Showing papers by "University of Vienna published in 2005"

Evolution of indirect reciprocity.

Abstract: Natural selection is conventionally assumed to favour the strong and selfish who maximize their own resources at the expense of others. But many biological systems, and especially human societies, are organized around altruistic, cooperative interactions. How can natural selection promote unselfish behaviour? Various mechanisms have been proposed, and a rich analysis of indirect reciprocity has recently emerged: I help you and somebody else helps me. The evolution of cooperation by indirect reciprocity leads to reputation building, morality judgement and complex social interactions with ever-increasing cognitive demands.

Musculoskeletal ultrasound including definitions for ultrasonographic pathology

Abstract: Ultrasound (US) has great potential as an outcome in rheumatoid arthritis trials for detecting bone erosions, synovitis, tendon disease, and enthesopathy. It has a number of distinct advantages over magnetic resonance imaging, including good patient tolerability and ability to scan multiple joints in a short period of time. However, there are scarce data regarding its validity, reproducibility, and responsiveness to change, making interpretation and comparison of studies difficult. In particular, there are limited data describing standardized scanning methodology and standardized definitions of US pathologies. This article presents the first report from the OMERACT ultrasound special interest group, which has compared US against the criteria of the OMERACT filter. Also proposed for the first time are consensus US definitions for common pathological lesions seen in patients with inflammatory arthritis.

SAPS 3—From evaluation of the patient to evaluation of the intensive care unit. Part 2: Development of a prognostic model for hospital mortality at ICU admission

Abstract: Objective To develop a model to assess severity of illness and predict vital status at hospital discharge based on ICU admission data.

Experimental One-Way Quantum Computing

Abstract: Standard quantum computation is based on sequences of unitary quantum logic gates that process qubits. The one-way quantum computer proposed by Raussendorf and Briegel is entirely different. It has changed our understanding of the requirements for quantum computation and more generally how we think about quantum physics. This new model requires qubits to be initialized in a highly entangled cluster state. From this point, the quantum computation proceeds by a sequence of single-qubit measurements with classical feedforward of their outcomes. Because of the essential role of measurement, a one-way quantum computer is irreversible. In the one-way quantum computer, the order and choices of measurements determine the algorithm computed. We have experimentally realized four-qubit cluster states encoded into the polarization state of four photons. We characterize the quantum state fully by implementing experimental four-qubit quantum state tomography. Using this cluster state, we demonstrate the feasibility of one-way quantum computing through a universal set of one- and two-qubit operations. Finally, our implementation of Grover's search algorithm demonstrates that one-way quantum computation is ideally suited for such tasks.

Toward a Neoproterozoic composite carbon-isotope record

Abstract: Glacial deposits of Sturtian and Marinoan age occur in the well-studied Neoproterozoic successions of northern Namibia, South Australia, and northwestern Canada. In all three regions, the Marinoan glaciation is presaged by a large negative δ 13 C anomaly, and the cap carbonates to both glacial units share a suite of unique sedimentological, stratigraphic, and geochemical features. These global chronostratigraphic markers are the bases of a new correlation scheme for the Neoproterozoic that corroborates radiometric data that indicate that there were three glacial epochs between ca. 750 and 580 Ma. Intraregional correlation of Neoproterozoic successions in the present-day North Atlantic region suggests that glacial diamictite pairs in the Polarisbreen Group in northeastern Svalbard and the Tillite Group in eastern Greenland were deposited during the Marinoan glaciation, whereas the younger of a pair of glacials (Mortensnes Formation) in the Vestertana Group of northern Norway was deposited during the third (Gaskiers) Neoproterozoic glaciation. Gaskiers-aged glacial deposits are neither globally distributed nor overlain by a widespread cap carbonate but are associated with an extremely negative δ 13 C anomaly. framework for a new, high-resolution model carbon-isotope record for the Neoproterozoic comprising new δ 13 C (carbonate) data from Svalbard (Akademikerbreen Group) and Namibia (Otavi Group) and data in the literature from Svalbard, Namibia, and Oman. A new U-Pb zircon age of 760 ± 1 Ma from an ash bed in the Ombombo Subgroup in Namibia provides the oldest direct time-calibration point in the compilation, but the time scale of this preliminary δ 13 C record remains

