Showing papers by "University of Antwerp published in 2002"

Introduction to the CoNLL-2002 shared task: language-independent named entity recognition

Abstract: We describe the CoNLL-2002 shared task: language-independent named entity recognition. We give background information on the data sets and the evaluation method, present a general overview of the systems that have taken part in the task and discuss their performance.

The snowmass Points and slopes: benchmarks for SUSY searches

Abstract: The ”Snowmass Points and Slopes” (SPS) are a set of benchmark points and parameter lines in the MSSM parameter space corresponding to different scenarios in the search for Supersymmetry at present and future experiments. This set of benchmarks was agreed upon at the 2001 ”Snowmass Workshop on the Future of Particle Physics” as a consensus based on different existing proposals.

Identification of a 52 kb deletion downstream of the SOST gene in patients with van Buchem disease.

Abstract: Van Buchem disease is an autosomal recessive skeletal dysplasia characterised by generalised bone overgrowth, predominantly in the skull and mandible. Clinical complications including facial nerve palsy, optic atrophy, and impaired hearing occur in most patients. These features are very similar to those of sclerosteosis and the two conditions are only differentiated by the hand malformations and the tall stature appearing in sclerosteosis. Using an extended Dutch inbred van Buchem family and two inbred sclerosteosis families, we mapped both disease genes to the same region on chromosome 17q12-q21, supporting the hypothesis that van Buchem disease and sclerosteosis are caused by mutations in the same gene. In a previous study, we positionally cloned a novel gene, called SOST, from the linkage interval and identified three different, homozygous mutations in the SOST gene in sclerosteosis patients leading to loss of function of the underlying protein. The present study focuses on the identification of a 52 kb deletion in all patients from the van Buchem family. The deletion, which results from a homologous recombination between Alu sequences, starts approximately 35 kb downstream of the SOST gene. Since no evidence was found for the presence of a gene within the deleted region, we hypothesise that the presence of the deletion leads to a down regulation of the transcription of the SOST gene by a cis regulatory action or a position effect.

The Two Sides of Euroscepticism Party Positions on European Integration in East Central Europe

Abstract: This article aims to make a three-fold contribution to the study of Euroscepticism in the wider Europe. First, it presents a two-dimensional conceptualization of party positions on European integra...

Object-oriented reengineering patterns

Abstract: The rapid growth of object-oriented development over the past twenty years has given rise to many object-oriented systems that are large, complex and hard to maintain. These systems exhibit a range of problems, effectively preventing them from satisfying the evolving requirements imposed by their customers. In our paper, we address problem of understanding and reengineering such object-oriented legacy systems. The material is presented as a set of "reengineering patterns" - recurring solutions that experts apply while reengineering and maintaining object-oriented systems. The patterns distill successful techniques in planning a reengineering project, reverse-engineering, problem detection, migration strategies and software redesign. The principles and techniques described have been observed and validated in a number of industrial projects, and reflect best practice in object-oriented reengineering.

Elevated Levels of Oxidative DNA Damage and DNA Repair Enzymes in Human Atherosclerotic Plaques

Abstract: Background— The formation of reactive oxygen species is a critical event in atherosclerosis because it promotes cell proliferation, hypertrophy, growth arrest, and/or apoptosis and oxidation of LDL. In the present study, we investigated whether reactive oxygen species-induced oxidative damage to DNA occurs in human atherosclerotic plaques and whether this is accompanied by the upregulation of DNA repair mechanisms. Methods and Results— We observed increased immunoreactivity against the oxidative DNA damage marker 7,8-dihydro-8-oxo-2′-deoxyguanosine (8-oxo-dG) in plaques of the carotid artery compared with the adjacent inner media and nonatherosclerotic mammary arteries. Strong 8-oxo-dG immunoreactivity was found in all cell types of the plaque including macrophages, smooth muscle cells, and endothelial cells. As shown by competitive ELISA, carotid plaques contained 160±29 8-oxo-dG residues/105 dG versus 3±1 8-oxo-dG residues/105 dG in mammary arteries. Single-cell gel electrophoresis showed elevated level...

