Showing papers by "Bielefeld University published in 2009"

Equation of state and QCD transition at finite temperature

Abstract: We calculate the equation of state in $2+1$ flavor QCD at finite temperature with physical strange quark mass and almost physical light quark masses using lattices with temporal extent ${N}_{\ensuremath{\tau}}=8$. Calculations have been performed with two different improved staggered fermion actions, the asqtad and p4 actions. Overall, we find good agreement between results obtained with these two $O({a}^{2})$ improved staggered fermion discretization schemes. A comparison with earlier calculations on coarser lattices is performed to quantify systematic errors in current studies of the equation of state. We also present results for observables that are sensitive to deconfining and chiral aspects of the QCD transition on ${N}_{\ensuremath{\tau}}=6$ and 8 lattices. We find that deconfinement and chiral symmetry restoration happen in the same narrow temperature interval. In an appendix we present a simple parametrization of the equation of state that can easily be used in hydrodynamic model calculations. In this parametrization we include an estimate of current uncertainties in the lattice calculations which arise from cutoff and quark mass effects.

A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis

Abstract: The microRNA pathway has been implicated in the regulation of synaptic protein synthesis and ultimately in dendritic spine morphogenesis, a phenomenon associated with long-lasting forms of memory. However, the particular microRNAs (miRNAs) involved are largely unknown. Here we identify specific miRNAs that function at synapses to control dendritic spine structure by performing a functional screen. One of the identified miRNAs, miR-138, is highly enriched in the brain, localized within dendrites and negatively regulates the size of dendritic spines in rat hippocampal neurons. miR-138 controls the expression of acyl protein thioesterase 1 (APT1), an enzyme regulating the palmitoylation status of proteins that are known to function at the synapse, including the alpha(13) subunits of G proteins (Galpha(13)). RNA-interference-mediated knockdown of APT1 and the expression of membrane-localized Galpha(13) both suppress spine enlargement caused by inhibition of miR-138, suggesting that APT1-regulated depalmitoylation of Galpha(13) might be an important downstream event of miR-138 function. Our results uncover a previously unknown miRNA-dependent mechanism in neurons and demonstrate a previously unrecognized complexity of miRNA-dependent control of dendritic spine morphogenesis.

Shared Reality: Experiencing Commonality With Others' Inner States About the World.

Abstract: Humans have a fundamental need to experience a shared reality with others. We present a new conceptualization of shared reality based on four conditions. We posit (a) that shared reality involves a (subjectively perceived) commonality of individuals' inner states (not just observable behaviors); (b) that shared reality is about some target referent; (c) that for a shared reality to occur, the commonality of inner states must be appropriately motivated; and (d) that shared reality involves the experience of a successful connection to other people's inner states. In reviewing relevant evidence, we emphasize research on the saying-is-believing effect, which illustrates the creation of shared reality in interpersonal communication. We discuss why shared reality provides a better explanation of the findings from saying-is-believing studies than do other formulations. Finally, we examine relations between our conceptualization of shared reality and related constructs (including empathy, perspective taking, theory of mind, common ground, embodied synchrony, and socially distributed knowledge) and indicate how our approach may promote a comprehensive and differentiated understanding of social-sharing phenomena.

Detection of 140 clinically relevant antibiotic-resistance genes in the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to selected antibiotics

Abstract: To detect plasmid-borne antibiotic-resistance genes in wastewater treatment plant (WWTP) bacteria, 192 resistance-gene-specific PCR primer pairs were designed and synthesized. Subsequent PCR analyses on total plasmid DNA preparations obtained from bacteria of activated sludge or the WWTP's final effluents led to the identification of, respectively, 140 and 123 different resistance-gene-specific amplicons. The genes detected included aminoglycoside, β-lactam, chloramphenicol, fluoroquinolone, macrolide, rifampicin, tetracycline, trimethoprim and sulfonamide resistance genes as well as multidrug efflux and small multidrug resistance genes. Some of these genes were only recently described from clinical isolates, demonstrating genetic exchange between clinical and WWTP bacteria. Sequencing of selected resistance-gene-specific amplicons confirmed their identity or revealed that the amplicon nucleotide sequence is very similar to a gene closely related to the reference gene used for primer design. These results demonstrate that WWTP bacteria are a reservoir for various resistance genes. Moreover, detection of about 64 % of the 192 reference resistance genes in bacteria obtained from the WWTP's final effluents indicates that these resistance determinants might be further disseminated in habitats downstream of the sewage plant.

