals. Conversely, mean serum cystatin did not differ between these two groups. A multivariate analysis of covariance showed that lean mass was significantly related to serum and urinary creatinine but not with cystatin, even after adjustment for protein/meat intake and physical activity. Conclusions: Cystatin C may represent a more adequate alternative to assess renal function in individuals with higher muscle mass when mild kidney impairment is suspected. 10.2215/CJN.02870707 Influence of Muscle Mass and Physical Activity on Serum and Urinary Creatinine and Serum Cystatin C Alessandra Baxmann Marion Ahmed Natalia Marques Viviane Menon Aparecido Pereira Gianna Kirsztajn Ita Heilberg doi:10.2215/CJN.02870707 Clin J Am Soc Nephrol, Vol. 3, No. 2. (1 March 2008), pp. 348-354. 2008-04-15T13:06:46-00:00 2008 Clin J Am Soc Nephrol 3 2 348 354 no-tag http://www.citeulike.org/user/rschulz/article/2622902 <i>PLoS Biology, Vol. 6, No. 4. (1 April 2008), e80.</i><br /><br />Mammalian sex chromosomes stem from ancestral autosomes and have substantially differentiated. It was shown that X-linked genes have generated duplicate intronless gene copies (retrogenes) on autosomes due to this differentiation. However, the precise driving forces for this out-of-X gene “movement” and its evolutionary onset are not known. Based on expression analyses of male germ-cell populations, we here substantiate and extend the hypothesis that autosomal retrogenes functionally compensate for the silencing of their X-linked housekeeping parental genes during, but also after, male meiotic sex chromosome inactivation (MSCI). Thus, sexually antagonistic forces have not played a major role for the selective fixation of X-derived gene copies in mammals. Our dating analyses reveal that although retrogenes were produced ever since the common mammalian ancestor, selectively driven retrogene export from the X only started later, on the placental mammal (eutherian) and marsupial (metatherian) lineages, respectively. Together, these observations suggest that chromosome-wide MSCI emerged close to the eutherian–marsupial split approximately 180 million years ago. Given that MSCI probably reflects the spread of the recombination barrier between the X and Y, crucial for their differentiation, our data imply that these chromosomes became more widely differentiated only late in the therian ancestor, well after the divergence of the monotreme lineage. Thus, our study also provides strong independent support for the recent notion that our sex chromosomes emerged, not in the common ancestor of all mammals, but rather in the therian ancestor, and therefore are much younger than previously thought. Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes Lukasz Potrzebowski Nicolas Vinckenbosch Ana Marques Frédéric Chalmel Bernard Jégou Henrik Kaessmann doi:10.1371/journal.pbio.0060080 PLoS Biology, Vol. 6, No. 4. (1 April 2008), e80. 2008-04-02T10:27:25-00:00 2008 PLoS Biology 6 4 e80 chrx evolution msci retrotransposition sex http://www.citeulike.org/user/djkt/article/2528548 <i>Genome Biology, Vol. 9 (12 March 2008), R54.</i> Functional diversification of duplicate genes through subcellular adaptation of encoded proteins Ana Marques Nicolas Vinckenbosh David Brawand Henrik Kaessmann doi:10.1186/gb-2008-9-3-r54 Genome Biology, Vol. 9 (12 March 2008), R54. 2008-03-13T17:09:06-00:00 2008 Genome Biology 1465-6906 9 R54 evolution localization proteins http://www.citeulike.org/user/dcastro/article/2648172 <i>Microwave and Wireless Components Letters, IEEE, Vol. 14, No. 1. (2004), pp. 10-12.</i><br /><br />A new type of compact band pass filters based on planar structures with three metal levels is proposed. The central layer consists on a coplanar waveguide (CPW) with periodic wire connections between the central strip and ground planes. In the upper and lower metal levels, split ring resonators (SRRs) are etched and aligned with the slots. The wires make the structure to behave as a microwave plasma, with a negative effective permittivity covering a wide frequency range. SRRs, which are magnetically coupled to the CPW, provide a negative magnetic permeability in a narrow frequency range above their resonant frequency. The result is a band pass structure which supports wave propagation in a frequency interval where negative permittivity and permeability coexist. The bandwidth of the structure can be controlled by tuning the resonant frequency of the upper and lower SRRs and the distance between SRRs. Fabricated prototype devices exhibit very low insertion losses in the pass band (<1.5 dB) and high frequency selectivity. Left handed coplanar waveguide band pass filters based on bi-layer split ring resonators F Falcone F Martin J Bonache R Marques T Lopetegi M Sorolla doi:10.1109/LMWC.2003.821512 Microwave and Wireless Components Letters, IEEE, Vol. 14, No. 1. (2004), pp. 10-12. 