Showing papers by "Bielefeld University published in 2006"

RNAhybrid: microRNA target prediction easy, fast and flexible

Abstract: In the elucidation of the microRNA regulatory network, knowledge of potential targets is of highest importance. Among existing target prediction methods, RNAhybrid [M. Rehmsmeier, P. Steffen, M. Hochsmann and R. Giegerich (2004) RNA, 10, 1507-1517] is unique in offering a flexible online prediction. Recently, some useful features have been added, among these the possibility to disallow G:U base pairs in the seed region, and a seed-match speed-up, which accelerates the program by a factor of 8. In addition, the program can now be used as a webservice for remote calls from user-implemented programs. We demonstrate RNAhybrid's flexibility with the prediction of a non-canonical target site for Caenorhabditis elegans miR-241 in the 3'-untranslated region of lin-39. RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid.

Introducing MASC: a movie for the assessment of social cognition.

Abstract: In the present study we introduce a sensitive video-based test for the evaluation of subtle mindreading difficulties: the Movie for the Assessment of Social Cognition (MASC). This new mindreading tool involves watching a short film and answering questions referring to the actors' mental states. A group of adults with Asperger syndrome (n = 19) and well-matched control subjects (n = 20) were administered the MASC and three other mindreading tools as part of a broader neuropsychological testing session. Compared to control subjects, Asperger individuals exhibited marked and selective difficulties in social cognition. A Receiver Operating Characteristic (ROC) analysis for the mindreading tests identified the MASC as discriminating the diagnostic groups most accurately. Issues pertaining to the multidimensionality of the social cognition construct are discussed.

Control of Electron Localization in Molecular Dissociation

Abstract: We demonstrated how the subcycle evolution of the electric field of light can be used to control the motion of bound electrons. Results are presented for the dissociative ionization of deuterium molecules (D2 ⇒ D+ + D), where asymmetric ejection of the ionic fragment reveals that light-driven intramolecular electronic motion before dissociation localizes the electron on one of the two D+ ions in a controlled way. The results extend subfemtosecond electron control to molecules and provide evidence of its usefulness in controlling reaction dynamics.

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

Abstract: Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. Although barely detectable in unpolluted environments, A. borkumensis becomes the dominant microbe in oil-polluted waters. A. borkumensis SK2 has a streamlined genome with a paucity of mobile genetic elements and energy generation-related genes, but with a plethora of genes accounting for its wide hydrocarbon substrate range and efficient oil-degradation capabilities. The genome further specifies systems for scavenging of nutrients, particularly organic and inorganic nitrogen and oligo-elements, biofilm formation at the oil-water interface, biosurfactant production and niche-specific stress responses. The unique combination of these features provides A. borkumensis SK2 with a competitive edge in oil-polluted environments. This genome sequence provides the basis for the future design of strategies to mitigate the ecological damage caused by oil spills.

The function of peroxiredoxins in plant organelle redox metabolism

Abstract: In 1996, cDNA sequences referred to as plant peroxiredoxins (Prx), i.e. a 1-Cys Prx and a 2-Cys Prx, were reported from barley. Ten years of research have advanced our understanding of plant Prx as thiol-based peroxide reductases with a broad substrate specificity, ranging from hydrogen peroxide to alkyl hydroperoxides and peroxinitrite. Prx have several features in common. (i) They are abundant proteins that are routinely detected in proteomics approaches. (ii) They interact with proteins such as glutaredoxins, thioredoxins, and cyclophilins as reductants, but also non-dithioldisulphide exchange proteins. By work with transgenic plants, their activity was shown to (iii) affect metabolic integrity, (iv) protect DNA from damage in vitro and as shown here in vivo, and (v) modulate intracellular signalling related to reactive oxygen species and reactive nitrogen species. (vi) In all organisms Prx are encoded by small gene families that are of particular complexity in higher plants. A comparison of the Prx gene families in rice and Arabidopsis thaliana supports previous suggestions on Prx function in specific subcellular and metabolic context. (vii) Prx gene expression and activity are subjected to complex regulation realized by an integration of various signalling pathways. 2-Cys Prx expression depends on redox signals, abscisic acid, and protein kinase cascades. Besides these general properties, the chloroplast Prx have acquired specific roles in the context of photosynthesis. The thioredoxin-dependent peroxidase activity can be measured in crude plant extracts and contributes significantly to the overall H2O2 detoxification capacity. Thus organellar Prx proteins enable an alternative water–water cycle for detoxification of photochemically produced H2O2, which acts independently from the ascorbatedependent Asada–Halliwell–Foyer cycle. 2-Cys Prx and Prx Q associate with thylakoid membrane components. The mitochondrial PrxII F is essential for root growth under stress. Following a more general introduction, the paper summarizes present knowledge on plant organellar Prx, addressing Prx in signalling, and also suggests some lines for future research.

