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Search Results: 1 - 10 of 8494 matches for " Oliver Sch?ffmann "
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Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
Mario Stanke, Oliver Schffmann, Burkhard Morgenstern, Stephan Waack
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-62
Abstract: We present a fairly general method for integration of external information. Our method is based on the evaluation of hints to potentially protein-coding regions by means of a Generalized Hidden Markov Model (GHMM) that takes both intrinsic and extrinsic information into account. We used this method to extend the ab initio gene prediction program AUGUSTUS to a versatile tool that we call AUGUSTUS+. In this study, we focus on hints derived from matches to an EST or protein database, but our approach can be used to include arbitrary user-defined hints. Our method is only moderately effected by the length of a database match. Further, it exploits the information that can be derived from the absence of such matches. As a special case, AUGUSTUS+ can predict genes under user-defined constraints, e.g. if the positions of certain exons are known. With hints from EST and protein databases, our new approach was able to predict 89% of the exons in human chromosome 22 correctly.Sensitive probabilistic modeling of extrinsic evidence such as sequence database matches can increase gene prediction accuracy. When a match of a sequence interval to an EST or protein sequence is used it should be treated as compound information rather than as information about individual positions.Finding protein-coding genes in eukaryotic genomic sequences with in-silico methods remains an important challenge in computational genomics, despite many years of intensive research work. Existing methods fall into two groups with respect to the data they utilize. The first group consists of ab initio programs which use only the query genomic sequence as input. Examples are the programs GENSCAN [1], AUGUSTUS [2] and HMMGene [3] which are HMM-based and GENEID [4]. The second group of gene-finding methods, extrinsic methods, comprises all programs which use data other than the query genomic sequence. Some extrinsic methods use genomic sequences from other species. A cross-species comparison of genomic sequences
Medical and health economic evaluation of prevention- and control measures related to MRSA infections or -colonisations at hospitals
Korczak, Dieter,Schffmann, Christine
GMS Health Technology Assessment , 2010,
Abstract: Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) are dangerous agents of nosocomial infections. In 2007 the prevalence of MRSA is 20.3% in Germany (Oxacilline-resistance according to EUCAST-criteria [EUCAST = European Committee on Antimicrobial Susceptibility Testing]). Objectives: * Which measurements are effective in the prevention and control of MRSA-infections in the hospital? * How effective are contact precautions, screening, decolonisation, education and surveillance? * Which recommendations can be given to health care politics on the basis of cost-effectiveness studies? * Have there been any adverse effects on patients and clinical staff? * What kind of liability problems exist?MethodsBased on a systematic review of the literature studies are included which have been published in German or English language since 2004. Results: 1,508 articles have been found. After having surveyed the full text, 33 medical, eight economic and four ethical/juridical studies are included for the Health Technology Assessment (HTA) report. The key result of the HTA report is that different measurements are effective in the prevention and control of MRSA-infections in hospitals, though the majority of the studies has a low quality. Effective are the conduction of differentiated screening measurements if they take into account the specific endemic situation, the use of antibiotic-control programs and the introduction and control of hygienic measurements. The break even point of preventive and control measurements cannot be defined because the study results differ too much. In the future it has to be more considered that MRSA-infections and contact precautions lead to a psycho-social strain for patients. Discussion: It is hardly possible to describe causal efficacies because in the majority of the studies confounders are not sufficiently considered. In many cases bundles of measurements have been established but not analyzed individually. The internal and external validity of the studies is too weak to evaluate single interventions. Hygienic measurements prove to be effective in combination with other measurements. But it cannot be said which of the single measurements (gloves, washing hands, wearing gowns or masks) has the strongest effect on the reduction of MRSA. It is irritating that there are high differences in the compliance concerning hand hygiene between different studies. A general decolonisation is questionable for different reasons: first because of the side-effects for patients, second because of the high rate of spontaneous remissions in the
Reduced dimensionality in layered quantum dimer magnets: Frustration vs. inhomogeneous condensates
Oliver R?sch,Matthias Vojta
Physics , 2007, DOI: 10.1103/PhysRevB.76.224408
Abstract: Motivated by recent experiments on BaCuSi2O6, we investigate magnetic excitations and quantum phase transitions of layered dimer magnets with inter-layer frustration. We consider two scenarios, (A) a lattice with one dimer per unit cell and perfect inter-layer frustration, and (B) an enlarged unit cell with inequivalent layers, with and without perfect frustration. In all situations, the critical behavior at asymptotically low temperatures is three-dimensional, but the corresponding crossover scale may be tiny. Magnetic ordering in case (B) can be discussed in terms of two condensates; remarkably, perfect frustration renders the proximity effect ineffective. Then, the ordering transition will be generically split, with clear signatures in measurable properties. Using a generalized bond-operator method, we calculate the low-temperature magnetic properties in the paramagnetic and antiferromagnetic phases. Based on the available experimental data on BaCuSi2O6, we propose that scenario (B) with inequivalent layers and imperfect frustration is realized in this material, likely with an additional modulation of the inter-layer couling along the c axis.
SPHINX TT - Monte Carlo Program for Nucleon-Nucleon Collisions with Transverse Polarization
Oliver Martin,Andreas Sch?fer
Physics , 1996,
Abstract: We present the program summary and long write-up for SPHINX TT, a new Monte Carlo simulation for transversely polarized nucleon-nucleon scattering. The program is based on Pythia/Jetset.