2008-04-10T06:51:14-00:00 2004 Microwave and Wireless Components Letters, IEEE 14 1 10 12 coplanar filter lh metamaterial http://www.citeulike.org/user/dmmarinlo/article/1506121 <i>IEEE Transactions on Image Processing, Vol. 16, No. 5. (May 2007), pp. 1339-1354.</i><br /><br />This paper considers the issues of scheduling and caching JPEG2000 data in client/server interactive browsing applications, under memory and channel bandwidth constraints. It analyzes how the conveyed data have to be selected at the server and managed within the client cache so as to maximize the reactivity of the browsing application. Formally, to render the dynamic nature of the browsing session, we assume the existence of a reaction model that defines when the user launches a novel command as a function of the image quality displayed at the client. As a main outcome, our work demonstrates that, due to the latency inherent to client/server exchanges, a priori expectation about future navigation commands may help to improve the overall reactivity of the system. In our study, the browsing session is defined by the evolution of a rectangular window of interest (WoI) along the time. At any given time, the WoI defines the position and the resolution of the image data to display at the client. The expectation about future navigation commands is then formalized based on a stochastic navigation model, which defines the probability that a given WoI is requested next, knowing previous WoI requests. Based on that knowledge, several scheduling scenarios are considered. The first scenario is conventional and transmits all the data corresponding to the current WoI before prefetching the most promising data outside the current WoI. Alternative scenarios are then proposed to anticipate prefetching, by scheduling data expected to be requested in the future before all the current WoI data have been sent out. Our results demonstrate that, for predictable navigation commands, anticipated prefetching improves the overall reactivity of the system by up to 30% compared to the conventional scheduling approach. They also reveal that an accurate knowledge of the reaction model is not required to get these significant improvements Prefetching and Caching Strategies for Remote and Interactive Browsing of JPEG2000 Images A Descampe C De Vleeschouwer M Iregui B Macq F Marques doi:10.1109/TIP.2007.894258 IEEE Transactions on Image Processing, Vol. 16, No. 5. (May 2007), pp. 1339-1354. 2007-07-27T04:46:52-00:00 2007 IEEE Transactions on Image Processing 16 5 1339 1354 caching jpeg2000 navigation prefetching http://www.citeulike.org/user/p0ol/article/2629161 <i></i><br /><br />The field of Content-Based Visual Information Retrieval (CBVIR) has experienced tremendous growth in the recent years and many research groups are currently working on solutions to the problem of finding a desired image or video clip in a huge archive without resorting to metadata. This paper describes the ongoing development of a CBVIR system for image search and retrieval with relevance feedback capabilities. Index Terms Content-based image search and retrieval, Relevance feedback,... Content-Based Image Search and Retrieval Using Relevance Feedback: the MUSE Project Oge Marques Fabio Costa Borko Furht 2008-04-04T09:40:24-00:00 no-tag http://www.citeulike.org/user/djkt/article/2620740 <i>PLoS Biology, Vol. 6, No. 4. (1 April 2008), e80.