RNAshapes: an integrated RNA analysis package based on abstract shapes

Abstract: Summary: We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach. Availability: RNAshapes is freely available at http://bibiserv.techfak.uni-bielefeld.de/rnashapes/ as C source code, and as compiled binaries for the most common computer architectures. For Microsoft Windows, we also offer a graphical user interface with convenient access to the complete functionality of the package. Contact: psteffen@techfak.uni-bielefeld.de

Generic health-related quality-of-life assessment in children and adolescents: methodological considerations.

Abstract: The health-related quality of life (HR-QOL) of children and adolescents is increasingly considered a relevant topic for research. Instruments to assess quality of life in children and adolescents of a generic as well as disease- or condition-specific nature are being developed and applied in epidemiological surveys, clinical studies, quality assurance and health economics. This paper attempts to give an overview on the state of the art of HR-QOL assessment in children as it relates to methodological and conceptual challenges. Instruments available in international or cross-cultural research to assess HR-QOL in generic terms were identified and described according to psychometric data provided and the width of application.

Is the genetic structure of human personality universal? A cross-cultural twin study from North America, Europe, and Asia.

Abstract: This study examined whether universality of the 5-factor model (FFM) of personality operationalized by the Revised NEO Personality Inventory is due to genetic influences that are invariant across diverse nations. Factor analyses were conducted on matrices of phenotypic, genetic, and environmental correlations estimated in a sample of 1,209 monozygotic and 701 dizygotic twin pairs from Canada, Germany, and Japan. Five genetic and environmental factors were extracted for each sample. High congruence coefficients were observed when phenotypic, genetic, and environmental factors were compared in each sample as well as when each factor was compared across samples. These results suggest that the FFM has a solid biological basis and may represent a common heritage of the human species.

The transition temperature in QCD

Abstract: We present a detailed calculation of the transition temperature in QCD with two light and one heavier (strange) quark mass on lattices with temporal extent N_t =4 and 6. Calculations with improved staggered fermions have been performed for various light to strange quark mass ratios in the range, 0.05 0) and continuum (aT = 1/N_t -> 0) limits we find for the transition temperature at the physical point T_c r_0 = 0.457(7) where the scale is set by the Sommer-scale parameter r_0 defined as the distance in the static quark potential at which the slope takes on the value, (dV_qq(r)/dr)_r=r_0 = 1.65/r_0^2. Using the currently best known value for r_0 this translates to a transition temperature T_c = 192(7)(4)MeV. The transition temperature in the chiral limit is about 3% smaller. We discuss current ambiguities in the determination of T_c in physical units and also comment on the universal scaling behavior of thermodynamic quantities in the chiral limit.

A unifying view of genome rearrangements

Abstract: Genome rearrangements have been modeled by a variety of operations such as inversions, translocations, fissions, fusions, transpositions and block interchanges. The double cut and join operation, introduced by Yancopoulos et al., allows to model all the classical operations while simplifying the algorithms. In this paper we show a simple way to apply this operation to the most general type of genomes with a mixed collection of linear and circular chromosomes. We also describe a graph structure that allows simplifying the theory and distance computation considerably, as neither capping nor concatenation of the linear chromosomes are necessary.

European Perspectives on Men and Masculinities: National and Transnational Approaches

Abstract: The social relations of home and work represent some of the most fundamental aspects of gender relations in society, and thus some of the most important elements in the construction of men and masculinities. The separation of home and work is both a very real one and an ideological construction. It is at the root of much liberal social science, as well as figuring, in more or less sophisticated ways, in non-feminist (Habermas, 1984, 1987) and feminist (Fraser, 1989) critical theory. In some ways it refers to the distinction between production and reproduction; but an over-simple division into dual spheres has been shown to be theoretically flawed, historically inaccurate (Bose, 1987; Hearn, 1992) and contrary to the experience of some people and some social categories, for example, women of colour (Collins, 1990).