Fast and reliable prediction of noncoding RNAs

Abstract: We report an efficient method for detecting functional RNAs. The approach, which combines comparative sequence analysis and structure prediction, already has yielded excellent results for a small number of aligned sequences and is suitable for large-scale genomic screens. It consists of two basic components: (i) a measure for RNA secondary structure conservation based on computing a consensus secondary structure, and (ii) a measure for thermodynamic stability, which, in the spirit of a z score, is normalized with respect to both sequence length and base composition but can be calculated without sampling from shuffled sequences. Functional RNA secondary structures can be identified in multiple sequence alignments with high sensitivity and high specificity. We demonstrate that this approach is not only much more accurate than previous methods but also significantly faster. The method is implemented in the program rnaz, which can be downloaded from www.tbi.univie.ac.at/~wash/RNAz. We screened all alignments of length n ≥ 50 in the Comparative Regulatory Genomics database, which compiles conserved noncoding elements in upstream regions of orthologous genes from human, mouse, rat, Fugu, and zebrafish. We recovered all of the known noncoding RNAs and cis-acting elements with high significance and found compelling evidence for many other conserved RNA secondary structures not described so far to our knowledge.

The Perdew–Burke–Ernzerhof exchange-correlation functional applied to the G2-1 test set using a plane-wave basis set

Abstract: Present local and semilocal functionals show significant errors, for instance, in the energetics of small molecules and in the description of band gaps. One possible solution to these problems is the introduction of exact exchange and hybrid functionals. A plane-wave-based algorithm was implemented in VASP (Vienna ab-initio simulation package) to allow for the calculation of the exact exchange. To systematically assess the precision of the present implementation, calculations for the 55 molecules of the G2-1 quantum chemical test set were performed applying the PBE and PBE0 functionals. Excellent agreement for both atomization energies and geometries compared with the results obtained by GAUSSIAN 03 calculations using large basis sets (augmented correlation consistent polarized valence quadruple zeta for the geometry optimization and augmented correlation-consistent polarized valence quintuple zeta for the energy calculations) was found. The mean absolute error for atomization energies between VASP and the experiment is 8.6 and 3.7 kcalmol, as calculated with the PBE and PBE0 functionals, respectively. The mean deviations between VASP and GAUSSIAN are 0.46 and 0.49 kcalmol for the PBE and PBE0 functionals, respectively.

Model selection and inference: facts and fiction

Abstract: Model selection has an important impact on subsequent inference. Ignoring the model selection step leads to invalid inference. We discuss some intricate aspects of data-driven model selection that do not seem to have been widely appreciated in the literature. We debunk some myths about model selection, in particular the myth that consistent model selection has no effect on subsequent inference asymptotically. We also discuss an “impossibility” result regarding the estimation of the finite-sample distribution of post-model-selection estimators.

Prediction of BRCA1 Status in Patients with Breast Cancer Using Estrogen Receptor and Basal Phenotype

Abstract: Purpose: To investigate the proportion of breast cancers arising inpatients with germ line BRCA1 and BRCA2 mutations expressing basal markers and developing predictive tests for identification of high-risk patients. Experimental Design: Histopathologic material from 182 tumors in BRCA1 mutation carriers, 63 BRCA2 carriers, and 109 controls, collected as part of the international Breast Cancer Linkage Consortium were immunohistochemically stained for CK14, CK5/6, CK17, epidermal growth factor receptor (EGFR), and osteonectin. Results: All five basal markers were commoner in BRCA1 tumors than in control tumors (CK14: 61% versus 12%; CK5/6: 58% versus 7%; CK17: 53% versus 10%; osteonectin: 43% versus 19%; EGFR: 67% versus 21%; P < 0.0001 in each case). In a multivariate analysis, CK14, CK5/6, and estrogen receptor (ER) remained significant predictors of BRCA1 carrier status. In contrast, the frequency of basal markers in BRCA2 tumors did not differ significant from controls. Conclusion: The use of cytokeratin staining in combination with ER and morphology provides a more accurate predictor of BRCA1 mutation status than previously available, that may be useful in selecting patients for BRCA1 mutation testing. The high percentage of BRCA1 cases positive for EGFR suggests that specific anti-tyrosine kinase therapy may be of potential benefit in these patients.