</i><br /><br />Mammalian sex chromosomes stem from ancestral autosomes and have substantially differentiated. It was shown that X-linked genes have generated duplicate intronless gene copies (retrogenes) on autosomes due to this differentiation. However, the precise driving forces for this out-of-X gene “movement” and its evolutionary onset are not known. Based on expression analyses of male germ-cell populations, we here substantiate and extend the hypothesis that autosomal retrogenes functionally compensate for the silencing of their X-linked housekeeping parental genes during, but also after, male meiotic sex chromosome inactivation (MSCI). Thus, sexually antagonistic forces have not played a major role for the selective fixation of X-derived gene copies in mammals. Our dating analyses reveal that although retrogenes were produced ever since the common mammalian ancestor, selectively driven retrogene export from the X only started later, on the placental mammal (eutherian) and marsupial (metatherian) lineages, respectively. Together, these observations suggest that chromosome-wide MSCI emerged close to the eutherian–marsupial split approximately 180 million years ago. Given that MSCI probably reflects the spread of the recombination barrier between the X and Y, crucial for their differentiation, our data imply that these chromosomes became more widely differentiated only late in the therian ancestor, well after the divergence of the monotreme lineage. Thus, our study also provides strong independent support for the recent notion that our sex chromosomes emerged, not in the common ancestor of all mammals, but rather in the therian ancestor, and therefore are much younger than previously thought. Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes Lukasz Potrzebowski Nicolas Vinckenbosch Ana Marques Frédéric Chalmel Bernard Jégou Henrik Kaessmann doi:10.1371/journal.pbio.0060080#special PLoS Biology, Vol. 6, No. 4. (1 April 2008), e80. 2008-04-01T18:25:49-00:00 2008 PLoS Biology 6 4 e80 chromosome evolution mammals sex http://www.citeulike.org/user/biomcgary/article/2620486 <i>PLoS Biology, Vol. 6, No. 4. (1 April 2008), e80.</i><br /><br />Mammalian sex chromosomes stem from ancestral autosomes and have substantially differentiated. It was shown that X-linked genes have generated duplicate intronless gene copies (retrogenes) on autosomes due to this differentiation. However, the precise driving forces for this out-of-X gene “movement” and its evolutionary onset are not known. Based on expression analyses of male germ-cell populations, we here substantiate and extend the hypothesis that autosomal retrogenes functionally compensate for the silencing of their X-linked housekeeping parental genes during, but also after, male meiotic sex chromosome inactivation (MSCI). Thus, sexually antagonistic forces have not played a major role for the selective fixation of X-derived gene copies in mammals. Our dating analyses reveal that although retrogenes were produced ever since the common mammalian ancestor, selectively driven retrogene export from the X only started later, on the placental mammal (eutherian) and marsupial (metatherian) lineages, respectively. Together, these observations suggest that chromosome-wide MSCI emerged close to the eutherian–marsupial split approximately 180 million years ago. Given that MSCI probably reflects the spread of the recombination barrier between the X and Y, crucial for their differentiation, our data imply that these chromosomes became more widely differentiated only late in the therian ancestor, well after the divergence of the monotreme lineage. Thus, our study also provides strong independent support for the recent notion that our sex chromosomes emerged, not in the common ancestor of all mammals, but rather in the therian ancestor, and therefore are much younger than previously thought. Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes Lukasz Potrzebowski Nicolas Vinckenbosch Ana Marques Frédéric Chalmel Bernard Jégou Henrik Kaessmann doi:10.1371%2Fjournal.pbio.0060080 PLoS Biology, Vol. 6, No. 4. (1 April 2008), e80. 2008-04-01T16:10:01-00:00 2008 PLoS Biology 6 4 e80 chromosomal_rearrangement evolution http://www.citeulike.org/user/damiantrj/article/2599199 <i>Nat Immunol, Vol. 3, No. 8. (August 2002), pp. 733-740.</i><br /><br />The murine gamma-herpesvirus-68 (MHV-68) K3 protein, like that of the Kaposi's sarcoma associated herpesvirus, down-regulates major histocompatibility complex (MHC) class I expression. However, how this contributes to viral replication in vivo is unclear. After intranasal MHV-68 infection, K3 was transcribed both during acute lytic infection in the lung and during latency establishment in lymphoid tissue. K3-deficient viruses were not cleared more rapidly from the lung, but the number of latently infected spleen cells was reduced and the frequency of virus-specific CD8(+) cytotoxic T lymphocytes (CTLs) was increased. CTL depletion reversed the viral latency deficit. Thus, a major function of K3 appears to be CTL evasion during viral latency expansion. K3-mediated evasion of CD8(+) T cells aids amplification of a latent gamma-herpesvirus. PG Stevenson JS May XG Smith S Marques H Adler UH Koszinowski JP Simas S Efstathiou doi:10.1038/ni818 Nat Immunol, Vol. 3, No. 8. (August 2002), pp. 733-740. 