Fluorescence quenching by photoinduced electron transfer: a reporter for conformational dynamics of macromolecules.

Abstract: Photoinduced electron transfer (PET) between organic fluorophores and suitable electron donating moieties, for example, the amino acid tryptophan or the nucleobase guanine, can quench fluorescence upon van der Waals contact and thus report on molecular contact. PET-quenching has been used as reporter for monitoring conformational dynamics in polypeptides, proteins, and oligonucleotides. Whereas dynamic quenching transiently influences quantum yield and fluorescence lifetime of the fluorophore, static quenching in pi-stacked complexes efficiently suppresses fluorescence emission over time scales longer than the fluorescence lifetime. Static quenching therefore provides sufficient contrast to be observed at the single-molecule level. Here, we review complex formation and static quenching of different fluorophores by various molecular compounds, discuss applications as reporter system for macromolecular dynamics, and give illustrating examples.

Amorphous and crystalline aerosol particles interacting with water vapor: conceptual framework and experimental evidence for restructuring, phase transitions and kinetic limitations

Abstract: . Interactions with water are crucial for the properties, transformation and climate effects of atmospheric aerosols. Here we present a conceptual framework for the interaction of amorphous aerosol particles with water vapor, outlining characteristic features and differences in comparison to crystalline particles. We used a hygroscopicity tandem differential mobility analyzer (H-TDMA) to characterize the hydration and dehydration of crystalline ammonium sulfate, amorphous oxalic acid and amorphous levoglucosan particles (diameter ~100 nm, relative humidity 5–95% at 298 K). The experimental data and accompanying Kohler model calculations provide new insights into particle microstructure, surface adsorption, bulk absorption, phase transitions and hygroscopic growth. The results of these and related investigations lead to the following conclusions: (1) Many organic substances, including carboxylic acids, carbohydrates and proteins, tend to form amorphous rather than crystalline phases upon drying of aqueous solution droplets. Depending on viscosity and microstructure, the amorphous phases can be classified as glasses, rubbers, gels or viscous liquids. (2) Amorphous organic substances tend to absorb water vapor and undergo gradual deliquescence and hygroscopic growth at lower relative humidity than their crystalline counterparts. (3) In the course of hydration and dehydration, certain organic substances can form rubber- or gel-like structures (supramolecular networks) and undergo transitions between swollen and collapsed network structures. (4) Organic gels or (semi-)solid amorphous shells (glassy, rubbery, ultra-viscous) with low molecular diffusivity can kinetically limit the uptake and release of water and may influence the hygroscopic growth and activation of aerosol particles as cloud condensation nuclei (CCN) and ice nuclei (IN). Moreover, (semi-)solid amorphous phases may influence the uptake of gaseous photo-oxidants and the chemical transformation and aging of atmospheric aerosols. (5) The shape and porosity of amorphous and crystalline particles formed upon dehydration of aqueous solution droplets depend on chemical composition and drying conditions. The apparent volume void fractions of particles with highly porous structures can range up to ~50% or more (xerogels, aerogels). (6) For efficient description of water uptake and phase transitions of aerosol particles, we propose not to limit the terms deliquescence and efflorescence to equilibrium phase transitions of crystalline substances. Instead we propose generalized definitions according to which amorphous and crystalline components can undergo gradual or prompt, partial or full deliquescence or efflorescence. We suggest that (semi-)solid amorphous phases may be important not only in the upper atmosphere as suggested in recent studies of glass formation at low temperatures. Depending on relative humidity, (semi-)solid phases and moisture-induced glass transitions may also play a role in gas-particle interactions at ambient temperatures in the lower atmosphere.

EDGAR: a software framework for the comparative analysis of prokaryotic genomes.

Abstract: The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. To support these studies EDGAR – "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http://edgar.cebitec.uni-bielefeld.de , where the precomputed data sets can be browsed.