On the large-angle anomalies of the microwave sky

Abstract: We apply the multipole vector framework to full-sky maps derived from the first-year Wilkinson Microwave Anisotropy Probe (WMAP) data. We significantly extend our earlier work showing that the two lowest cosmologically interesting multipoles, � = 2 and 3, are not statistically isotropic. These results are compared to the findings obtained using related methods. In particular, we show that the planes of the quadrupole and the octopole are unexpectedly aligned. Moreover, the combined quadrupole plus octopole is surprisingly aligned with the geometry and direction of motion of the Solar system: the plane they define is perpendicular to the ecliptic plane and to the plane defined by the dipole direction, and the ecliptic plane carefully separates stronger from weaker extrema, running within a couple of degrees of the null-contour between a maximum and a minimum over more than 120 ◦ of the sky. Even given the alignment of the quadrupole and octopole with each other, we find that their alignment with the ecliptic is unlikely at >98 per cent confidence level (CL), and argue that it is in fact unlikely at >99.9 per cent CL. Most of the � = 2 and 3 multipole vectors of the known Galactic foregrounds are located far from those of the observed sky, strongly suggesting that residual contamination by such foregrounds is unlikely to be the cause of the observed correlations. Multipole vectors,

Four-loop decoupling relations for the strong coupling

Abstract: We compute the matching relation for the strong coupling constant within the framework of QCD up to four-loop order. This allows a consistent five-loop running (once the β function is available to this order) taking into account threshold effects. As a side product we obtain the effective coupling of a Higgs boson to gluons with five-loop accuracy.

CO Fixation to Stable Acyclic and Cyclic Alkyl Amino Carbenes: Stable Amino Ketenes with a Small HOMO–LUMO Gap