A detailed study of thermal, hydrothermal, and mechanical stabilities of a wide range of surfactant assembled mesoporous silicas

Abstract: The thermal, hydrothermal, and mechanical stabilities of a wide range of ordered mesoporous materials, in particular, the molecular sieves MCM-41, MCM-48, HMS, FSM-16, KIT-1, PCH, and SBA-15, have been studied in detail using X-ray diffraction (XRD) and nitrogen sorption. The thermal stability was found to be strongly related to the wall thickness and the silica precursor used during synthesis, and the following stability trend was observed: MCM-41 (fumed silica), MCM-48 (fumed silica), KIT-1 (colloid silica) > SBA-15 (TEOS) > FSM-16 (layered silicate), PCH (layered silicate) > MCM-41 (TEOS), MCM-48 (TEOS), HMS (TEOS). The hydrothermal stability is influenced by the wall thickness and the polymerization degree and decreases according to the following trend: KIT-1 > SBA-15 > MCM-48 (fumed silica and TEOS), PCH > FSM-16, MCM-41 (fumed silica and TEOS), HMS. The mechanical stability is little influenced by the nature of the mesoporous molecular sieves. All materials collapsed at a maximum pelletizing press...

Rat C6 glioma as experimental model system for the study of glioblastoma growth and invasion

Abstract: Infiltration of the central nervous system by neoplastic cells in patients with glioblastoma multiforme (GBM) leads to neurological dysfunction and eventually to death. The elucidation of the mechanisms underlying the aggressive nature of GBM aims at improving radio-, chemo- and gene therapy. This review is focused on the use of rat C6 glioma as an experimental model system for GBM and provides an overview of the experimental data published in the literature using this cell line in elucidating the mechanism of tumor growth, angiogenesis and invasion, and in the design and evaluation of anticancer therapies. Understanding the stages of malignant brain tumor progression requires a series of experimental approaches with a varying degree of complexity. Implantation of malignant cells into animal brain tissue closely resembles in vivo tumor growth and has the advantage over simplified models that inflammatory and vascular mechanisms are activated. However, the complexity of these models makes it difficult to identify the individual processes involved in sustained tumor growth, angiogenesis and invasion. In cell culture models, the effect of growth factors, extracellular matrix components, proteases and adhesion molecules can be investigated. The secretion of tumor-derived factors into the medium can also be analyzed when simplified models are used. This review is a compilation of experimental data focused on the characterization of tumor-related processes and on the evaluation of new therapies for the treatment of malignant glial neoplasms using rat C6 glioma as a model system.

The Role of Auxin, pH, and Stress in the Activation of Embryogenic Cell Division in Leaf Protoplast-Derived Cells of Alfalfa

Abstract: Culturing leaf protoplast-derived cells of the embryogenic alfalfa ( Medicago sativa subsp. varia A2) genotype in the presence of low (1 μm) or high (10 μm) 2, 4-dichlorophenoxyacetic acid (2,4-D) concentrations results in different cell types. Cells exposed to high 2,4-D concentration remain small with dense cytoplasm and can develop into proembryogenic cell clusters, whereas protoplasts cultured at low auxin concentration elongate and subsequently die or form undifferentiated cell colonies. Fe stress applied at nonlethal concentrations (1 mm) in the presence of 1 μm2,4-D also resulted in the development of the embryogenic cell type. Although cytoplasmic alkalinization was detected during cell activation of both types, embryogenic cells could be characterized by earlier cell division, a more alkalic vacuolar pH, and nonfunctional chloroplasts as compared with the elongated, nonembryogenic cells. Buffering of the 10 μm 2,4-D-containing culture medium by 10 mm2-( N -morpholino)ethanesulfonic acid delayed cell division and resulted in nonembryogenic cell-type formation. The level of endogenous indoleacetic acid (IAA) increased transiently in all protoplast cultures during the first 4 to 5 d, but an earlier peak of IAA accumulation correlated with the earlier activation of the division cycle in embryogenic-type cells. However, this IAA peak could also be delayed by buffering of the medium pH by 2-( N -morpholino)ethanesulfonic acid. Based on the above data, we propose the involvement of stress responses, endogenous auxin synthesis, and the establishment of cellular pH gradients in the formation of the embryogenic cell type.