Update of the preclinical situation of anticancer platinum complexes: novel design strategies and innovative analytical approaches.

Abstract: Research in the field of bioinorganic chemistry has been stimulated by the worldwide success of the anticancer drug cisplatin. 40 years after the first report about its biological activity, carboplatin and oxaliplatin are in routine clinical use today, whereas nedaplatin, lobaplatin, and heptaplatin (SKI2053R) are only approved in Japan, China, and South Korea, respectively. Up to now, about 35 platinum complexes entered clinical trials in order to circumvent the side-effects and the problem of tumor resistance to cisplatin. Additionally, improvement of tumor selectivity as well as the need for a broader spectrum of indications are the motivations for tremendous efforts in the development of novel anticancer platinum-based drugs. New synthetic strategies and innovative analytical approaches provide a basis for a deeper understanding of the pharmacological profile of cisplatin and analogues (biodistribution, clearance, detoxification, sideeffects, tumor specificity, cellular uptake, acquired or intrinsic resistance, platinum-DNA adduct removal by the cellular machinery) and give rise to a rational design of promising anticancer platinum coordination compounds. This article reviews the recent development of preclinical platinum complexes with interesting in vitro and in vivo tumor inhibiting properties. It focuses also on innovative synthetic strategies leading to novel classes of platinum complexes. A small part of the review is dedicated to new analytical approaches which have been supplied to or emerged in this field of research.

KIDSCREEN-52 quality-of-life measure for children and adolescents.

Abstract: This study describes the development and reports the first psychometric results of the European KIDSCREEN-52 generic health-related quality-of-life questionnaire for children and adolescents. The KIDSCREEN-52, including ten dimensions, was applied in a European survey involving 12 countries (i.e., Austria, Switzerland, Czech Republic, Germany, Greece, Spain, France, Hungary, The Netherlands, Poland, Sweden and the UK) and 22,110 children and adolescents aged between 8 and 18 years of age. Questionnaire development included a literature search, expert consultation, and focus group discussions with children and adolescents. After definition of dimensions and collection of items, a translation process following international translation guidelines, cognitive interviews and a pilot test were performed. Analysis regarding psychometric properties showed Cronbach-α ranged from 0.77 to 0.89. Correlation coefficients between KINDLR and KIDSCREEN-52 dimensions were high for those assessing similar constructs (r = 0.51-0.68). All KIDSCREEN-52 dimensions showed a gradient according to socioeconomic status and most dimensions showed a gradient according to psychosomatic health complaints. The first results demonstrate that the KIDSCREEN-52 questionnaire is a promising cross-cultural measure of health-related quality-of-life assessment for children and adolescents in Europe. © 2005 Future Drugs Ltd.

Light-induced charge separation in anatase TiO2 particles.

Abstract: Ultraviolet light-induced electron−hole pair excitations in anatase TiO2 powders were studied by a combination of electron paramagnetic resonance and infrared spectroscopy measurements. During continuous UV irradiation in the mW.cm-2 range, photogenerated electrons are either trapped at localized sites, giving paramagnetic Ti3+ centers, or remain in the conduction band as EPR silent species which may be observed by their IR absorption. Using low temperatures (90 K) to reduce the rate of the electron−hole recombination processes, trapped electrons and conduction band electrons exhibit lifetimes of hours. The EPR-detected holes produced by photoexcitation are O- species, produced from lattice O2- ions. It is found that under high vacuum conditions, the major fraction of photoexcited electrons remains in the conduction band. At 298 K, all stable hole and electron states are lost from TiO2. Defect sites produced by oxygen removal during annealing of anatase TiO2 are found to produce a Ti3+ EPR spectrum identi...