Abstract: Reactive intermediates play a central role in modern chemistry.[1] Since 1900, and the discovery by Gomberg of a stable radical,[2] many species that were thought to be too short-lived for observation have been isolated. The availability of stable versions of reactive intermediates has allowed for a superior control of their reactivity and a better understanding of the mechanism of chemical reactions. Even more importantly, new applications of these species have been found, for example, the successful use of stable carbenes as ligands for transition-metal catalysts,[3] and even as organic catalysts.[4] There are still several families of synthetically important reactive intermediates, the preparation of which has been impeded by the belief that they are incapable of existence, or has eluded the synthetic skills of investigators. Because of their very high reactivity, ketenes are key intermediates in synthetic organic chemistry, and have even found industrial applications.[5–7] Despite the isolation of diphenylketene as early as the beginning of the 20th century,[8] most ketenes are intrinsically unstable and cannot be isolated.[5] Calculations have predicted that σ-electron-withdrawing substituents, as well as π-donor groups destabilize ketenes.[9] Accordingly, alkoxy ketenes have only been characterized at low temperature or by fast-spectroscopic methods,[10] whereas amino ketenes have never been observed.[11] Transient triplet carbenes, such as methylene, react with CO to give the corresponding ketenes.[12] In contrast, although the carbonylation of singlet carbenes is spin-allowed, there are very few examples of ketene formation using this route.[13] In 1994 it was claimed that the imidazol-2-ylidene 1a reacts with carbon monoxide to give the stable diamino ketene 2a (Scheme 1).[14] However, a year later Arduengo et al.[15] were not able to duplicate these experimental results. They demonstrated computationally that the parent compound 2b is not even a transition state, and found that there is no stable structure associated with the combination of 1b and CO, other than “a non-bonded weakly interacting (van der Waals) complex” 3b (scheme 1). Moreover, the calculations showed that the CO addition leading to 2b is not favored thermodynamically [ΔH(298 K) =+15.9 kcalmol−1].[15] Scheme 1 N-heterocyclic carbenes (NHCs) do not react with CO; the structure of van der Waals complex 3 b. Herein we report that, in marked contrast with cyclic diamino carbenes 1, stable acyclic 4a[16] and 4b, and cyclic alkyl amino carbenes (CAACs) 6[17] react with CO to afford amino ketenes 5a,b and 7, respectively (see Scheme 2), which are indefinitely stable at room temperature both in solution and in the solid state. We show that the ring structure forces the planarization of the amino fragment of 7, and therefore causes the destabilizing n–π donation from the amino group. Consequently, the HOMO of the ketene 7 is raised and the singlet–triplet gap considerably reduced, which induces unusual optical and NMR spectroscopic properties. Scheme 2 Addition of CO to carbenes 4 a,b and 6. According to calculations,[16] the singlet–triplet gap (26.7 kcalmol−1) and the HOMO (−4.3 eV) for acyclic alkyl amino carbenes 4 are much smaller and higher in energy, respectively, than for NHCs 1 (79.6 kcalmol−1 and −5.4 eV).[18] Consequently, carbenes 4 are more nucleophilic but also more electrophilic than NHCs 1, and are therefore better candidates for a carbonylation reaction. Indeed, when carbon monoxide was bubbled at room temperature through a THF solution of acyclic carbene 4a, a clean reaction occurred, and after evaporation of the solvent under vacuum, ketene 5a was obtained in good yield as a pale yellow oil (Scheme 2). The IR spectrum of 5a shows a very strong C=C=O stretching vibration at 2066 cm−1, and the 13C NMR signals for the ketene group appear at δ =213.95 (CCO) and 60.90 (CCO) ppm; all these values are expected for a ketene bearing a σ-electron-withdrawing group.[9] Only one set of NMR signals was observed for the isopropyl substituents, which suggests free rotation around the N–CCO bond. Starting from carbene 4b, which has cyclohexyl instead of isopropyl groups, ketene 5b was isolated as pale yellow crystals (m.p.: <20°C) suitable for X-ray diffraction (Figure 1).[19] Interestingly, the N–C1 bond (ca. 1.43 A) is much longer than in carbene 4a (1.30 A), suggesting again the absence of interaction between the nitrogen lone pair and the CCO fragment. Indeed, molecule 5b escapes the destabilizing n–π donation, by pyramidalization of the amino group (sum of the angles: 347.7°), and by directing the nitrogen lone pair 180°away from the CCO moiety. Consequently, the observed geometric parameters of the CCO fragment of 5b are very similar to those calculated for the parent ketene H2CCO (Table 1).[20] Figure 1 Molecular view of the crystal structure of 5 b. Selected bond lengths [A] and angles [°]: N–C1 1.426(4), C1–C2 1.310(5), C2–O 1.174(4), C1–C3 1.517(4), N–C6a 1.417(7); N-C1-C3 122.6(3), C3-C1-C2 ... Table 1 Comparison of the spectroscopic data, geometric parameters, and singlet–triplet (S/T) energy gap for ketenes. The next challenge was to synthesize an amino ketene in which the nitrogen lone pair would be forced to stay parallel to the C=C π system. We have recently shown that despite the reluctance of phosphorus to be planar (inversion barrier 35 kcalmol−1 for PH3 compared to 5 kcalmol−1 for NH3), its incorporation into a ring, in addition to the use of bulky substituents, allowed us to force its planarization.[21,22] Applying the same concept, the CAAC 6 (Scheme 2)appeared to be the ideal precursor. As soon as carbon monoxide was bubbled at room temperature through a THF solution of CAAC 6, a very deep blue color appeared. After evaporation of the solvent under vacuum, ketene 7 crystallizes from hexane at −20°C as blue crystals (65%, m.p.: 95–97°C) suitable for X-ray diffraction (Figure 2).[19] As expected, the nitrogen atom is in a planar environment (sum of the angles: 357.3°), and the lone pair is coplanar with the C=C π system. Although the N1a–C1 bond (ca. 1.40 A) is much longer than that of carbene 6(1.31 A), it is similar to that observed for ketene 5b. Similarly, in the IR spectrum, the C=C=O stretching vibration for 7 is at 2073 cm−1, very close to that observed for 5 (Δν =7 cm−1). These results suggest only a weak interaction between the nitrogen lone pair and the CCO fragment. However, compared to other ketenes, a dramatic red-shifted UV absorption is observed (very intense band from 500 to 700 nm, λmax 598 nm), as well as a spectacular downfield shift of the 13C NMR signal of the CCO carbon of 7 (δ ≈ 278 ppm; Table 1). Figure 2 Molecular view of the crystal structure of 7. Selected bond lengths [A] and angles [°]: N1a–C1a 1.405(2), C1a–C2aa 1.334(5), C2aa–O1aa 1.186(5) C1a–C5a 1.524(2), N1a–C11a 1.437(2); N1a-C1a-C5a 110.80(14), ... To gain further insight into the electronic structure of amino ketenes 5 and 7, density functional theory (DFT) calculations at triple-zeta basis set quality[20] were performed on the parent acyclic amino ketenes 5cpyr and 5cpla (Scheme 3), which feature a nitrogen atom in a pyramidal (pyr) and planar (pla) environment, respectively. The calculated geometry and NMR chemical shifts for 5cpyr are similar to those observed experimentally for 5a,b (Table 1). Of particular interest, the lone pair of 5cpyr is also directed 180° away from the CCO fragment. Forcing the nitrogen to be in a planar geometry, with the lone pair parallel to the C=C π system, costs 6.8 kcalmol−1, and 5cpla is not even an energy minimum on the electronic hypersurface. In 5cpla the π-conjugation of the amino group with the adjacent C=C π bond has a drastic effect on the frontier orbitals. It raises the HOMO (π-C=C) while the LUMO (π*-C=O), is not affected. The resulting smaller HOMO–LUMO gap is in line with the smaller value of the adiabatic singlet–triplet energy separation, which decreases from 23.9 for 5cpyr to 17.0 kcalmol−1 for 5cpla. In other words, forcing the π-conjugation with the adjacent amino substituent, as in the calculated 5cpla and observed ketenes 7, induces a biradical character. The reduction of the HOMO–LUMO energy gap readily explains the red-shift of the π(C=C)-→ π*(C=O) optical transition. The small singlet–triplet energy gap leads to the enhancement of the paramagnetic term, and therefore the downfield shift of the 13C NMR signal of the CO carbon of 5cpla and 7. Scheme 3 Schematic representations of the calculated parent amino ketenes 5 cpyr and 5 cpla. In conclusion, cumulenes 5 and 7 are the first ketenes prepared from CO fixation to stable carbenes. When compared to the parent ketene (H2CCO), the presence of a pyramidal amino group as in 5 reduces the singlet–triplet energy gap by about 50%, and the planarization of the amino group as in 7 induces another 30% reduction to reach 17 kcalmol−1. The small HOMO–LUMO energy gap induces unusual optical and NMR spectroscopic properties.[26] The design of ketenes featuring an even more pronounced diradical character is under active investigation.

