Showing papers by "University of Antwerp published in 2008"

The CMS experiment at the CERN LHC

Abstract: The Compact Muon Solenoid (CMS) detector is described. The detector operates at the Large Hadron Collider (LHC) at CERN. It was conceived to study proton-proton (and lead-lead) collisions at a centre-of-mass energy of 14 TeV (5.5 TeV nucleon-nucleon) and at luminosities up to 10(34)cm(-2)s(-1) (10(27)cm(-2)s(-1)). At the core of the CMS detector sits a high-magnetic-field and large-bore superconducting solenoid surrounding an all-silicon pixel and strip tracker, a lead-tungstate scintillating-crystals electromagnetic calorimeter, and a brass-scintillator sampling hadron calorimeter. The iron yoke of the flux-return is instrumented with four stations of muon detectors covering most of the 4 pi solid angle. Forward sampling calorimeters extend the pseudo-rapidity coverage to high values (vertical bar eta vertical bar <= 5) assuring very good hermeticity. The overall dimensions of the CMS detector are a length of 21.6 m, a diameter of 14.6 m and a total weight of 12500 t.

Platinum-Based Chemotherapy plus Cetuximab in Head and Neck Cancer

Abstract: Background Cetuximab is effective in platinum-resistant recurrent or metastatic squamous-cell carcinoma of the head and neck. We investigated the efficacy of cetuximab plus platinum-based chemotherapy as first-line treatment in patients with recurrent or metastatic squamous-cell carcinoma of the head and neck. Methods We randomly assigned 220 of 442 eligible patients with untreated recurrent or metastatic squamous-cell carcinoma of the head and neck to receive cisplatin (at a dose of 100 mg per square meter of body-surface area on day 1) or carboplatin (at an area under the curve of 5 mg per milliliter per minute, as a 1-hour intravenous infusion on day 1) plus fluorouracil (at a dose of 1000 mg per square meter per day for 4 days) every 3 weeks for a maximum of 6 cycles and 222 patients to receive the same chemotherapy plus cetuximab (at a dose of 400 mg per square meter initially, as a 2-hour intravenous infusion, then 250 mg per square meter, as a 1-hour intravenous infusion per week) for a maximum of 6 cycles. Patients with stable disease who received chemotherapy plus cetuximab continued to receive cetuximab until disease progression or unacceptable toxic effects, whichever occurred first. Results

Social contacts and mixing patterns relevant to the spread of infectious diseases.

Abstract: Background Mathematical modelling of infectious diseases transmitted by the respiratory or close-contact route (e.g., pandemic influenza) is increasingly being used to determine the impact of possible interventions. Although mixing patterns are known to be crucial determinants for model outcome, researchers often rely on a priori contact assumptions with little or no empirical basis. We conducted a population-based prospective survey of mixing patterns in eight European countries using a common paper-diary methodology.

Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Abstract: Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms Recent reviews have described the range of assays that have been used for this purpose(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi) Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response

Old-growth forests as global carbon sinks.

Abstract: Old-growth forests remove carbon dioxide from the atmosphere at rates that vary with climate and nitrogen deposition. The sequestered carbon dioxide is stored in live woody tissues and slowly decomposing organic matter in litter and soil. Old-growth forests therefore serve as a global carbon dioxide sink, but they are not protected by international treaties, because it is generally thought that ageing forests cease to accumulate carbon. Here we report a search of literature and databases for forest carbon-flux estimates. We find that in forests between 15 and 800 years of age, net ecosystem productivity (the net carbon balance of the forest including soils) is usually positive. Our results demonstrate that old-growth forests can continue to accumulate carbon, contrary to the long-standing view that they are carbon neutral. Over 30 per cent of the global forest area is unmanaged primary forest, and this area contains the remaining old-growth forests. Half of the primary forests (6 times 10 8 hectares) are located in the boreal and temperate regions of the Northern Hemisphere. On the basis of our analysis, these forests alone sequester about 1.3 plusminus 0.5 gigatonnes of carbon per year. Thus, our findings suggest that 15 per cent of the global forest area, which is currently not considered when offsetting increasing atmospheric carbon dioxide concentrations, provides at least 10 per cent of the global net ecosystem productivity. Old-growth forests accumulate carbon for centuries and contain large quantities of it. We expect, however, that much of this carbon, even soil carbon, will move back to the atmosphere if these forests are disturbed