2008-03-26T17:05:53-00:00 2002 Nat Immunol 1529-2908 3 8 733 740 k3 latency mhv68 http://www.citeulike.org/user/damiantrj/article/2599174 <i>J Virol, Vol. 77, No. 13. (July 2003), pp. 7308-7318.</i><br /><br />Intranasal infection of mice with murine gammaherpesvirus 68 (MHV-68), a virus genetically related to the human pathogen Kaposi's sarcoma-associated herpesvirus, results in a persistent, latent infection in the spleen and other lymphoid organs. Here, we have determined the frequency of virus infection in splenic dendritic cells, macrophages, and several B-cell subpopulations, and we quantified cell type-dependent virus transcription patterns. The frequencies of virus genome positive cells were maximal at 14 days postinfection in all splenic cell populations analyzed. Marginal zone and germinal center B cells harbored the highest frequency of infection and the former population accounted for approximately half the total number of infected B cells. Analysis of virus transcription during the establishment of latency revealed that virus gene expression in B cells was restricted and dependent on the differentiation stage of the B cell. Notably, transcription of ORF73 was detected in germinal center B cells, a finding in agreement with the predicted latent genome maintenance function of ORF73 in dividing cells. At late times after infection, virus DNA could only be detected in newly formed and germinal center B cells, which suggests that B cells play a critical role in facilitating life-long latency. Selective gene expression of latent murine gammaherpesvirus 68 in B lymphocytes. S Marques S Efstathiou KG Smith M Haury JP Simas doi:10.1128/JVI.77.13.7308-7318.2003 J Virol, Vol. 77, No. 13. (July 2003), pp. 7308-7318. 2008-03-26T16:54:52-00:00 2003 J Virol 0022-538X 77 13 7308 7318 latency mhv68 http://www.citeulike.org/user/damiantrj/article/2573820 <i>J Gen Virol, Vol. 86, No. Pt 1. (January 2005), pp. 31-40.</i><br /><br />The gammaherpesviruses are characteristically latent in lymphocytes and exploit lymphocyte proliferation to establish a large, persistent pool of latent genomes. Murine gammaherpesvirus 68 (MHV-68) allows the in vivo analysis of viral genes that contribute to this and other aspects of host colonization. In this study, the MHV-68 bcl-2 homologue, M11, was disrupted either in its BH1 homology domain or upstream of its membrane-localizing C-terminal domain. Each M11 mutant showed normal lytic replication in vitro and in vivo, but had a reduction in peak splenic latency. Lower infectious-centre titres correlated with lower in vivo B-cell activation, lower viral genome loads and reduced viral tRNA expression. This was therefore a true latency deficit, rather than a deficit in ex vivo reactivation. Stable, long-term levels of splenic latency were normal. M11 function therefore contributed specifically to viral latency amplification in infected lymphoid tissue. Murine gammaherpesvirus 68 bcl-2 homologue contributes to latency establishment in vivo. BD de Lima JS May S Marques JP Simas PG Stevenson doi:10.1099/vir.0.80480-0 J Gen Virol, Vol. 86, No. Pt 1. (January 2005), pp. 31-40. 2008-03-23T07:04:31-00:00 2005 J Gen Virol 0022-1317 86 Pt 1 31 40 bcl-2 mhv68 http://www.citeulike.org/user/robertlischke/article/2560655 <i>Knowledge Acquisition, Vol. 3, No. 2. (June 1991), pp. 117-135.</i><br /><br />Our research goal is to make programming easier. A central focus in our research is developing programming constructs, called mechanisms, that are both (1) usable and (2) reusable. A mechanism is usable if it can be used to automate a task by someone who understands and performs that task, but who does not necessarily know how to program. A mechanism is reusable, if it can be employed for several domains and tasks. Focusing on usability can lead to application-specific mechanisms, that is, can reduce reusability. On the other hand, focusing on reusability can lead to task-independent structures, that is, lessen their usability. The trick is to come up with mechanisms satisfying both requirements: usability and reusability. We have identified some quantitative characteristics describing such mechanisms. Usable and reusable programming constructs Georg Klinker Carlos Bhola Geoffroy Dallemagne David Marques John Mcdermott doi:10.1016/1042-8143(91)90001-4 Knowledge Acquisition, Vol. 3, No. 2. (June 1991), pp. 117-135. 