Food consumption frequency and perceived stress and depressive symptoms among students in three European countries

Abstract: Certain foods might be more frequently eaten under stress or when higher levels of depressive symptoms are experienced. We examined whether poor nutritional habits are associated with stress and depressive symptoms and whether the relationships differ by country and gender in a sample from three European countries collected as part of a Cross National Student Health Survey. A cross-sectional survey was conducted among first-year students in Germany (N = 696), Poland (N = 489) and Bulgaria (N = 654). Self-administered questionnaires included a 12-item food frequency questionnaire, Cohen's Perceived Stress Scale, and a modified Beck Depression Index. Linear regression analyses were conducted for two outcomes, perceived stress and depressive symptoms. Food consumption frequencies differed by country and gender, as did depressive symptoms and perceived stress. For male students, none of the food consumption groups were associated with perceived stress or depressive symptoms. In females, perceived stress was associated with more frequent consumption of sweets/fast foods and less frequent consumption of fruits/vegetables. Additionally, depressive symptoms were associated with less frequent consumption of fruits/vegetables and meat. Our data show consistent associations between unhealthy food consumption and depressive symptoms and perceived stress among female students from three European countries, but not among male students. This suggests that efforts to reduce depressive symptoms and stress among female students may also lead to the consumption of healthier foods and/or vice-versa.

Plant chemistry and insect sequestration.

Abstract: Most plant families are distinguished by characteristic secondary metabolites, which can function as putative defence against herbivores. However, many herbivorous insects of different orders can make use of these plant-synthesised compounds by ingesting and storing them in their body tissue or integument. Such sequestration of putatively unpalatable or toxic metabolites can enhance the insects’ own defence against enemies and may also be involved in reproductive behaviour. This review gives a comprehensive overview of all groups of secondary plant metabolites for which sequestration by insect herbivores belonging to different orders has been demonstrated. Sequestered compounds include various aromatic compounds, nitrogen-containing metabolites such as alkaloids, cyanogenic glycosides, glucosinolates and other sulphur-containing metabolites, and isoprenoids such as cardiac glycosides, cucurbitacins, iridoid glycosides and others. Sequestration of plant compounds has been investigated most in insects feeding or gathering on Apocynaceae s.l. (Apocynoideae, Asclepiaoideae), Aristolochiaceae, Asteraceae, Boraginaceae, Fabaceae and Plantaginaceae, but it also occurs for some gymnosperms and even lichens. In total, more than 250 insect species have been shown to sequester plant metabolites from at least 40 plant families. Sequestration predominates in the Coleoptera and Lepidoptera, but also occurs frequently in the orders Heteroptera, Hymenoptera, Orthoptera and Sternorrhyncha. Patterns of sequestration mechanisms for various compound classes and common or individual features occurring in different insect orders are highlighted. More research is needed to elucidate the specific transport mechanisms and the physiological processes of sequestration in various insect species.

Baryon number, strangeness, and electric charge fluctuations in QCD at high temperature

Abstract: We analyze baryon number, strangeness, and electric charge fluctuations as well as their correlations in QCD at high temperature. We present results obtained from lattice calculations performed with an improved staggered fermion action (p4 action) at two values of the lattice cutoff with almost physical up and down quark masses and a physical value for the strange quark mass. We compare these results, with an ideal quark gas at high temperature and a hadron resonance gas model at low temperature. We find that fluctuations and correlations are well described by the former already for temperatures about 1.5 times the transition temperature. At low temperature qualitative features of the lattice results are quite well described by a hadron resonance gas model. Higher order cumulants, which become increasingly sensitive to the light pions, however, show deviations from a resonance gas in the vicinity of the transition temperature.