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

Abstract: Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a surprisingly low degree of synteny. Coding sequences involved in the synthesis of surface components potentially important for plant-microbe interactions were more closely related to those of plant-associated bacteria. Strain BH72 appears to be 'disarmed' compared to plant pathogens, having only a few enzymes that degrade plant cell walls; it lacks type III and IV secretion systems, related toxins and an N-acyl homoserine lactones-based communication system. The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment.

bZIP10-LSD1 antagonism modulates basal defense and cell death in Arabidopsis following infection

Abstract: Plants use sophisticated strategies to balance responses to oxidative stress. Programmed cell death, including the hypersensitive response (HR) associated with successful pathogen recognition, is one cellular response regulated by reactive oxygen in various cellular contexts. The Arabidopsis basic leucine zipper (bZIP) transcription factor AtbZIP10 shuttles between the nucleus and the cytoplasm and binds consensus G- and C-box DNA sequences. Surprisingly, AtbZIP10 can be retained outside the nucleus by LSD1, a protein that protects Arabidopsis cells from death in the face of oxidative stress signals. We demonstrate that AtbZIP10 is a positive mediator of the uncontrolled cell death observed in lsd1 mutants. AtbZIP10 and LSD1 act antagonistically in both pathogen-induced HR and basal defense responses. LSD1 likely functions as a cellular hub, where its interaction with AtbZIP10 and additional, as yet unidentified, proteins contributes significantly to plant oxidative stress responses.

Baryogenesis in the Two-Higgs Doublet Model

Abstract: We consider the generation of the baryon asymmetry in the two-Higgs doublet model. Investigating the thermal potential in the presence of CP violation, as relevant for baryogenesis, we find a strong first-order phase transition if the extra Higgs states are heavier than about 300 GeV. The mass of the lightest Higgs can be as large as about 200 GeV. We compute the bubble wall properties, including the profile of the relative complex phase between the two Higgs vevs. The baryon asymmetry is generated by top transport, which we treat in the WKB approximation. We find a baryon asymmetry consistent with observations. The neutron electric dipole moment is predicted to be larger than about 10(-27) ecm and can reach the current experimental bound. Low values of tan beta are favored.