2008-03-19T13:25:43-00:00 1991 Knowledge Acquisition 3 2 117 135 da http://www.citeulike.org/user/toppi/article/2548209 <i>ECOOP 2007 – Object-Oriented Programming (2007), pp. 151-175.</i><br /><br />Most modern programming languages rely on exceptions for dealing with abnormal situations. Although exception handling was a significant improvement over other mechanisms like checking return codes, it is far from perfect. In fact, it can be argued that this mechanism is seriously limited, if not, flawed. This paper aims to contribute to the discussion by providing quantitative measures on how programmers are currently using exception handling. We examined 32 different applications, both for Java and .NET. The major conclusion for this work is that exceptions are not being correctly used as an error recovery mechanism. Exception handlers are not specialized enough for allowing recovery and, typically, programmers just do one of the following actions: logging, user notification and application termination. To our knowledge, this is the most comprehensive study done on exception handling to date, providing a quantitative measure useful for guiding the development of new error handling mechanisms. Exception Handling: A Field Study in Java and .NET Bruno Cabral Paulo Marques doi:10.1007/978-3-540-73589-2_8 ECOOP 2007 – Object-Oriented Programming (2007), pp. 151-175. 2008-03-18T04:19:10-00:00 2007 ECOOP 2007 – Object-Oriented Programming 151 175 exception java net programming_language http://www.citeulike.org/user/Montrachet/article/2532872 <i>Trends in Genetics, Vol. 23, No. 7. (July 2007), pp. 359-364.</i><br /><br />Virus infection is generally disadvantageous to the host and strongly selects for host antiviral mechanisms. Therefore, viruses must develop counter-mechanisms to guarantee their survival. This arms race between pathogen and host leads to positive selection for both cellular antiviral mechanisms and viral inhibitors of such mechanisms. Here, we characterize this arms race in the context of the RNA interference (RNAi) pathway, which is used as an innate immune response against viral infection by animals. We review how RNAi is used as an antiviral strategy and the mechanisms that viruses have evolved to suppress the RNAi response. A call to arms: coevolution of animal viruses and host innate immune responses Joao Marques Richard Carthew doi:10.1016/j.tig.2007.04.004 Trends in Genetics, Vol. 23, No. 7. (July 2007), pp. 359-364. 2008-03-14T15:14:59-00:00 2007 Trends in Genetics 23 7 359 364 coevolution immunology mirna sirna http://www.citeulike.org/user/jlh64/article/2507796 <i>Proteins: Structure, Function, and Genetics, Vol. 23, No. 4. (1995), pp. 557-560.</i><br /><br />A normal mode analysis of the closed form of dimeric citrate synthase has been performed. The largest-amplitude collective motion predicted by this method compares well with the crystallographically observed hinge-bending motion. Such a result supports those obtained previously in the case of hinge-bending motions of smaller systems, such as lysozyme or hexokinase. Taken together, all these results suggest that low-frequency normal modes may become useful for determining a first approximation of the conformational path between the closed and open forms of these proteins. © 1995 Wiley-Liss, Inc. Hinge-bending motion in citrate synthase arising from normal mode calculations Osni Marques Yves-Henri Sanejouand doi:10.1002/prot.340230410 Proteins: Structure, Function, and Genetics, Vol. 23, No. 4. (1995), pp. 557-560. 