Adsorption of H 2 O , N H 3 , CO, N O 2 , and NO on graphene: A first-principles study

Abstract: Motivated by the recent realization of graphene sensors to detect individual gas molecules, we investigate the adsorption of ${\mathrm{H}}_{2}\mathrm{O}$, $\mathrm{N}{\mathrm{H}}_{3}$, CO, $\mathrm{N}{\mathrm{O}}_{2}$, and NO on a graphene substrate using first-principles calculations. The optimal adsorption position and orientation of these molecules on the graphene surface is determined and the adsorption energies are calculated. Molecular doping, i.e., charge transfer between the molecules and the graphene surface, is discussed in light of the density of states and the molecular orbitals of the adsorbates. The efficiency of doping of the different molecules is determined and the influence of their magnetic moment is discussed.

Net carbon dioxide losses of northern ecosystems in response to autumn warming

Abstract: The carbon balance of terrestrial ecosystems is particularly sensitive to climatic changes in autumn and spring(1-4), with spring and autumn temperatures over northern latitudes having risen by about 1.1 degrees C and 0.8 degrees C, respectively, over the past two decades(5). A simultaneous greening trend has also been observed, characterized by a longer growing season and greater photosynthetic activity(6,7). These observations have led to speculation that spring and autumn warming could enhance carbon sequestration and extend the period of net carbon uptake in the future(8). Here we analyse interannual variations in atmospheric carbon dioxide concentration data and ecosystem carbon dioxide fluxes. We find that atmospheric records from the past 20 years show a trend towards an earlier autumn- to- winter carbon dioxide build- up, suggesting a shorter net carbon uptake period. This trend cannot be explained by changes in atmospheric transport alone and, together with the ecosystem flux data, suggest increasing carbon losses in autumn. We use a process- based terrestrial biosphere model and satellite vegetation greenness index observations to investigate further the observed seasonal response of northern ecosystems to autumnal warming. We find that both photosynthesis and respiration increase during autumn warming, but the increase in respiration is greater. In contrast, warming increases photosynthesis more than respiration in spring. Our simulations and observations indicate that northern terrestrial ecosystems may currently lose carbon dioxide in response to autumn warming, with a sensitivity of about 0.2 PgC degrees C-1, offsetting 90% of the increased carbon dioxide uptake during spring. If future autumn warming occurs at a faster rate than in spring, the ability of northern ecosystems to sequester carbon may be diminished earlier than previously suggested(9,10).

Classification of Traumatic Brain Injury for Targeted Therapies

Abstract: The heterogeneity of traumatic brain injury (TBI) is considered one of the most significant barriers to finding effective therapeutic interventions. In October, 2007, the National Institute of Neurological Disorders and Stroke, with support from the Brain Injury Association of America, the Defense and Veterans Brain Injury Center, and the National Institute of Disability and Rehabilitation Research, convened a workshop to outline the steps needed to develop a reliable, efficient and valid classification system for TBI that could be used to link specific patterns of brain and neurovascular injury with appropriate therapeutic interventions. Currently, the Glasgow Coma Scale (GCS) is the primary selection criterion for inclusion in most TBI clinical trials. While the GCS is extremely useful in the clinical management and prognosis of TBI, it does not provide specific information about the pathophysiologic mechanisms which are responsible for neurological deficits and targeted by interventions. On th...

Tuberculosis-associated immune reconstitution inflammatory syndrome: case definitions for use in resource-limited settings.