Does flight morphology relate to flight performance? An experimental test with the butterfly **Pararge aegeria**

Abstract: 1. The relationship between maximal acceleration capacity and flight morphology was tested experimentally in the butterfly Pararge aegeria. Such relations are often assumed but seldom tested. 2. In both sexes acceleration capacity was positively correlated with total body mass, thorax mass, forewing area, forewing length, wing loading, aspect ratio and centre of forewing area (centroid). Relationships with total body mass, forewing area, forewing length and wing loading were stronger in males. This can be explained by different mass allocation: males allocate proportionally more mass to the thorax, females more to the abdomen. 3. Evidence for the combined effect of morphological traits on acceleration capacity was found by multivariate analysis. In males and females, a more distant relative centroid and higher relative thorax mass were related to a higher flight capacity. In addition, aspect ratio was positively related to acceleration capacity in males only. 4. Our results support the assumed mechanism behind the relationship between flight morphology and mate-locating behaviour.

Testing the beneficial acclimation hypothesis

Abstract: Recent developments in evolutionary physiology have seen many of the long-held assumptions within comparative physiology receive rigorous experimental analysis. Studies of the adaptive significance of physiological acclimation exemplify this new evolutionary approach. The beneficial acclimation hypothesis (BAH) was proposed to describe the assumption that all acclimation changes enhance the physiological performance or fitness of an individual organism. To the surprise of most physiologists, all empirical examinations of the BAH have rejected its generality. However, we suggest that these examinations are neither direct nor complete tests of the functional benefit of acclimation. We consider them to be elegant analyses of the adaptive significance of developmental plasticity, a type of phenotypic plasticity that is very different from the traditional concept of acclimation that is used by comparative physiologists.

Mining All Non-Derivable Frequent Itemsets

Abstract: Recent studies on frequent itemset mining algorithms resulted in significant performance improvements. However, if the minimal support threshold is set too low, or the data is highly correlated, the number of frequent itemsets itself can be prohibitively large. To overcome this problem, recently several proposals have been made to construct a concise representation of the frequent itemsets, instead of mining all frequent itemsets. The main goal of this paper is to identify redundancies in the set of all frequent itemsets and to exploit these redundancies in order to reduce the result of a mining operation. We present deduction rules to derive tight bounds on the support of candidate itemsets. We show how the deduction rules allow for constructing a minimal representation for all frequent itemsets. We also present connections between our proposal and recent proposals for concise representations and we give the results of experiments on real-life datasets that show the effectiveness of the deduction rules. In fact, the experiments even show that in many cases, first mining the concise representation, and then creating the frequent itemsets from this representation outperforms existing frequent set mining algorithms.

Mutations of the Selenoprotein N Gene, Which Is Implicated in Rigid Spine Muscular Dystrophy, Cause the Classical Phenotype of Multiminicore Disease: Reassessing the Nosology of Early-Onset Myopathies

Abstract: Multiminicore disease (MmD) is an autosomal recessive congenital myopathy characterized by the presence of multiple, short core lesions (known as "minicores") in most muscle fibers. MmD is a clinically heterogeneous condition, in which four subgroups have been distinguished. Homozygous RYR1 mutations have been recently identified in the moderate form of MmD with hand involvement. The genes responsible for the three other forms (including the most prevalent phenotype, termed the "classical" phenotype) remained, so far, unknown. To further characterize the genetic basis of MmD, we analyzed a series of 62 patients through a combined positional/candidate-gene approach. On the basis of clinical and morphological data, we suspected a relationship between classical MmD and the selenoprotein N gene (SEPN1), which is located on chromosome 1p36 (RSMD1 locus) and is responsible for the congenital muscular dystrophy with rigid spine syndrome (RSMD). A genomewide screening, followed by the analysis of 1p36 microsatellite markers in 27 informative families with MmD, demonstrated linkage to RSMD1 in eight families. All showed an axial myopathy with scoliosis and respiratory failure, consistent with the most severe end of the classical MmD spectrum; spinal rigidity was evident in some, but not all, patients. We excluded linkage to RSMD1 in 19 families with MmD, including 9 with classical MmD. Screening of SEPN1 in the 8 families that showed linkage and in 14 patients with classical sporadic disease disclosed 9 mutations affecting 17 patients (12 families); 6 were novel mutations, and 3 had been described in patients with RSMD. Analysis of three deltoid biopsy specimens from patients with typical RSMD revealed a wide myopathological variability, ranging from a dystrophic to a congenital myopathy pattern. A variable proportion of minicores was found in all the samples. The present study represents the first identification of a gene responsible for classical MmD, demonstrates its genetic heterogeneity, and reassesses the nosological boundaries between MmD and RSMD.