Renormalisation of ϕ4-Theory on Noncommutative ℝ4 in the Matrix Base

Abstract: We prove that the real four-dimensional Euclidean noncommutative ϕ4-model is renormalisable to all orders in perturbation theory. Compared with the commutative case, the bare action of relevant and marginal couplings contains necessarily an additional term: an harmonic oscillator potential for the free scalar field action. This entails a modified dispersion relation for the free theory, which becomes important at large distances (UV/IR-entanglement). The renormalisation proof relies on flow equations for the expansion coefficients of the effective action with respect to scalar fields written in the matrix base of the noncommutative ℝ4. The renormalisation flow depends on the topology of ribbon graphs and on the asymptotic and local behaviour of the propagator governed by orthogonal Meixner polynomials.

SAPS 3-From evaluation of the patient to evaluation of the intensive care unit. Part 1. Objectives, methods and cohort description

Abstract: Objective Risk adjustment systems now in use were developed more than a decade ago and lack prognostic performance. Objective of the SAPS 3 study was to collect data about risk factors and outcomes in a heterogeneous cohort of intensive care unit (ICU) patients, in order to develop a new, improved model for risk adjustment.

Nomenclature for factors of the HLA system, 2004

Abstract: Correspondence to: Dr Steven G. E. Marsh Anthony Nolan Research Institute Royal Free Hospital Pond Street Hampstead London NW3 2QG UK Tel.: þ442072848321 Fax: þ442072848331 e-mail: marsh@ebi.ac.uk Following the decision to hold their next full meeting after the 14th International Histocompatibility Workshop in 2005, the WHO Nomenclature Committee for Factors of the HLA System has decided to publish an interim report listing updated tables of alleles including those assigned since the publication of the last full report in 2002 (1). The alleles named during the period follow the principles established in previous reports (1–17).

Amoebae as Training Grounds for Intracellular Bacterial Pathogens

Abstract: Free-living amoebae are important predators that control microbial communities. They are ubiquitous and have been isolated from various natural sources such as soil, freshwater, salt water, dust, and air. Although their abundance in soil is only limited, they have been implicated in the stimulation

The Yin and Yang of type I interferon activity in bacterial infection

Abstract: Interferons (IFNs) are cytokines that are important for immune responses, particularly to intracellular pathogens. They are divided into two structurally and functionally distinct types that interact with different cell-surface receptors. Classically, type I IFNs are potent antiviral immunoregulators, whereas the type II IFN enhances antibacterial immunity. However, as outlined here, type I IFNs are also produced in response to infection with other pathogens, and an increasing body of work shows that type I IFNs have an important role in the host response to bacterial infection. Strikingly, their activity can be either favourable or detrimental, and can influence various immune effector mechanisms.

The MAP kinase substrate MKS1 is a regulator of plant defense responses

Abstract: Arabidopsis MAP kinase 4 (MPK4) functions as a regulator of pathogen defense responses, because it is required for both repression of salicylic acid (SA)-dependent resistance and for activation of jasmonate (JA)-dependent defense gene expression. To understand MPK4 signaling mechanisms, we used yeast two-hybrid screening to identify the MPK4 substrate MKS1. Analyses of transgenic plants and genome-wide transcript profiling indicated that MKS1 is required for full SA-dependent resistance in mpk4 mutants, and that overexpression of MKS1 in wild-type plants is sufficient to activate SA-dependent resistance, but does not interfere with induction of a defense gene by JA. Further yeast two-hybrid screening revealed that MKS1 interacts with the WRKY transcription factors WRKY25 and WRKY33. WRKY25 and WRKY33 were shown to be in vitro substrates of MPK4, and a wrky33 knockout mutant was found to exhibit increased expression of the SA-related defense gene PR1. MKS1 may therefore contribute to MPK4-regulated defense activation by coupling the kinase to specific WRKY transcription factors.

Remission and active disease in rheumatoid arthritis: defining criteria for disease activity states.