Abstract: The immune reconstitution inflammatory syndrome (IRIS) has emerged as an important early complication of antiretroviral therapy (ART) in resource-limited settings, especially in patients with tuberculosis. However, there are no consensus case definitions for IRIS or tuberculosis-associated IRIS. Moreover, previously proposed case definitions are not readily applicable in settings where laboratory resources are limited. As a result, existing studies on tuberculosis-associated IRIS have used a variety of non-standardised general case definitions. To rectify this problem, around 100 researchers, including microbiologists, immunologists, clinicians, epidemiologists, clinical trialists, and public-health specialists from 16 countries met in Kampala, Uganda, in November, 2006. At this meeting, consensus case definitions for paradoxical tuberculosis-associated IRIS, ART-associated tuberculosis, and unmasking tuberculosis-associated IRIS were derived, which can be used in high-income and resource-limited settings. It is envisaged that these definitions could be used by clinicians and researchers in a variety of settings to promote standardisation and comparability of data.

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

Abstract: Human immunodeficiency virus type 1 (HIV-1) sequences that pre-date the recognition of AIDS are critical to defining the time of origin and the timescale of virus evolution. A viral sequence from 1959 (ZR59) is the oldest known HIV-1 infection. Other historically documented sequences, important calibration points to convert evolutionary distance into time, are lacking, however; ZR59 is the only one sampled before 1976. Here we report the amplification and characterization of viral sequences from a Bouin's-fixed paraffin-embedded lymph node biopsy specimen obtained in 1960 from an adult female in Leopoldville, Belgian Congo (now Kinshasa, Democratic Republic of the Congo (DRC)), and we use them to conduct the first comparative evolutionary genetic study of early pre-AIDS epidemic HIV-1 group M viruses. Phylogenetic analyses position this viral sequence (DRC60) closest to the ancestral node of subtype A (excluding A2). Relaxed molecular clock analyses incorporating DRC60 and ZR59 date the most recent common ancestor of the M group to near the beginning of the twentieth century. The sizeable genetic distance between DRC60 and ZR59 directly demonstrates that diversification of HIV-1 in west-central Africa occurred long before the recognized AIDS pandemic. The recovery of viral gene sequences from decades-old paraffin-embedded tissues opens the door to a detailed palaeovirological investigation of the evolutionary history of HIV-1 that is not accessible by other methods.

Defining cyberbullying: a qualitative research into the perceptions of youngsters.

Abstract: Data from 53 focus groups, which involved students from 10 to 18 years old, show that youngsters often interpret “cyberbullying” as “Internet bullying” and associate the phenomenon with a wide range of practices. In order to be considered “true” cyberbullying, these practices must meet several criteria. They should be intended to hurt (by the perpetrator) and perceived as hurtful (by the victim); be part of a repetitive pattern of negative offline or online actions; and be performed in a relationship characterized by a power imbalance (based on “real-life” power criteria, such as physical strength or age, and/or on ICT-related criteria such as technological know-how and anonymity).

Mass loss of galaxies due to an ultraviolet background

Abstract: We perform cosmological hydrodynamic simulations to determine to what extent galaxies lose their gas due to photoheating from an ionizing background. We find that the characteristic mass at which haloes on average have lost half of their baryons is M c ∼ 6.5 x 10 9 h -1 M ⊙ at z = 0, which corresponds to a circular velocity of 25 km s -1 . This is significantly lower than the filtering mass obtained by the linear theory, which is often used in semi-analytical models of galaxy formation. We demonstrate it is the gas temperature at the virial radius which determines whether a halo can accrete gas. A simple model that follows the merger history of the dark matter progenitors, and where gas accretion is not allowed when this temperature is higher than the virial temperature of the halo, reproduces the results from the simulation remarkably well. This model can be applied to any reionization history, and is easy to incorporate in semi-analytical models.

