Showing papers by "Ghent University published in 2004"

GATE : a simulation toolkit for PET and SPECT

Abstract: Monte Carlo simulation is an essential tool in emission tomography that can assist in the design of new medical imaging devices, the optimization of acquisition protocols and the development or assessment of image reconstruction algorithms and correction techniques. GATE, the Geant4 Application for Tomographic Emission, encapsulates the Geant4 libraries to achieve a modular, versatile, scripted simulation toolkit adapted to the field of nuclear medicine. In particular, GATE allows the description of time-dependent phenomena such as source or detector movement, and source decay kinetics. This feature makes it possible to simulate time curves under realistic acquisition conditions and to test dynamic reconstruction algorithms. This paper gives a detailed description of the design and development of GATE by the OpenGATE collaboration, whose continuing objective is to improve, document and validate GATE by simulating commercially available imaging systems for PET and SPECT. Large effort is also invested in the ability and the flexibility to model novel detection systems or systems still under design. A public release of GATE licensed under the GNU Lesser General Public License can be downloaded at http:/www-lphe.epfl.ch/GATE/. Two benchmarks developed for PET and SPECT to test the installation of GATE and to serve as a tutorial for the users are presented. Extensive validation of the GATE simulation platform has been started, comparing simulations and measurements on commercially available acquisition systems. References to those results are listed. The future prospects towards the gridification of GATE and its extension to other domains such as dosimetry are also discussed.

Lignins: Natural polymers from oxidative coupling of 4-hydroxyphenyl- propanoids

Abstract: Lignins are complex natural polymers resulting from oxidative coupling of, primarily, 4-hydroxyphenylpropanoids. An understanding of their nature is evolving as a result of detailed structural studies, recently aided by the availability of lignin-biosynthetic-pathway mutants and transgenics. The currently accepted theory is that the lignin polymer is formed by combinatorial-like phenolic coupling reactions, via radicals generated by peroxidase-H2O2, under simple chemical control where monolignols react endwise with the growing polymer. As a result, the actual structure of the lignin macromolecule is not absolutely defined or determined. The ``randomness'' of linkage generation (which is not truly statistically random but governed, as is any chemical reaction, by the supply of reactants, the matrix, etc.) and the astronomical number of possible isomers of even a simple polymer structure, suggest a low probability of two lignin macromolecules being identical. A recent challenge to the currently accepted theory of chemically controlled lignification, attempting to bring lignin into line with more organized biopolymers such as proteins, is logically inconsistent with the most basic details of lignin structure. Lignins may derive in part from monomers and conjugates other than the three primary monolignols (p-coumaryl, coniferyl, and sinapyl alcohols). The plasticity of the combinatorial polymerization reactions allows monomer substitution and significant variations in final structure which, in many cases, the plant appears to tolerate. As such, lignification is seen as a marvelously evolved process allowing plants considerable flexibility in dealing with various environmental stresses, and conferring on them a striking ability to remain viable even when humans or nature alter ``required'' lignin-biosynthetic-pathway genes/enzymes. The malleability offers significant opportunities to engineer the structures of lignins beyond the limits explored to date.

Formation of Secondary Organic Aerosols Through Photooxidation of Isoprene

Abstract: Detailed organic analysis of natural aerosols from the Amazonian rain forest showed considerable quantities of previously unobserved polar organic compounds, which were identified as a mixture of two diastereoisomeric 2-methyltetrols: 2-methylthreitol and 2-methylerythritol. These polyols, which have the isoprene skeleton, can be explained by OH radical-initiated photooxidation of isoprene. They have low vapor pressure, allowing them to condense onto preexisting particles. It is estimated that photooxidation of isoprene results in an annual global production of about 2 teragrams of the polyols, a substantial fraction of the Intergovernmental Panel on Climate Change estimate of between 8 and 40 teragrams per year of secondary organic aerosol from biogenic sources.