Relationships between head size, bite force, prey handling efficiency and diet in two sympatric lacertid lizards

Abstract: Summary 1. Relationships between morphology, bite force capacity, prey handling efficiency and trophic niche were explored in two sympatric species of lacertid lizards, Podarcis melisellensis (Braun 1877) and Lacerta oxycephala Dumeril & Bibron 1839. 2. Head shape showed little variation, but head size (absolute and relative to snout‐ vent length, SVL) differed between species and sexes. Males have larger heads than females, both absolute and relative to their SVL. In absolute terms, male P. melisellensis have larger heads than male L. oxycephala , but the reverse case was true for the females. Relative to SVL, L. oxycephala have larger heads than P. melisellensis . 3. Bite force capacity was estimated by having the lizards bite on two metal plates, connected to a piezoelectric force transducer. Differences in maximal bite force between species and sexes paralleled differences in absolute head size. Differences in body size and head size explain the higher bite force of males (compared with females), but not the higher bite force of P. melisellensis (compared with L. oxycephala ). Among individual lizards, bite force correlated with body size and head size. 4. Prey handling efficiency, estimated by the time and number of bites needed to subdue a cricket in experimental conditions, also showed intersexual and interspecific variation. This variation corresponded to the differences in maximal bite capacity, suggesting that bite force is a determining factor in prey handling. Among individual lizards, both estimates of handling efficiency correlated with maximal bite force capacity. 5. Faecal pellet analyses suggested that in field conditions, males of both sexes select larger and harder prey than females. There was no difference between the species. The proportion of hard-bodied and large-sized prey items found in a lizard’s faeces correlated positively with its bite force capacity. 6. It is concluded that differences in head and body size, through their effect on bite force capacity, may affect prey selection, either directly, or via handling efficiency.

Investigation of selected persistent organic pollutants in farmed Atlantic salmon (Salmo salar), salmon aquaculture feed, and fish oil components of the feed.

Abstract: There is extensive literature documenting the bioaccumulation of persistent organic pollutants in the marine environment, but relatively little data are available on contamination pathways in aquaculture systems such as that for farmed salmon. In recent years,the salmon industry has grown significantly in Europe. This study reports on the determination of a wide range of polychlorinated biphenyls (PCBs), organochlorine pesticides, and polybrominated diphenyl ethers (PBDEs) in farmed and wild European Atlantic salmon fish, aquaculture feeds, and fish oils used to supplement the feeds. The study confirms previous reports of relatively high concentrations of PCBs and indicates moderate concentrations of organochlorine pesticides and PBDEs in farmed Scottish and European salmon. Concentrations of the selected persistent organic pollutants varied among the samples: PCBs (salmon, 145-460 ng/g lipid; salmon feeds, 76-1153 ng/g lipid; fish oils, 9-253 ng/g lipid), S DDTs (salmon, 5-250 ng/g lipid; salmon feeds, 34-52 ng/g lipid; fish oils, 11-218 ng/g lipid), and PBDEs (salmon, 1-85 ng/g lipid: salmon feeds, 8-24 ng/g lipid; fish oils, ND-13 ng/g lipid). Comparison of the samples for all groups of contaminants, except for HCHs, showed an increase in concentration in the order fish oil < feed < salmon. Homologue profiles were similar, with an increase in contribution of hepta- and octa-PCBs in the fish, and profiles of DDTs were similar in all three types of samples. With a constant contribution to the total PCB content, the ICES 7 PCBs appear to be reliable predictors of the PCB contamination profile through all the samples. For PBDEs, BDE 47 dominated the profiles, with no significant difference in the PBDE profiles for the three matrixes. Samples with higher PCB contents generally showed higher levels of the pesticide residues, but this was not the case with the PBDEs, indicating the existence of different pollution sources.

Mining All Non-derivable Frequent Itemsets

Abstract: Recent studies on frequent itemset mining algorithms resulted in significant performance improvements. However, if the minimal support threshold is set too low, or the data is highly correlated, the number of frequent itemsets itself can be prohibitively large. To overcome this problem, recently several proposals have been made to construct a concise representation of the frequent itemsets, instead of mining all frequent itemsets. The main goal of this paper is to identify redundancies in the set of all frequent itemsets and to exploit these redundancies in order to reduce the result of a mining operation. We present deduction rules to derive tight bounds on the support of candidate itemsets. We show how the deduction rules allow for constructing a minimal representation for all frequent itemsets. We also present connections between our proposal and recent proposals for concise representations and we give the results of experiments on real-life datasets that show the effectiveness of the deduction rules. In fact, the experiments even show that in many cases, first mining the concise representation, and then creating the frequent itemsets from this representation outperforms existing frequent set mining algorithms.