2008-03-11T12:11:12-00:00 1995 Proteins: Structure, Function, and Genetics 23 4 557 560 no-tag http://www.citeulike.org/user/middledomain/article/2507028 <i>J. Phys. Chem. A (11 March 2008)</i><br /><br />Abstract: In the light of the recognized anticancer properties of cisplatin-type inorganic systems, the exact knowledge of their conformational preferences is of the utmost importance for understanding their biological activity. The present study reports the use of theoretical (quantum mechanical) calculations for achieving this goal. An alternative calculation method to the use of the AE basis sets, both accurate and computationally feasible, was presently tested for the conformational and vibrational study of cis-diamminedichloroplatinum(II). Effective core potentials (ECPs) were used, within the HF methodology and, within the B3LYP and mPW1PW DFT protocols. The DFT methods (particularly mPW1PW) were found to be the best choice for describing cDDP (as compared to the HF methodology). Use of Effective Core Potential Calculations for the Conformational and Vibrational Study of Platinum(II) Anticancer Drugs. cis-Diamminedichloroplatinum(II) as a Case Study SM Fiuza AM Amado MPM Marques LAE Batistadecarvalho doi:10.1021/jp710868p J. Phys. Chem. A (11 March 2008) 2008-03-11T10:47:09-00:00 2008 J. Phys. Chem. A conformation http://www.citeulike.org/user/dpareit/article/2483237 <i>Wireless Communications, IEEE [see also IEEE Personal Communications], Vol. 12, No. 1. (2005), pp. 47-53.</i><br /><br />Foreseeing a future where IPv6 and mobile terminals play an important role in public access communication networks, this article introduces a monitoring system capable of identifying relevant traffic flows and tracking them while terminal equipment moves between network attachment points. The mobile flows are characterized and represented so that individual users and flows can perceive the quality of service they receive, and operators can have global traffic views of their heterogeneous access networks. Monitoring emerging IPv6 wireless access networks P Marques H Castro M Ricardo doi:10.1109/MWC.2005.1404572 Wireless Communications, IEEE [see also IEEE Personal Communications], Vol. 12, No. 1. (2005), pp. 47-53. 2008-03-07T10:28:02-00:00 2005 Wireless Communications, IEEE [see also IEEE Personal Communications] 12 1 47 53 ipv6 wireless http://www.citeulike.org/group/4345/article/1159140 <i>Journal of Food Processing & Preservation, Vol. 31, No. 2. (April 2007), pp. 178-189.</i> STORAGE STABILITY OF A STIMULANT COCONUT WATER-CASHEW APPLE JUICE BEVERAGE DE Carvalho Joelia Marques Geraldo Maia DE Figueiredo Raimundo Wilane DE Brito EDY Sousa Sueli Rodrigues doi:10.1111/j.1745-4549.2007.00121.x Journal of Food Processing & Preservation, Vol. 31, No. 2. (April 2007), pp. 178-189. 2007-03-14T07:43:56-00:00 2007 Journal of Food Processing & Preservation 0145-8892 31 2 178 189 Blackwell Publishing apple cashew coconut juice water http://www.citeulike.org/user/yongchul/article/2382818 <i>SIGPLAN Not., Vol. 38, No. 10. (October 2003), pp. 84-94.</i> Automated application-level checkpointing of MPI programs Greg Bronevetsky Daniel Marques Keshav Pingali Paul Stodghill doi:10.1145/966049.781513 SIGPLAN Not., Vol. 38, No. 10. (October 2003), pp. 84-94. 2008-02-14T22:08:22-00:00 2003 SIGPLAN Not. 0362-1340 38 10 84 94 ACM application c3 checkpoint http://www.citeulike.org/user/yongchul/article/2382817 <i>(2003), pp. 234-243.</i> Collective operations in application-level fault-tolerant MPI Greg Bronevetsky Daniel Marques Keshav Pingali Paul Stodghill doi:10.1145/782814.782847 (2003), pp. 234-243. 2008-02-14T22:07:03-00:00 2003 234 243 ACM c3 checkpoint http://www.citeulike.org/user/yongchul/article/2361504 <i>Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International (2006), 8 pp..</i><br /><br />Checkpoint and recovery (CPR) systems have many uses in high-performance computing. Because of this, many developers have implemented it, by hand, into their applications. One of the uses of checkpointing is to help mitigate the effects of interruptions in computational service (both planned and unplanned) In fact, some supercomputing centers expect their users to use checkpointing as a matter of policy. And yet, few centers provide fully automatic checkpointing systems for their high-end production machines. The paper is a status report on our work on the family of C/sup 3/ systems for (almost) fully automatic checkpointing for scientific applications. To date, we have shown that our techniques can be used for checkpointing sequential, MPI and OpenMP applications written in C, Fortran, and several other languages. A novel aspect of our work is that we have not built a single checkpointing system, rather, we