Search asymmetries with real faces: testing the anger-superiority effect.

Abstract: The anger-superiority hypothesis states that angry faces are detected more efficiently than friendly faces. Previously research used schematized stimuli, which minimizes perceptual confounds, but violates ecological validity. The authors argue that a confounding of appearance and meaning is unavoidable and even unproblematic if real faces are presented. Four experiments tested carefully controlled photos in a search-asymmetry design. Experiments 1 and 2 revealed more efficient detection of an angry face among happy faces than vice versa. Experiment 3 indicated that the advantage was due to the mouth, but not to the eyes, and Experiment 4, using upright and inverted thatcherized faces, suggests a perceptual basis. The results are in line with a sensory-bias hypothesis that facial expressions evolved to exploit extant capabilities of the visual system.

Mindestindikatorensatz zur Erfassung des Migrationsstatus

Abstract: Nach wie vor fehlt eine Datenbasis, die Migranten und ihre gesundheitliche Situation angemessen reprasentiert. Einer der Grunde fur diesen Mangel ist die unzulangliche Erfassung des Migrationsstatus in der amtlichen Statistik und in epidemiologischen Studien. Voraussetzung fur eine adaquate und standardisierte Operationalisierung ist eine genaue Definition der Begriffe „Migrant“ und „Migrationshintergrund“. In unserem Beitrag diskutieren wir Konzepte zur begrifflichen Bestimmung und Erfassung ethnischer Minderheiten und Migranten und entwickeln auf dieser Grundlage einen Mindestindikatorensatz fur die epidemiologische Forschung. Der vorgeschlagene Mindestindikatorensatz zur Erfassung des Migrationsstatus enthalt die Merkmale Geburtsland von Vater und Mutter, Einreisejahr, Muttersprache, Deutschkenntnisse sowie den Aufenthaltsstatus. Zentraler Indikator zur Identifikation von Migranten ist das Geburtsland der Eltern und nicht – wie bislang zumeist ublich – die Staatsangehorigkeit. Die Klassifikation mittels der juristischen Kategorie Staatsangehorigkeit wird damit abgelost durch die Klassifikation anhand des lebensbiographischen Ereignisses „Migration“. Mit der Migration gehen spezifische Lebensbedingungen und Handlungsanforderungen einher, die uber mehrere Generationen fur die Gesundheit von Bedeutung sein konnen. Ein Instrument zur Erfassung des Migrationsstatus muss dahingehend weiterentwickelt werden, dass es diese aus dem Migrationsereignis resultierenden Besonderheiten in der Lebenssituation widerspiegelt und moglichst alle Aspekte eines Migrationshintergrundes berucksichtigt.

Graph-based analysis and visualization of experimental results with ONDEX

Abstract: Motivation: Assembling the relevant information needed to interpret the output from high-throughput, genome scale, experiments such as gene expression microarrays is challenging. Analysis reveals genes that show statistically significant changes in expression levels, but more information is needed to determine their biological relevance. The challenge is to bring these genes together with biological information distributed across hundreds of databases or buried in the scientific literature (millions of articles). Software tools are needed to automate this task which at present is labor-intensive and requires considerable informatics and biological expertise. Results: This article describes ONDEX and how it can be applied to the task of interpreting gene expression results. ONDEX is a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis. An overview of the ONDEX system is presented, concentrating on recently developed features for graph-based analysis and visualization. A case study is used to show how ONDEX can help to identify causal relationships between stress response genes and metabolic pathways from gene expression data. ONDEX also discovered functional annotations for most of the genes that emerged as significant in the microarray experiment, but were previously of unknown function. Availability: ONDEX is freely available under the GPL License and can be downloaded from SourceForge http://ondex.sourceforge.net/ Contact: Jacob.Koehler@bbsrc.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Social Norms and the Likelihood of Raping: Perceived Rape Myth Acceptance of Others Affects Men's Rape Proclivity

Abstract: Research showing that rape myth acceptance (RMA) causally affects rape proclivity (RP) was extended by examining the impact of RMA-related norms on RP. Male students (total N = 264) received feedback about the alleged responses of other students to RMA items either before (Experiment 1) or after (Experiment 2) they reported their own RMA, and then their RP was assessed using acquaintance-rape scenarios. The level of RMA feedback was varied. Results showed that higher norms led to higher RP. In Experiment 1, this effect was mediated via self-reported RMA. Experiment 2 yielded main effects of both RMA feedback and self-reported RMA and an interaction effect showing that RMA feedback was particularly influential at higher levels of own RMA. Theoretical and practical implications of these findings are discussed.