Biofuel Cells Select for Microbial Consortia That Self-Mediate Electron Transfer

Abstract: Microbial fuel cells hold great promise as a sustainable biotechnological solution to future energy needs. Current efforts to improve the efficiency of such fuel cells are limited by the lack of knowledge about the microbial ecology of these systems. The purposes of this study were (i) to elucidate whether a bacterial community, either suspended or attached to an electrode, can evolve in a microbial fuel cell to bring about higher power output, and (ii) to identify species responsible for the electricity generation. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a biofuel cell in which glucose was used increased the output from an initial level of 0.6 W m−2 of electrode surface to a maximal level of 4.31 W m−2 (664 mV, 30.9 mA) when plain graphite electrodes were used. This result was obtained with an average loading rate of 1 g of glucose liter−1 day−1 and corresponded to 81% efficiency for electron transfer from glucose to electricity. Cyclic voltammetry indicated that the enhanced microbial consortium had either membrane-bound or excreted redox components that were not initially detected in the community. Dominant species of the enhanced culture were identified by denaturing gradient gel electrophoresis and culturing. The community consisted mainly of facultative anaerobic bacteria, such as Alcaligenes faecalis and Enterococcus gallinarum, which are capable of hydrogen production. Pseudomonas aeruginosa and other Pseudomonas species were also isolated. For several isolates, electrochemical activity was mainly due to excreted redox mediators, and one of these mediators, pyocyanin produced by P. aeruginosa, could be characterized. Overall, the enrichment procedure, irrespective of whether only attached or suspended bacteria were examined, selected for organisms capable of mediating the electron transfer either by direct bacterial transfer or by excretion of redox components.

Biodiversity of Vibrios

Abstract: Vibrios are ubiquitous and abundant in the aquatic environment. A high abundance of vibrios is also detected in tissues and/or organs of various marine algae and animals, e.g., abalones, bivalves, corals, fish, shrimp, sponges, squid, and zooplankton. Vibrios harbour a wealth of diverse genomes as revealed by different genomic techniques including amplified fragment length polymorphism, multilocus sequence typing, repetetive extragenic palindrome PCR, ribotyping, and whole-genome sequencing. The 74 species of this group are distributed among four different families, i.e., Enterovibrionaceae, Photobacteriaceae, Salinivibrionaceae, and Vibrionaceae. Two new genera, i.e., Enterovibrio norvegicus and Grimontia hollisae, and 20 novel species, i.e., Enterovibrio coralii, Photobacterium eurosenbergii, V. brasiliensis, V. chagasii, V. coralliillyticus, V. crassostreae, V. fortis, V. gallicus, V. hepatarius, V. hispanicus, V. kanaloaei, V. neonatus, V. neptunius, V. pomeroyi, V. pacinii, V. rotiferianus, V. superstes, V. tasmaniensis, V. ezurae, and V. xuii, have been described in the last few years. Comparative genome analyses have already revealed a variety of genomic events, including mutations, chromosomal rearrangements, loss of genes by decay or deletion, and gene acquisitions through duplication or horizontal transfer (e.g., in the acquisition of bacteriophages, pathogenicity islands, and super-integrons), that are probably important driving forces in the evolution and speciation of vibrios. Whole-genome sequencing and comparative genomics through the application of, e.g., microarrays will facilitate the investigation of the gene repertoire at the species level. Based on such new genomic information, the taxonomy and the species concept for vibrios will be reviewed in the next years.

Toxic proteins released from mitochondria in cell death

Abstract: A plethora of apoptotic stimuli converge on the mitochondria and affect their membrane integrity. As a consequence, multiple death-promoting factors residing in the mitochondrial intermembrane space are liberated in the cytosol. Pro- and antiapoptotic Bcl-2 family proteins control the release of these mitochondrial proteins by inducing or preventing permeabilization of the outer mitochondrial membrane. Once released into the cytosol, these mitochondrial proteins activate both caspase-dependent and -independent cell death pathways. Cytochrome c was the first protein shown to be released from the mitochondria into the cytosol, where it induces apoptosome formation. Other released mitochondrial proteins include apoptosis-inducing factor (AIF) and endonuclease G, both of which contribute to apoptotic nuclear DNA damage in a caspase-independent way. Other examples are Smac/DIABLO (second mitochondria-derived activator of caspase/direct IAP-binding protein with low PI) and the serine protease HtrA2/OMI (high-temperature requirement protein A2), which both promote caspase activation and instigate caspase-independent cytotoxicity. The precise mode of action and importance of cytochrome c in apoptosis in mammalian cells has become clear through biochemical, structural and genetic studies. More recently identified factors, for example HtrA2/OMI and Smac/DIABLO, are still being studied intensively in order to delineate their functions in apoptosis. A better understanding of these functions may help to develop new strategies to treat cancer.