Quantized vortices in an exciton–polariton condensate

Abstract: When a superfluid—such as liquid helium—is set in rotation, vortices appear in which circulation around a closed loop can take only discrete values. Such quantized vortices have now been observed in a solid-state system—a Bose–Einstein condensate made of exciton polaritons. One of the most striking quantum effects in an interacting Bose gas at low temperature is superfluidity. First observed in liquid 4He, this phenomenon has been intensively studied in a variety of systems for its remarkable features such as the persistence of superflows and the proliferation of quantized vortices1. The achievement of Bose–Einstein condensation in dilute atomic gases2 provided the opportunity to observe and study superfluidity in an extremely clean and well-controlled environment. In the solid state, Bose–Einstein condensation of exciton polaritons has been reported recently3,4,5,6. Polaritons are strongly interacting light–matter quasiparticles that occur naturally in semiconductor microcavities in the strong-coupling regime and constitute an interesting example of composite bosons. Here, we report the observation of spontaneous formation of pinned quantized vortices in the Bose-condensed phase of a polariton fluid. Theoretical insight into the possible origin of such vortices is presented in terms of a generalized Gross–Pitaevskii equation. Whereas the observation of quantized vortices is, in itself, not sufficient for establishing the superfluid nature of the non-equilibrium polariton condensate, it suggests parallels between our system and conventional superfluids.

Fish invasions in the world's river systems: when natural processes are blurred by human activities.

Abstract: Because species invasions are a principal driver of the human-induced biodiversity crisis, the identification of the major determinants of global invasions is a prerequisite for adopting sound conservation policies. Three major hypotheses, which are not necessarily mutually exclusive, have been proposed to explain the establishment of non-native species: the “human activity” hypothesis, which argues that human activities facilitate the establishment of non-native species by disturbing natural landscapes and by increasing propagule pressure; the “biotic resistance” hypothesis, predicting that species-rich communities will readily impede the establishment of non-native species; and the “biotic acceptance” hypothesis, predicting that environmentally suitable habitats for native species are also suitable for non-native species. We tested these hypotheses and report here a global map of fish invasions (i.e., the number of non-native fish species established per river basin) using an original worldwide dataset of freshwater fish occurrences, environmental variables, and human activity indicators for 1,055 river basins covering more than 80% of Earth's surface. First, we identified six major invasion hotspots where non-native species represent more than a quarter of the total number of species. According to the World Conservation Union, these areas are also characterised by the highest proportion of threatened fish species. Second, we show that the human activity indicators account for most of the global variation in non-native species richness, which is highly consistent with the “human activity” hypothesis. In contrast, our results do not provide support for either the “biotic acceptance” or the “biotic resistance” hypothesis. We show that the biogeography of fish invasions matches the geography of human impact at the global scale, which means that natural processes are blurred by human activities in driving fish invasions in the world's river systems. In view of our findings, we fear massive invasions in developing countries with a growing economy as already experienced in developed countries. Anticipating such potential biodiversity threats should therefore be a priority.

Incapacitating Unilateral Tinnitus in Single-Sided Deafness Treated by Cochlear Implantation

Abstract: Objectives:Tinnitus is a well-known, difficult-to-treat symptom of hearing loss. Users of cochlear implants (CIs) have reported a reduction in tinnitus following implantation for bilateral severe-t...

Synthesis of few-layer graphene via microwave plasma-enhanced chemical vapour deposition

Abstract: If graphene is ever going to live up to the promises of future nanoelectronic devices, an easy and cheap route for mass production is an essential requirement. A way to extend the capabilities of plasma-enhanced chemical vapour deposition to the synthesis of freestanding few-layer graphene is presented. Micrometre-wide flakes consisting of four to six atomic layers of stacked graphene sheets have been synthesized by controlled recombination of carbon radicals in a microwave plasma. A simple and highly reproducible technique is essential, since the resulting flakes can be synthesized without the need for a catalyst on the surface of any substrate that withstands elevated temperatures up to 700 °C. A thorough structural analysis of the flakes is performed with electron microscopy, x-ray diffraction, Raman spectroscopy and scanning tunnelling microscopy. The resulting graphene flakes are aligned vertically to the substrate surface and grow according to a three-step process, as revealed by the combined analysis of electron microscopy and x-ray photoelectron spectroscopy.