Abstract: Objective Several composite scores are available to assess the activity of rheumatoid arthritis (RA). Criteria for remission and active RA based on these continuous scores are important for use in clinical practice and clinical trials. We aimed to reevaluate or to define such criteria for the Disease Activity Score in 28 joints (DAS28) and the Simplified Disease Activity Index (SDAI). Methods We sampled patient profiles from an observational RA database that included clinical and laboratory variables. Thirty-five rheumatology experts classified these profiles into 1 of 4 categories: remission, low, moderate, or high disease activity. Cutoff values were estimated by mapping scores on the DAS28 and SDAI to these ratings, and analyses of agreement (kappa statistics) and a diagnostic testing approach (receiver operating characteristic curves) were used to validate the estimates. The final criteria were validated using 2 observational cohorts (a routine cohort of 767 patients and an inception cohort of 91 patients). Results Results from the 3 analyses were very similar and were integrated. The criteria for separating remission, low, moderate, and high disease activity based on the SDAI were scores of 3.3, 11, and 26, respectively; those based on the DAS28 were scores of 2.4, 3.6, 5.5, respectively. In the routine cohort, these cutoff values showed substantial agreement (weighed κ = 0.70) and discriminated between groups of patients with clearly different functional capacities (P < 0.001). In the inception cohort, these cutoff scores differentiated responders (those with a 20% response on the American College of Rheumatology improvement criteria) from nonresponders (P < 0.01), as well as patients with and without radiologic progression (P < 0.05). Conclusion New criteria for levels of RA disease activity were determined and internally validated. These criteria, which are based on current and explicit expert judgment, are valuable in this era of rapidly advancing therapeutic approaches.

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.

Abstract: The RFAM database defines families of ncRNAs by means of sequence similarities that are sufficient to establish homology. In some cases, such as microRNAs and box H/ACA snoRNAs, functional commonalities define classes of RNAs that are characterized by structural similarities, and typically consist of multiple RNA families. Recent advances in high-throughput transcriptomics and comparative genomics have produced very large sets of putative noncoding RNAs and regulatory RNA signals. For many of them, evidence for stabilizing selection acting on their secondary structures has been derived, and at least approximate models of their structures have been computed. The overwhelming majority of these hypothetical RNAs cannot be assigned to established families or classes. We present here a structure-based clustering approach that is capable of extracting putative RNA classes from genome-wide surveys for structured RNAs. The LocARNA (local alignment of RNA) tool implements a novel variant of the Sankoff algorithm that is sufficiently fast to deal with several thousand candidate sequences. The method is also robust against false positive predictions, i.e., a contamination of the input data with unstructured or nonconserved sequences. We have successfully tested the LocARNA-based clustering approach on the sequences of the RFAM-seed alignments. Furthermore, we have applied it to a previously published set of 3,332 predicted structured elements in the Ciona intestinalis genome (Missal K, Rose D, Stadler PF (2005) Noncoding RNAs in Ciona intestinalis. Bioinformatics 21 (Supplement 2): i77–i78). In addition to recovering, e.g., tRNAs as a structure-based class, the method identifies several RNA families, including microRNA and snoRNA candidates, and suggests several novel classes of ncRNAs for which to date no representative has been experimentally characterized.

Intra-articular hyaluronic acid for the treatment of osteoarthritis of the knee: systematic review and meta-analysis

Abstract: Background: Osteoarthritis of the knee affects up to 10% of the elderly population. The condition is frequently treated by intra-articular injection of hyaluronic acid. We performed a systematic review and meta-analysis of randomized controlled trials to assess the effectiveness of this treatment. Methods: We searched MEDLINE, EMBASE, CINAHL, BIOSIS and the Cochrane Controlled Trial Register from inception until April 2004 using a combination of search terms for knee osteoarthritis and hyaluronic acid and a filter for randomized controlled trials. We extracted data on pain at rest, pain during or immediately after movement, joint function and adverse events. Results: Twenty-two trials that reported usable quantitative information on any of the predefined end points were identified and included in the systematic review. Even though pain at rest may be improved by hyaluronic acid, the data available from these studies did not allow an appropriate assessment of this end point. Patients who received the intervention experienced a reduction in pain during movement: the mean difference on a 100-mm visual analogue scale was –3.8 mm (95% confidence interval [CI] –9.1 to 1.4 mm) after 2–6 weeks, –4.3 mm (95% CI –7.6 to –0.9 mm) after 10–14 weeks and –7.1 mm (95% CI –11.8 to –2.4 mm) after 22–30 weeks. However, this effect was not compatible with a clinically meaningful difference (expected to be about 15 mm on the visual analogue scale). Furthermore, the effect was exaggerated by trials not reporting an intention-to-treat analysis. No improvement in knee function was observed at any time point. Even so, the effect of hyaluronic acid on knee function was more favourable when allocation was not concealed. Adverse events occurred slightly more often among patients who received the intervention (relative risk 1.08, 95% CI 1.01 to 1.15). Only 4 trials explicitly reported allocation concealment, had blinded outcome assessment and presented intention-to-treat data. Interpretation: According to the currently available evidence, intra-articular hyaluronic acid has not been proven clinically effective and may be associated with a greater risk of adverse events. Large trials with clinically relevant and uniform end points are necessary to clarify the benefit–risk ratio.