Quantum phase transitions and dimensional reduction in antiferromagnets with inter-layer frustration
Oliver R?sch,Matthias Vojta
Physics , 2007, DOI: 10.1103/PhysRevB.76.180401
Abstract: For magnets with a fully frustrated inter-layer interaction, we argue that the quantum phase transitions from a paramagnetic to an antiferromagnetic ground state, driven by pressure or magnetic field, are asymptotically three-dimensional, due to interaction-generated non-frustrated inter-layer couplings. However, the relevant crossover scale is tiny, such that two-dimensional behavior occurs in an experimentally relevant low-temperature regime. In the pressure-driven case the phase transition may split, in which case an Ising symmetry related to inter-layer bond order is broken before magnetism occurs. We discuss the relation of our results to recent experiments on BaCuSi2O6.
Superconducting d-wave stripes in cuprates: Valence bond order coexisting with nodal quasiparticles
Matthias Vojta,Oliver R?sch
Physics , 2007, DOI: 10.1103/PhysRevB.77.094504
Abstract: We point out that unidirectional bond-centered charge-density-wave states in cuprates involve electronic order in both s- and d-wave channels, with non-local Coulomb repulsion suppressing the s-wave component. The resulting bond-charge-density wave, coexisting with superconductivity, is compatible with recent photoemission and tunneling data and as well as neutron-scattering measurements, once long-range order is destroyed by slow fluctuations or glassy disorder. In particular, the real-space structure of d-wave stripes is consistent with the scanning-tunneling-microscopy measurements on both underdoped Bi2Sr2CaCu2O8+x and Ca2-xNaxCuO2Cl2 of Kohsaka et al. [Science 315, 1380 (2007), arXiv:cond-mat/0703309].
On representations of super coalgebras
A. Hüffmann
Physics , 1994, DOI: 10.1088/0305-4470/27/19/015
Abstract: The general structure of the representation theory of a $Z_2$-graded coalgebra is discussed. The result contains the structure of Fourier analysis on compact supergroups and quantisations thereof as a special case. The general linear supergroups serve as an explicit illustration and the simplest example is carried out in detail.
Analyzing Citation Frequencies of Leading Software Engineering Scholars
Oliver Hummel,Alexander Gerhart,Bernhard Sch?fer
Computer and Information Science , 2012, DOI: 10.5539/cis.v6n1p1
Abstract: It is understandable that sponsors of research activities are interested in assessing the work of scholars they (plan to) support although this is not a simple undertaking. Until today, there is no obvious approach for objectively measuring and comparing the quality of research results from different disciplines. Hence, counting publications has been used for long time as a substitute to deal with this challenge and only recent technological advances have fostered the usage of so-called citation indices (such as the h-index) for this purpose. Although this approach is as disputed as all previous ideas in this context, we feel it is about time to investigate the expressiveness of modern citation analysis approaches in computer science more closely. In order to do that, we have chosen the area of software engineering and created a first comprehensive ranking, illustrating citation values of world class scholars by analyzing the work of almost 700 researchers in this field. We have found that top h-index scores in software engineering are around 60 while top-notch g-indices start at around 130 when Google Scholar and Publish or Perish, the quasi standard tools for this purpose are used. Clearly, the results of our study are influenced by the coverage of these tools so that we have also analyzed Google Scholar and found it having a very high coverage of software engineering publications. Hence we are convinced to have collected good quality results that will allow our community to better judge and use citation numbers in the future.
Paternal Relatedness Predicts the Strength of Social Bonds among Female Rhesus Macaques
Oliver Schülke, Svenja Wenzel, Julia Ostner
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0059789
Abstract: Forming strong, equitable, and enduring social bonds with a few individuals in a group carries adaptive benefits in terms of increased longevity, offspring survival and paternity success in birds and mammals, including humans. These recent insights generated a new interest in the factors creating variation in the strength of social relationships. Whether and how animals discriminate paternal kin from non-kin and bias their social behavior accordingly is being debated. This study explores the relative importance of dominance rank, age, maternal and paternal relatedness in shaping dyadic affiliative relationships in a group of 30 captive rhesus macaque females. The strength of social relationships, measured by the composite sociality index from observational data, was independently predicted in GLMMs by both maternal and paternal relatedness as well as rank similarity. In addition, social bonds between paternal half-sisters were stronger than between distantly related kin suggesting that females biased their affiliative effort towards paternal relatives. Despite identical relatedness coefficients bonds between mothers and their daughters were three times as strong as those between full sisters. Together these results add to the growing body of evidence for paternal kin biases in affiliative behavior and highlight that females prefer descendent over lateral kin.
Phantom of Human Adipose Tissue and Studies of Light Propagation and Light Absorption for Parameterization and Evaluation of Noninvasive Optical Fat Measuring Devices  [PDF]
Stefan Hartmann, Matthias Moschall, Oliver Sch?fer, Frank Stüpmann, Ulrich Timm, David Klinger, Jens Kraitl, Hartmut Ewald
Optics and Photonics Journal (OPJ) , 2015, DOI: 10.4236/opj.2015.52005
Abstract: A method for noninvasive determination of fat and water content in the human body is examined. A spatially resolved spectroscopy method is used which can record low intensity near infrared spectra. This novel approach is compared to other methods for the determination of fat and water content. Monte Carlo simulations of light propagation in tissue are shown and the production and characterization of optical phantoms of adipose tissue are investigated.
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