Classification and control of the origin of photoluminescence from Si nanocrystals

Abstract: Silicon dominates the electronics industry, but its poor optical properties mean that III–V compound semiconductors are preferred for photonics applications. Photoluminescence at visible wavelengths was observed from porous Si at room temperature in 1990, but the origin of these photons (do they arise from highly localized defect states or quantum confinement effects?) has been the subject of intense debate ever since. Attention has subsequently shifted from porous Si to Si nanocrystals, but the same fundamental question about the origin of the photoluminescence has remained. Here we show, based on measurements in high magnetic fields, that defects are the dominant source of light from Si nanocrystals. Moreover, we show that it is possible to control the origin of the photoluminescence in a single sample: passivation with hydrogen removes the defects, resulting in photoluminescence from quantum-confined states, but subsequent ultraviolet illumination reintroduces the defects, making them the origin of the light again.

Antimicrobial drug use and resistance in Europe.

Abstract: Our study confronts the use of antimicrobial agents in ambulatory care with the resistance trends of 2 major pathogens, Streptococcus pneumoniae and Escherichia coli, in 21 European countries in 2000-2005 and explores whether the notion that antimicrobial drug use determines resistance can be supported by surveillance data at national aggregation levels. The data obtained from the European Surveillance of Antimicrobial Consumption and the European Antimicrobial Resistance Surveillance System suggest that variation of consumption coincides with the occurrence of resistance at the country level. Linear regression analysis showed that the association between antimicrobial drug use and resistance was specific and robust for 2 of 3 compound pathogen combinations, stable over time, but not sensitive enough to explain all of the observed variations. Ecologic studies based on routine surveillance data indicate a relation between use and resistance and support interventions designed to reduce antimicrobial drug consumption at a national level in Europe.

Meta-analyses of genetic studies on major depressive disorder.

Abstract: The genetic basis of major depressive disorder (MDD) has been investigated extensively, but the identification of MDD genes has been hampered by conflicting results from underpowered studies. We review all MDD case-control genetic association studies published before June 2007 and perform meta-analyses for polymorphisms that had been investigated in at least three studies. The study selection and data extraction were performed in duplicate by two independent investigators. The 183 papers that met our criteria studied 393 polymorphisms in 102 genes. Twenty-two polymorphisms (6%) were investigated in at least three studies. Seven polymorphisms had been evaluated in previous meta-analyses, 5 of these had new data available. Hence, we performed meta-analyses for 20 polymorphisms in 18 genes. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. Statistically significant associations were found for the APOE varepsilon2 (OR, 0.51), GNB3 825T (OR, 1.38), MTHFR 677T (OR, 1.20), SLC6A4 44 bp Ins/Del S (OR, 1.11) alleles and the SLC6A3 40 bpVNTR 9/10 genotype (OR, 2.06). To date, there is statistically significant evidence for six MDD susceptibility genes (APOE, DRD4, GNB3, MTHFR, SLC6A3 and SLC6A4).

Ram pressure stripping the hot gaseous haloes of galaxies in groups and clusters

Abstract: We use a large suite of carefully controlled full hydrodynamic simulations to study the ram pressure stripping of the hot gaseous haloes of galaxies as they fall into massive groups and clusters. The sensitivity of the results to the orbit, total galaxy mass, and galaxy structural properties is explored. For typical structural and orbital parameters, we find that ∼30 per cent of the initial hot galactic halo gas can remain in place after 10 Gyr. We propose a physically simple analytic model that describes the stripping seen in the simulations remarkably well. The model is analogous to the original formulation of Gunn & Gott, except that it is appropriate for the case of a spherical (hot) gas distribution (as opposed to a face-on cold disc) and takes into account that stripping is not instantaneous but occurs on a characteristic time-scale. The model reproduces the results of the simulations to within ≈10 per cent at almost all times for all the orbits, mass ratios, and galaxy structural properties we have explored. The one exception involves unlikely systems where the orbit of the galaxy is highly non-radial and its mass exceeds about 10 per cent of the group or cluster into which it is falling (in which case the model underpredicts the stripping following pericentric passage). The proposed model has several interesting applications, including modelling the ram pressure stripping of both observed and cosmologically simulated galaxies and as a way to improve present semi-analytic models of galaxy formation. One immediate consequence is that the colours and morphologies of satellite galaxies in groups and clusters will differ significantly from those predicted with the standard assumption of complete stripping of the hot coronae.