Treating children traumatized by war and Tsunami: A comparison between exposure therapy and meditation-relaxation in North-East Sri Lanka

Abstract: The North-Eastern part of Sri Lanka had already been affected by civil war when the 2004 Tsunami wave hit the region, leading to high rates of posttraumatic stress disorder (PTSD) in children. In the acute aftermath of the Tsunami we tested the efficacy of two pragmatic short-term interventions when applied by trained local counselors. A randomized treatment comparison was implemented in a refugee camp in a severely affected community. 31 children who presented with a preliminary diagnosis of PTSD were randomly assigned either to six sessions Narrative Exposure Therapy for children (KIDNET) or six sessions of meditation-relaxation (MED-RELAX). Outcome measures included severity of PTSD symptoms, level of functioning and physical health. In both treatment conditions, PTSD symptoms and impairment in functioning were significantly reduced at one month post-test and remained stable over time. At 6 months follow-up, recovery rates were 81% for the children in the KIDNET group and 71% for those in the MED-RELAX group. There was no significant difference between the two therapy groups in any outcome measure. As recovery rates in the treatment groups exceeded the expected rates of natural recovery, the study provides preliminary evidence for the effectiveness of NET as well as meditation-relaxation techniques when carried out by trained local counselors for the treatment of PTSD in children in the direct aftermath of mass disasters. ClinicalTrials.gov Identifier:NCT00820391

Can electroweak bubble walls run away

Abstract: In extensions of the Standard Model with SU(2) singlet scalar fields, there can be regions of parameter space for which the electroweak phase transition is first order already at the mean-field level of analysis. We show that in this case the phase interface (bubble wall) can become ultra-relativistic, with the relativistic gamma factor {gamma} = (1-v{sub wall}{sup 2}){sup -1/2} growing linearly with the wall's propagation distance. We provide a simple criterion for determining whether the bubble wall ''runs away'' in this way or if {gamma} approaches a terminal value.

Spin polarization in half-metals probed by femtosecond spin excitation.

Abstract: Knowledge of the spin polarization is of fundamental importance for the use of a material in spintronics applications. Here, we used femtosecond optical excitation of half-metals to distinguish between half-metallic and metallic properties. Because the direct energy transfer by Elliot-Yafet scattering is blocked in a half-metal, the demagnetization time is a measure for the degree of half-metallicity. We propose that this characteristic enables us vice versa to establish a novel and fast characterization tool for this highly important material class used in spin-electronic devices. The technique has been applied to a variety of materials where the spin polarization at the Fermi level ranges from 45 to 98%: Ni, Co(2)MnSi, Fe(3)O(4), La(0.66)Sr(0.33)MnO(3) and CrO(2).

Patterns and sources of adult personality development: growth curve analyses of the NEO PI-R scales in a longitudinal twin study.

Abstract: The present study examined the patterns and sources of 10-year stability and change of adult personality assessed by the 5 domains and 30 facets of the Revised NEO Personality Inventory. Phenotypic and biometric analyses were performed on data from 126 identical and 61 fraternal twins from the Bielefeld Longitudinal Study of Adult Twins (BiLSAT). Consistent with previous research, LGM analyses revealed significant mean-level changes in domains and facets suggesting maturation of personality. There were also substantial individual differences in the change trajectories of both domain and facet scales. Correlations between age and trait changes were modest and there were no significant associations between change and gender. Biometric extensions of growth curve models showed that 10-year stability and change of personality were influenced by both genetic as well as environmental factors. Regarding the etiology of change, the analyses uncovered a more complex picture than originally stated, as findings suggest noticeable differences between traits with respect to the magnitude of genetic and environmental effects.

One Nanometer Thin Carbon Nanosheets with Tunable Conductivity and Stiffness

Abstract: Atomically thin (similar to 1 nm) carbon films and membranes whose electrical behavior can be tuned from insulating to conducting are fabricated by a novel route. These films present arbitrary size and shape based on molecular self-assembly, electron irradiation, and pyrolysis, and their technical applicability is demonstrated by their incorporation into a microscopic pressure sensor.

TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach.

Abstract: Background Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning.

Optimal Stopping With Multiple Priors

Abstract: We develop a theory of optimal stopping under Knightian uncertainty. A suitable martingale theory for multiple priors is derived that extends the classical dynamic programming or Snell envelope approach to multiple priors. We relate the multiple prior theory to the classical setup via a minimax theorem. In a multiple prior version of the classical model of independent and identically distributed random variables, we discuss several examples from microeconomics, operation research, and finance. For monotone payoffs, the worst-case prior can be identified quite easily with the help of stochastic dominance arguments. For more complex payoff structures like barrier options, model ambiguity leads to stochastic changes in the worst-case beliefs.