Prevalence of Drug-Resistant HIV-1 Variants in Untreated Individuals in Europe: Implications for Clinical Management

Abstract: BackgroundInfection with drug-resistant human immunodeficiency virus type 1 (HIV-1) can impair the response to combination therapy. Widespread transmission of drug-resistant variants has the disturbing potential of limiting future therapy options and affecting the efficacy of postexposure prophylaxispenta increase-spacing 1>MethodsWe determined the baseline rate of drug resistance in 2208 therapy-naive patients recently and chronically infected with HIV-1 from 19 European countries during 1996–2002ResultsIn Europe, 1 of 10 antiretroviral-naive patients carried viruses with ⩾1 drug-resistance mutation. Recently infected patients harbored resistant variants more often than did chronically infected patients (13.5% vs. 8.7%; P=.006). Non-B viruses (30%) less frequently carried resistance mutations than did subtype B viruses (4.8% vs. 12.9%; P<.01). Baseline resistance increased over time in newly diagnosed cases of non-B infection: from 2.0% (1/49) in 1996–1998 to 8.2% (16/194) in 2000–2001ConclusionsDrug-resistant variants are frequently present in both recently and chronically infected therapy-naive patients. Drug-resistant variants are most commonly seen in patients infected with subtype B virus, probably because of longer exposure of these viruses to drugs. However, an increase in baseline resistance in non-B viruses is observed. These data argue for testing all drug-naive patients and are of relevance when guidelines for management of postexposure prophylaxis and first-line therapy are updated

Intersphincteric resection for low rectal tumours.

Abstract: Preface .- Preoperative diagnostic procedures: Pathology of rectal cancer .- MRT for staging .- Preoperative therapeutic options: Preoperative chemoradiotherapy .- Rectal surgery: Surgical anatomy of the pelvis .- Basics of rectal cancer surgery .- Development of intersphincteric resection .- Surgical technique of ISR .- Laparoscopic technique .- Experience in France .- Modification of ISR .- Our technique of ISR .- Experience in Japan .- Experience in China .- Experience in Germany .- Sphincter restoration after APR .- Laparoscopic ISR .- ISR with reconstruction of the internal sphincter .- Quality of life after very low rectal resections .- Do we need a pouch for reconstruction?

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome

Abstract: In contrast to the fairly reliable and complete annotation of the protein coding genes in the human genome, comparable information is lacking for noncoding RNAs (ncRNAs). We present a comparative screen of vertebrate genomes for structural noncoding RNAs, which evaluates conserved genomic DNA sequences for signatures of structural conservation of base-pairing patterns and exceptional thermodynamic stability. We predict more than 30,000 structured RNA elements in the human genome, almost 1,000 of which are conserved across all vertebrates. Roughly a third are found in introns of known genes, a sixth are potential regulatory elements in untranslated regions of protein-coding mRNAs and about half are located far away from any known gene. Only a small fraction of these sequences has been described previously. A comparison with recent tiling array data shows that more than 40% of the predicted structured RNAs overlap with experimentally detected sites of transcription. The widespread conservation of secondary structure points to a large number of functional ncRNAs and cis-acting mRNA structures in the human genome.