The State of the Art of Nurse Rostering

Abstract: Nurse rostering is a complex scheduling problem that affects hospital personnel on a daily basis all over the world. The need for quality software solutions is acute for a number of reasons. In particular, it is very important to efficiently utilise time and effort, to evenly balance the workload among people and to attempt to satisfy personnel preferences. A high quality roster can lead to a more contented and thus more effective workforce. In this review, we discuss nurse rostering within the global personnel scheduling problem in healthcare. We begin by briefly discussing the review and overview papers that have appeared in the literature and by noting the role that nurse rostering plays within the wider context of longer term hospital personnel planning. The main body of the paper describes and critically evaluates solution approaches which span the interdisciplinary spectrum from operations research techniques to artificial intelligence methods. We conclude by drawing on the strengths and weaknesses of the literature to outline the key issues that need addressing in future nurse rostering research.

Endogenous DNA damage in humans: a review of quantitative data

Abstract: DNA damage plays a major role in mutagenesis, carcinogenesis and ageing. The vast majority of mutations in human tissues are certainly of endogenous origin. A thorough knowledge of the types and prevalence of endogenous DNA damage is thus essential for an understanding of the interactions of endogenous processes with exogenous agents and the influence of damage of endogenous origin on the induction of cancer and other diseases. In particular, this seems important in risk evaluation concerning exogenous agents that also occur endogenously or that, although chemically different from endogenous ones, generate the same DNA adducts. This knowledge may also be crucial to the development of rational chemopreventive strategies. A list of endogenous DNA-damaging agents, processes and DNA adduct levels is presented. For the sake of comparison, DNA adduct levels are expressed in a standardized way, including the number of adducts per 10(6) nt. This list comprises numerous reactive oxygen species and products generated as a consequence (e.g. lipid peroxides), endogenous reactive chemicals (e.g. aldehydes and S-adenosylmethionine), and chemical DNA instability (e.g. depurination). The respective roles of endogenous versus exogenous DNA damage in carcinogenesis are discussed.

Duplication and Divergence: The Evolution of New Genes and Old Ideas

Abstract: ▪ Abstract Over 35 years ago, Susumu Ohno stated that gene duplication was the single most important factor in evolution (97). He reiterated this point a few years later in proposing that without duplicated genes the creation of metazoans, vertebrates, and mammals from unicellular organisms would have been impossible. Such big leaps in evolution, he argued, required the creation of new gene loci with previously nonexistent functions (98). Bold statements such as these, combined with his proposal that at least one whole-genome duplication event facilitated the evolution of vertebrates, have made Ohno an icon in the literature on genome evolution. However, discussion on the occurrence and consequences of gene and genome duplication events has a much longer, and often neglected, history. Here we review literature dealing with the occurence and consequences of gene duplication, begining in 1911. We document conceptual and technological advances in gene duplication research from this early research in comparat...

Rhinosinusitis: Establishing definitions for clinical research and patient care

Abstract: Background There is a need for more research on all forms of rhinosinusitis. Progress in this area has been hampered by a lack of consensus definitions and the limited number of published clinical trials. Objectives To develop consensus definitions for rhinosinusitis and outline strategies useful in clinical trials. Methods Five national societies, The American Academy of Allergy, Asthma and Immunology; The American Academy of Otolaryngic Allergy; The American Academy of Otolaryngology Head and Neck Surgery; The American College of Allergy, Asthma and Immunology; and the American Rhinologic Society formed an expert panel from multiple disciplines. Over two days, the panel developed definitions for rhinosinusitis and outlined strategies for design of clinical trials. Results Committee members agreed to adopt the term "rhinosinusitis" and reached consensus on definitions and strategies for clinical research on acute presumed bacterial rhinosinusitis, chronic rhinosinusitis without polyposis, chronic rhinosinusitis with polyposis, and classic allergic fungal rhinosinusitis. Symptom and objective criteria, measures for monitoring research progress, and use of symptom scoring tools, quality-of-life instruments, radiologic studies, and rhinoscopic assessment were outlined for each condition. Conclusion The recommendations from this conference should improve accuracy of clinical diagnosis and serve as a starting point for design of rhinosinusitis clinical trials.

How specific are executive functioning deficits in attention deficit hyperactivity disorder and autism

Abstract: Background: The objective of this study is to identify intact and deficient cognitive processes in children with attention deficit hyperactivity disorder (ADHD) and children with high functioning autism (HFA). Method: Three rigorously diagnosed groups of children aged between 6 and 12 years (54 ADHD, 41 HFA, and 41 normal controls) were tested on a wide range of tasks related to five major domains of executive functioning (EF): inhibition, visual working memory, planning, cognitive flexibility, and verbal fluency. In addition, the role of comorbid oppositional defiant disorder (ODD) and comorbid conduct disorder (CD) in ADHD was investigated by directly comparing 20 children with ADHD and 34 children with comorbid ADHD + ODD/CD. Results: ADHD was associated with EF deficits in inhibiting a prepotent response and verbal fluency. Children with HFA demonstrated deficits in all EF domains, except interference control and working memory. The HFA group showed more difficulties than the ADHD group with planning and cognitive flexibility. The comorbid ADHD + ODD/CD group did not show a distinctive pattern of performance on the EF tests compared to the ADHD group. Conclusion: The present study indicates that children with HFA exhibit more generalised and profound problems with EF tasks compared to children with ADHD. © Association for Child Psychology and Psychiatry, 2004.