have developed a methodology and a set of techniques that have enabled us to develop a number of systems, each meeting different design goals and efficiency requirements. Recent advances in checkpoint/recovery systems G Bronevetsky R Fernandes D Marques K Pingali P Stodghill doi:10.1109/IPDPS.2006.1639575 Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International (2006), 8 pp.. 2008-02-11T06:37:12-00:00 2006 Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International 8 pp. c3 checkpoint report http://www.citeulike.org/user/yongchul/article/2354942 <i>(2004)</i> Implementation and Evaluation of a Scalable Application-Level Checkpoint-Recovery Scheme for MPI Programs Martin Schulz Greg Bronevetsky Rohit Fernandes Daniel Marques Keshav Pingali Paul Stodghill doi:10.1109/SC.2004.29 (2004) 2008-02-08T21:56:46-00:00 2004 IEEE Computer Society application checkpoint mpi http://www.citeulike.org/user/yongchul/article/2354934 <i>SIGARCH Comput. Archit. News, Vol. 32, No. 5. (December 2004), pp. 235-247.</i> Application-level checkpointing for shared memory programs Greg Bronevetsky Daniel Marques Keshav Pingali Peter Szwed Martin Schulz doi:10.1145/1037947.1024421 SIGARCH Comput. Archit. News, Vol. 32, No. 5. (December 2004), pp. 235-247. 2008-02-08T21:54:01-00:00 2004 SIGARCH Comput. Archit. News 0163-5964 32 5 235 247 ACM application checkpoint mpi http://www.citeulike.org/user/briordan/article/2343195 <i>Cognition, Vol. 85, No. 3. (October 2002), pp. 251-275.</i><br /><br />The present paper evaluates different hypotheses for explaining the living/nonliving things dissociation phenomenon in terms of feature type, considering the role of this dimension in the organization of conceptual semantic representations and in the activation of name representations. For this purpose we used Sloman and associates' (Memory and Cognition 27(3) (1999) 526; Cognitive Science 22(2) (1998) 189) name centrality and conceptual centrality tasks and asked subjects to judge functional and perceptual/visual features of living and nonliving items. Conceptual centrality results are more in accordance with a "single feature-domain connection hypothesis" where visual features are more important than functional features for the representation of living things and no feature type advantage is found for nonliving things. Name centrality results show that functional features are more important than sensory/visual features overall, a result that is not predicted by any of the hypotheses considered. The fact that the two judgments diverge emphasizes their importance for evaluating the role of feature type in the living/nonliving dissociation. Implications for explaining this phenomenon are also discussed. Names, concepts, features and the living/nonliving things dissociation Frederico Marques doi:10.1016/S0010-0277(02)00123-3 Cognition, Vol. 85, No. 3. (October 2002), pp. 251-275. 2008-02-06T19:45:20-00:00 2002 Cognition 85 3 251 275 semantic-association semantic-features semantic-measures semantic-organization http://www.citeulike.org/user/yongchul/article/2295270 <i>(2003), pp. 84-94.</i> Automated application-level checkpointing of MPI programs Greg Bronevetsky Daniel Marques Keshav Pingali Paul Stodghill doi:10.1145/781498.781513 (2003), pp. 84-94. 2008-01-27T19:21:13-00:00 2003 84 94 ACM application checkpoint mpi http://www.citeulike.org/user/Prodiana/article/2272302 <i>Computers in Cardiology 2000 (2000), pp. 375-378.</i><br /><br />Episodes of hypoglycaemia in adults and children with Type I diabetes induce abnormalities in cardiac repolarization, including lengthening of the QT interval and QT dispersion. The authors have used a computerised ECG system to measure overnight changes in the heart rate corrected QT interval (QTc) in diabetic patients. The aim of the study was to determine whether QT prolongation is associated with nocturnal hypoglycaemia (blood glucose <3.5 mmol/l) and to investigate whether such changes might be used as the basis for a hypoglycaemia alarm. The authors used a Hewlett Packard 200LX (pocket PC attached to a single channel high gain amplifier with a serial data interface. Recordings were made for 30 seconds at 15 minute intervals throughout the night and the data downloaded to a PC for analysis. Patients were asked to measure their blood glucose at 23:00, 03:00 and 07:00 hours. The authors have studied 20 