Ruthenium Nanoparticles inside Porous [Zn4O(bdc)3] by Hydrogenolysis of Adsorbed [Ru(cod)(cot)]: A Solid-State Reference System for Surfactant-Stabilized Ruthenium Colloids

Abstract: The gas-phase loading of [Zn4O(bdc)3] (MOF-5; bdc = 1,4-benzenedicarboxylate) with the volatile compound [Ru(cod)(cot)] (cod = 1,5-cyclooctadiene, cot = 1,3,5-cyclooctatriene) was followed by solid-state 13C magic angle spinning (MAS) NMR spectroscopy. Subsequent hydrogenolysis of the adsorbed complex inside the porous structure of MOF-5 at 3 bar and 150 °C was performed, yielding ruthenium nanoparticles in a typical size range of 1.5–1.7 nm, embedded in the intact MOF-5 matrix, as confirmed by transmission electron microscopy (TEM), selected area electron diffraction (SAED), powder X-ray diffraction (PXRD), and X-ray absorption spectroscopy (XAS). The adsorption of CO molecules on the obtained Ru@MOF-5 nanocomposite was followed by IR spectroscopy. Solid-state 2H NMR measurements indicated that MOF-5 was a stabilizing support with only weak interactions with the embedded particles, as deduced from the surprisingly high mobility of the surface Ru−D species in comparison to surfactant-stabilized colloidal ...

Coagulation disorders after traumatic brain injury

Abstract: Background. Over the past decade new insights in our understanding of coagulation have identified the prominent role of tissue factor. The brain is rich in tissue factor, and injury to the brain may initiate disturbances in local and systemic coagulation. We aimed to review the current knowledge on the pathophysiology, incidence, nature, prognosis and treatment of coagulation disorders following traumatic brain injury (TBI). Methods. We performed a MEDLINE search from 1966 to April 2007 with various MESH headings, focusing on head trauma and coagulopathy. We identified 441 eligible English language studies. These were reviewed for relevance by two independent investigators. A meta-analysis was performed to calculate the frequencies of coagulopathy after TBI and to determine the association of coagulopathy and outcome, expressed as odds ratios. Results. Eighty-two studies were relevant for the purpose of this review. Meta-analysis of 34 studies reporting the frequencies of coagulopathy after TBI, showed an overall prevalence of 32.7%. The presence of coagulopathy after TBI was related both to mortality (OR 9.0; 95%CI: 7.3–11.6) and unfavourable outcome (OR 36.3; 95%CI: 18.7–70.5). Conclusions. We conclude that coagulopathy following traumatic brain injury is an important independent risk factor related to prognosis. Routine determination of the coagulation status should therefore be performed in all patients with traumatic brain injury. These data may have important implications in patient management. Well-performed prospective clinical trials should be undertaken as a priority to determine the beneficial effects of early treatment of coagulopathy.

Social value orientation and cooperation in social dilemmas: a review and conceptual model.

Abstract: Social psychologists have long recognized that people fundamentally differ with respect to their social value orientation (SVO), that is, self-regarding versus other regarding preferences, and that these differences affect cooperative behaviour in situations of interdependence. In this paper, we systematically review the vast number of findings on SVO and cooperation, and synthesize the state of the art by presenting an integrated conceptual model that may explain why and when people with different social values select different behavioural strategies in social dilemmas. Specifically, building on Pruitt and Kimmel's (1977) goal/expectation theory and our review of the literature, we suggest that the relationship between SVO and cooperative behaviour is mediated by (1) a cooperative goal and (2) the specific expectations concerning alters' behaviour. We also propose that trust and goal alignment are important contextual moderators of this relationship: for prosocials, cues signalling trust are necessary to generate positive expectations regarding alters' behaviour, whereas proselfs need external incentives to align their personal interest with a cooperative goal. We conclude this review by pointing to several avenues for future research that would help to deepen our understanding of the role of SVO in human cooperation.