IFCC Reference System for Measurement of Hemoglobin A1c in Human Blood and the National Standardization Schemes in the United States, Japan, and Sweden: A Method-Comparison Study

Abstract: Background: The national programs for the harmonization of hemoglobin (Hb)A1c measurements in the US [National Glycohemoglobin Standardization Program (NGSP)], Japan [Japanese Diabetes Society (JDS)/Japanese Society of Clinical Chemistry (JSCC)], and Sweden are based on different designated comparison methods (DCMs). The future basis for international standardization will be the reference system developed by the IFCC Working Group on HbA1c Standardization. The aim of the present study was to determine the relationships between the IFCC Reference Method (RM) and the DCMs. Methods: Four method-comparison studies were performed in 2001–2003. In each study five to eight pooled blood samples were measured by 11 reference laboratories of the IFCC Network of Reference Laboratories, 9 Secondary Reference Laboratories of the NGSP, 3 reference laboratories of the JDS/JSCC program, and a Swedish reference laboratory. Regression equations were determined for the relationship between the IFCC RM and each of the DCMs. Results: Significant differences were observed between the HbA1c results of the IFCC RM and those of the DCMs. Significant differences were also demonstrated between the three DCMs. However, in all cases the relationship of the DCMs with the RM were linear. There were no statistically significant differences between the regression equations calculated for each of the four studies; therefore, the results could be combined. The relationship is described by the following regression equations: NGSP-HbA1c = 0.915(IFCC-HbA1c) + 2.15% ( r 2 = 0.998); JDS/JSCC-HbA1c = 0.927(IFCC-HbA1c) + 1.73% ( r 2 = 0.997); Swedish-HbA1c = 0.989(IFCC-HbA1c) + 0.88% ( r 2 = 0.996). Conclusion: There is a firm and reproducible link between the IFCC RM and DCM HbA1c values.

Compact efficient broadband grating coupler for silicon-on-insulator waveguides.

Abstract: We have designed a high-efficiency broadband grating coupler for coupling between silicon-on-insulator (SOI) waveguides and optical fibers. The grating is only 13 µm long and 12 µm wide, and the size of the grooves is optimized numerically. For TE polarization the coupling loss to single-mode fiber is below 1 dB over a 35-nm wavelength range when using SOI with a two-pair bottom reflector. The tolerances to fabrication errors are also calculated.

Meat fatty acid composition as affected by fatness and genetic factors: a review

Abstract: Meat fatty acid composition is influenced by genetic factors, although to a lower extent than dietary factors. The species is the major source of variation in fatty acid composition with ruminant meats being more saturated as a result of biohydrogenation in the rumen compared to the meat of monogastric animals. The level of fatness also has an effect on the meat fatty acid composition. The contents of saturated (SFA) and monounsaturated (MUFA) fatty acids increase faster with increasing fatness than does the content of PUFA, resulting in a decrease in the relative proportion of PUFA and consequently in the polyunsaturated/saturated fatty acids (P/S) ratio. The dilution of phospholipids with triacylglycerols and the distinct differences in fatty acid composition of these fractions explain the decrease in the P/S ratio with increasing fatness. An exponential model was fitted to the literature data for beef and showed a sharply increasing P/S ratio at low levels of intramuscular fat. Lowering the fat level of beef is thus more efficient in increasing the P/S ratio than dietary interventions. For pork, the intramuscular fat level also affects the P/S ratio, but nutrition will have a larger impact. The fat level also influences the n-6/n-3 PUFA ratio, due to the difference of this ratio in polar and neutral lipids. However, these effects are much smaller than the effects that can be achieved by dietary means. Differences in fatty acid composition between breeds and genotypes can be largely explained by differences in fatness. However, after correction for fat level, breed or genotype differences in the MUFA/SFA ratio and in the longer chain C20 and C22 PUFA metabolism have been reported, reflecting the possible genetic differences in fatty acid metabolism. Breed differences in meat conjugated linoleic acid (CLA) content have not yet been reported, but the c9t11CLA content in meat is positively related to the total fat content. Heritabilities and genetic correlations for the proportion of certain fatty acids have been estimated in a few studies, and correspond to the observations at the phenotypic level in relation to the intramuscular fat level. Although there is potential for genetic change, incorporating fatty acid composition as a goal in classical breeding programs does not seem worthwhile at the present. Enzyme activities have been measured in a few studies, but are not able to explain between-animal variation in fatty acid composition. Biochemical and molecular genetic studies should be encouraged to unravel the mechanisms responsible for differences in the metabolism and incorporation of specific fatty acids in meat. fatty acids / meat / genetics / P/S ratio