Neuroglobin and cytoglobin. Fresh blood for the vertebrate globin family.

Abstract: Neuroglobin and cytoglobin are two recently discovered members of the vertebrate globin family. Both are intracellular proteins endowed with hexacoordinated heme-Fe atoms, in their ferrous and ferric forms, and display O2 affinities comparable with that of myoglobin. Neuroglobin, which is predominantly expressed in nerve cells, is thought to protect neurons from hypoxic–ischemic injury. It is of ancient evolutionary origin, and is homologous to nerve globins of invertebrates. Cytoglobin is expressed in many different tissues, although at varying levels. It shares common ancestry with myoglobin, and can be traced to early vertebrate evolution. The physiological roles of neuroglobin and cytoglobin are not completely understood. Although supplying cells with O2 is the likely function, it is also possible that both globins act as O2-consuming enzymes or as O2 sensors. Here, we review what is currently known about neuroglobin and cytoglobin in terms of their function, tissue distribution and relatedness to the well-known hemoglobin and myoglobin. Strikingly, the data reveal that O2 metabolism in cells is more complicated than was thought before, requiring unexpected O2-binding proteins with potentially novel functional features.

Fluctuating asymmetry as an indicator of fitness: can we bridge the gap between studies?

Abstract: There is growing evidence from both experimental and non-experimental studies that fluctuating asymmetry does not consistently index stress or fitness. The widely held ‐ yet poorly substantiated ‐ belief that fluctuating asymmetry can act as a universal measure of developmental stability and predictor of stressmediated changes in fitness, therefore staggers. Yet attempts to understand why the reported relationships between fluctuating asymmetry, stress and fitness are so heterogeneous ‐ i.e. whether the associations are truly weak or non-existent or whether they become confounded during different stages of the analytical pathways ‐ remain surprisingly scarce. Hence, we attempt to disentangle these causes, by reviewing the various statistical and conceptual factors that are suspected to confound potential relationships between fluctuating asymmetry, stress and fitness. Two main categories of factors are discerned: those associated with the estimation of developmental stability through fluctuating asymmetry, and those associated with the effects of genotype and environment on developmental stability. Next, we describe a series of statistical tools that have recently been developed to help reduce this noise. We argue that the current lack of a theoretical framework that predicts if and when relationships with developmental stability can be expected, urges for further theoretical and empirical research, such as on the genetic architecture of developmental stability in stressed populations. If the underlying developmental mechanisms are better understood, statistical patterns of asymmetry variation may become a biologically meaningful tool.

The European database on small subunit ribosomal RNA

Abstract: The European database on SSU rRNA can be consulted via the World WideWeb at http://rrna.uia.ac.be/ssu/ and compiles all complete or nearly complete small subunit ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also available.

New media, new movements?

Abstract: Collective action and social movement protest has become commonplace in our ‘demonstration‐democracy’ and no longer surprises the media or the public. However, as will be shown, this was not the case with the recent anti‐globalization protests that attracted demonstrators from countries all over the world. The battles of Seattle, Washington, Prague and Genoa, with an unforeseen mixture of nationalities and movements, became world news. Interestingly, the new media seemed to play a crucial role in the organization of these global protests. This article maps this movement‐in‐progress via an analysis of the websites of anti‐globalization, or more specifically anti‐neo‐liberal globalization organizations. It examines the contribution of these sites to three different conditions that establish movement formation; collective identity; actual mobilization and a network of organizations. This ongoing, explorative research indicates signs of an integration of different organizations involved and attribute...

Integrating optimal foraging and optimal oviposition theory in plant–insect research

Abstract: The current approach for studying host selection by phytophagous insects is mainly based on optimal oviposition theory, i.e. the preference-performance hypothesis. Almost no attention has been given to optimal foraging theory. However, recent papers and additional evidence given in this work illustrate that also optimal foraging may shape host preference patterns of phytophagous insects. Therefore and because optimal foraging and optimal oviposition may oppose conflicting needs to phytophagous insects, we plea for an integration of optimal foraging and optimal oviposition in plant-insect research. We argue how this may improve our understanding of plant-insect interactions.