Photosynthetic hydrogen production by a hybrid complex of photosystem I and [NiFe]-hydrogenase.

Abstract: Nature provides key components for generating fuels from renewable resources in the form of enzymatic nanomachines which catalyze crucial steps in biological energy conversion, for example, the photosynthetic apparatus, which transforms solar power into chemical energy, and hydrogenases, capable of generating molecular hydrogen. As sunlight is usually used to synthesize carbohydrates, direct generation of hydrogen from light represents an exception in nature. On the molecular level, the crucial step for conversion of solar energy into H(2) lies in the efficient electronic coupling of photosystem I and hydrogenase. Here we show the stepwise assembly of a hybrid complex consisting of photosystem I and hydrogenase on a solid gold surface. This device gave rise to light-induced H(2) evolution. Hydrogen production is possible at far higher potential and thus lower energy compared to those of previously described (bio)nanoelectronic devices that did not employ the photosynthesis apparatus. The successful demonstration of efficient solar-to-hydrogen conversion may serve as a blueprint for the establishment of this system in a living organism with the paramount advantage of self-replication.

Dynamic Plastid Redox Signals Integrate Gene Expression and Metabolism to Induce Distinct Metabolic States in Photosynthetic Acclimation in Arabidopsis

Abstract: Plants possess acclimation responses in which structural reconfigurations adapt the photosynthetic apparatus to fluctuating illumination. Long-term acclimation involves changes in plastid and nuclear gene expression and is controlled by redox signals from photosynthesis. The kinetics of these signals and the adjustments of energetic and metabolic demands to the changes in the photosynthetic apparatus are currently poorly understood. Using a redox signaling system that preferentially excites either photosystem I or II, we measured the time-dependent impact of redox signals on the transcriptome and metabolome of Arabidopsis thaliana. We observed rapid and dynamic changes in nuclear transcript accumulation resulting in differential and specific expression patterns for genes associated with photosynthesis and metabolism. Metabolite pools also exhibited dynamic changes and indicate readjustments between distinct metabolic states depending on the respective illumination. These states reflect reallocation of energy resources in a defined and reversible manner, indicating that structural changes in the photosynthetic apparatus during long-term acclimation are additionally supported at the level of metabolism. We propose that photosynthesis can act as an environmental sensor, producing retrograde redox signals that trigger two parallel adjustment loops that coordinate photosynthesis and metabolism to adapt plant primary productivity to the environment.

Understanding Social Robots

Abstract: Research on social robots is mainly comprised of research into algorithmic problems in order to expand a robot´s capabilities to improve communication with human beings. Also, a large body of research concentrates on the appearance, i.e. aesthetic form of social robots. However, only little reference to their definition is made. In this paper we argue that form, function, and context have to be taken systematically into account in order to develop a model to help us understand social robots. Therefore, we address the questions: What is a social robot, what are the interdisciplinary research aspects of social robotics, and how are these different aspects interlinked? In order to present a comprehensive and concise overview of the various aspects we present a framework for a definition towards social robots.

No large-angle correlations on the non-Galactic microwave sky

Abstract: We investigate the angular two-point correlation function of temperature in the Wilkinson Microwave Anisotropy Probe (WMAP) maps. Updating and extending earlier results, we confirm firm the lack of correlations outside the Galaxy on angular scales greater than about 600 at a level that would occur in 0.025 per cent of realizations of the concordance model. This represents a dramatic increase in significance from the original observations by the Cosmic Background Explorer Differential Microwave Radiometer (COBE-DMR) and a marked increase in significance from the first-year WMAP maps. Given the rest of the reported angular power spectrum C-l, the lack of large-angle correlations that one infers outside the plane of the Galaxy requires covariance among the C-l up to l = 5. Alternately, it requires both the unusually small (5 per cent of realizations) full-sky large-angle correlations and an Unusual coincidence of alignment of the Galaxy with the pattern of cosmological fluctuations (less than 2 per cent of those 5 per cent). We argue that unless there is Some undiscovered systematic error in their collection or reduction, the data point towards a violation of statistical isotropy. The near-vanishing of the large-angle correlations in the cut-sky maps, together with their disagreement with results inferred from full-sky maps, remains open problems, and are very difficult to understand within the concordance model.