Fear-related avoidance of activities, falls and physical frailty. A prospective community-based cohort study

Abstract: Objective: to investigate the relationship between fear-related avoidance of activities and physical frailty. Subjects and methods: fear-related avoidance of activities, physical performance, maximal isometric muscle strength and postural control were assessed in 225 community-living elderly (94 men and 131 women), aged between 61 and 92 years of age. Results: bivariate analyses revealed significant correlations between avoidance of activities on the one hand, and physical performance, muscle strength, forward endpoint excursion of the centre of gravity, and previous falls on the other hand. Logistic regression analysis revealed that fear of falling and avoidance of activities in daily life were predictive of falls within a 1-year follow-up, together with general fear of falling, old age and being female. Conclusions: fear-related avoidance of activities may have negative effects on physical abilities and may also be predictive for future falls. Avoidance of activities is therefore an important additional psychological variable in the development of physical frailty and falling in community-living elderly.

Mutant small heat-shock protein 27 causes axonal Charcot-Marie-Tooth disease and distal hereditary motor neuropathy

Abstract: Charcot-Marie-Tooth disease (CMT) is the most common inherited neuromuscular disease and is characterized by considerable clinical and genetic heterogeneity. We previously reported a Russian family with autosomal dominant axonal CMT and assigned the locus underlying the disease (CMT2F; OMIM 606595) to chromosome 7q11-q21 (ref. 2). Here we report a missense mutation in the gene encoding 27-kDa small heat-shock protein B1 (HSPB1, also called HSP27) that segregates in the family with CMT2F. Screening for mutations in HSPB1 in 301 individuals with CMT and 115 individuals with distal hereditary motor neuropathies (distal HMNs) confirmed the previously observed mutation and identified four additional missense mutations. We observed the additional HSPB1 mutations in four families with distal HMN and in one individual with CMT neuropathy. Four mutations are located in the Hsp20-alpha-crystallin domain, and one mutation is in the C-terminal part of the HSP27 protein. Neuronal cells transfected with mutated HSPB1 were less viable than cells expressing the wild-type protein. Cotransfection of neurofilament light chain (NEFL) and mutant HSPB1 resulted in altered neurofilament assembly in cells devoid of cytoplasmic intermediate filaments.

Clostridium perfringens in poultry: an emerging threat for animal and public health

Abstract: The incidence of Clostridium perfringens-associated necrotic enteritis in poultry has increased in countries that stopped using antibiotic growth promoters. Necrotic enteritis and the subclinical form of C. perfringens infection in poultry are caused by C. perfringens type A, producing the alpha toxin, and to a lesser extent type C, producing both alpha toxin and beta toxin. Some strains of C. perfringens type A produce an enterotoxin at the moment of sporulation and are responsible for foodborne disease in humans. The mechanisms of colonization of the avian small intestinal tract and the factors involved in toxin production are largely unknown. It is generally accepted, however, that predisposing factors are required for these bacteria to colonize and cause disease in poultry. The best known predisposing factor is mucosal damage, caused by coccidiosis. Diets with high levels of indigestible, water-soluble non-starch polysaccharides, known to increase the viscosity of the intestinal contents, also predispose to necrotic enteritis. Standardized models are being developed for the reproduction of colonization of poultry by C. perfringens and the C. perfringens-associated necrotic enteritis. One such model is a combined infection with Eimeria species and C. perfringens. Few tools and strategies are available for prevention and control of C. perfringens in poultry. Vaccination against the pathogen and the use of probiotic and prebiotic products has been suggested, but are not available for practical use in the field at the present time. The most cost-effective control will probably be achieved by balancing the composition of the feed.

Rhinosinusitis: Establishing definitions for clinical research and patient care

Abstract: Objectives: to develop consensus definitions for rhinosinusitis and outline strategies useful in clinical trials