non-diabetic subjects (8F/12M), with a mean age 32 years and 14 patients with diabetes (7 M/7F), with a mean age 49 years. In nondiabetic subjects, the QTc remained stable throughout the night with a mean change in QC of 2.8 (SD 22.1) ms. In the diabetic patients, the mean change in QTc during 13 normoglycaemic nights was 6.9 (SD 10.0) ms and during hypoglycaemic nights 6.5 (SD 8.9) ms. The QTc cumulative mean change and SD was calculated throughout the night. Episodes where there were two consecutive increases in QTc above mean +2 SD within an hour were considered significant. Using these criteria, there was I significant event during the normoglycaemic nights but only 4 episodes were correctly identified out of 6 hypoglycaemic nights. Automated measurements of nocturnal QT interval can be used to monitop changes in cardiac repopulation associated with hypoglycaemia but more sophisticated analysis of T wave morphology or other factors will be required if such a system is to be used to reliably detect the onset of hypoglycaemia Can changes in QT interval be used to predict the onset of hypoglycemia in type 1 diabetes? ND Harris RH Ireland JLB Marques S Hudson C Davies S Lee RT Robinson SR Heller doi:10.1109/CIC.2000.898535 Computers in Cardiology 2000 (2000), pp. 375-378. 2008-01-22T08:13:44-00:00 2000 Computers in Cardiology 2000 375 378 diabetes qt_interval http://www.citeulike.org/user/marcusfrean/article/2248166 <i>(5 Jul 2006)</i><br /><br />The shapes of flat pebbles may be characterized in terms of the statistical distribution of curvatures measured along their contours. We illustrate this new method for clay pebbles eroded in a controlled laboratory apparatus, and also for naturally-occurring rip-up clasts formed and eroded in the Mont St.-Michel bay. We find that the curvature distribution allows finer discrimination than traditional measures of aspect ratios. Furthermore, it connects to the microscopic action of erosion processes that are typically faster at protruding regions of high curvature. We discuss in detail how the curvature may be reliable deduced from digital photographs. The shape and erosion of pebbles DJ Durian H Bideaud P Duringer A Schroder CM Marques (5 Jul 2006) 2008-01-18T00:25:31-00:00 2006 rocks http://www.citeulike.org/user/epigenetics/article/2211495 <i>Mol. Hum. Reprod. (4 January 2008), gam093.</i><br /><br />Genomic imprinting marks in the male germ line are already established in the adult germinal stem cell population. We studied the methylation patterns of H19 and MEST imprinted genes in sperm of control and oligozoospermic patients, by bisulphite genomic sequencing. We here report that 7 out of 15 (46.7%) patients with a sperm count below 10 x 106/ml display defective methylation of H19 and/or MEST imprinted genes. In these cases, hypomethylation was observed in 5.54% (1.28.3%) and complete unmethylation in 2.95% (05.9%) of H19 clones. Similarly, for the CTCF binding site 6, hypomethylation occurred in 4.8% (1.28.9%) and complete unmethylation in 3.7% (06.9%) of the clones. Conversely, hypermethylation occurred in 8.3% (3.812.2%) and complete methylation in 6.1% (3.87.6%) of MEST clones. Of the 7 patients presenting imprinting errors, two had both H19 hypomethylation and MEST hypermethylation whereas five displayed only one imprinted gene affected. The frequency of patients with MEST hypermethylation was highest in the severe oligozoospermia group (2/5 patients) whereas H19 hypomethylation was more frequent in the moderate oligozoospermia (2/5 patients). In all cases, global sperm genome methylation analysis (LINE1 transposon) suggested that defects were specific for imprinted genes. These findings could contribute to an explanation of the cause of Silver Russell syndrome in children born with H19 hypomethylation after assisted reproductive technologies (ART). Additionally, unmethylation of the CTCF binding site could lead to inactivation of the paternal IGF2 gene, and be linked to decreased embryo quality and birth weight, often associated with ART. 10.1093/molehr/gam093 Abnormal methylation of imprinted genes in human sperm is associated with oligozoospermia CJ Marques P Costa B Vaz F Carvalho S Fernandes A Barros M Sousa doi:10.1093/molehr/gam093 Mol. Hum. Reprod. (4 January 2008), gam093. 2008-01-09T17:28:04-00:00 2008 Mol. Hum. Reprod. gam093 epigenetics methylation reproduction