Collective non-Abelian instabilities in a melting color glass condensate.

Abstract: We present first results for ($3+1$)D simulations of SU(2) Yang-Mills equations for matter expanding into the vacuum after a heavy ion collision. Violations of boost invariance cause a non-Abelian Weibel instability leading soft modes to grow with proper time $\ensuremath{\tau}$ as $\mathrm{exp} (\ensuremath{\Gamma}\sqrt{{g}^{2}\ensuremath{\mu}\ensuremath{\tau}})$, where ${g}^{2}\ensuremath{\mu}$ is a scale arising from the saturation of gluons in the nuclear wave function. The scale for the growth rate $\ensuremath{\Gamma}$ is set by a plasmon mass, defined as ${\ensuremath{\omega}}_{\mathrm{pl}}={\ensuremath{\kappa}}_{0}\sqrt{{g}^{2}\ensuremath{\mu}/\ensuremath{\tau}}$, generated dynamically in the collision. We compare the numerical ratio $\ensuremath{\Gamma}/{\ensuremath{\kappa}}_{0}$ to the corresponding value predicted by the hard thermal loop formalism for anisotropic plasmas.

Arousal and cortisol interact in modulating memory consolidation in healthy young men.

Abstract: Animal studies indicate that adrenal glucocorticoids enhance memory consolidation while impairing memory retrieval. In humans, beneficial effects on consolidation have been observed infrequently. In the current double-blind study, subjects (N = 29) received placebo or cortisol (30 mg) 10 min before viewing emotionally arousing or neutral pictures. Cortisol treatment had no effects on immediate recall. In the 24-hr delayed recall condition, cortisol led to an enhanced emotional memory facilitation because of decreased neutral and increased emotional memory recall. No effects of cortisol treatment were observed for recognition memory or mood. Results support the notion that glucocorticoids specifically enhance the consolidation of emotional material.

Heterogeneous nucleation of ice on surrogates of mineral dust

Abstract: [1] Field studies have shown that mineral dust particles can act as ice nuclei in cirrus clouds. Here, we present a laboratory investigation of heterogeneous ice nucleation on surrogates of mineral dust particles, in particular pure Arizona test dust (ATD) particles, and ATD particles coated with sulfuric acid. The experiments have been performed using a new apparatus in which ice formation on the particles is determined by optical microscopy at temperatures between 197 and 260 K and relative humidities up to water saturation. The experiments reveal that pure and sulfuric acid coated ATD particles nucleate ice at considerably lower relative humidities than required for homogeneous ice nucleation in liquid aerosols. Nucleation occurred over a broad relative humidity range indicating that the different minerals contained in ATD have different ice nucleation thresholds. No significant difference in the ice nucleation ability of pure and H2SO4 coated ATD particles was observed. Below 240 K, ice nucleated on ATD particles apparently by deposition nucleation. Preactivation of ATD particles, that is, a reduction in supersaturation, required for heterogeneous ice nucleation after a previous ice nucleation event on the same particle, has been observed for temperatures as low as 200 K. Differences of 10–30% in the onset RHice values were obtained for particles with or without preactivation. The results indicate that pure and sulfuric acid coated mineral dust particles may act as efficient ice nuclei in the atmosphere. Preactivation of the particles should be considered when modeling long-range transport of mineral dust particles and their impact on cloud formation.

Dissipative hydrodynamics and heavy-ion collisions

Abstract: Recent discussions of RHIC data emphasized the exciting possibility that the matter produced in nucleus-nucleus collisions shows properties of a near-perfect fluid. Here, we aim at delineating the applicability of fluid dynamics, which is needed to quantify the size of corresponding dissipative effects. We start from the equations for dissipative fluid dynamics, which we derive from kinetic theory up to second order (Israel-Stewart theory) in a systematic gradient expansion. In model studies, we then establish that for too early initialization of the hydrodynamic evolution (${\ensuremath{\tau}}_{0}\ensuremath{\lesssim}1\phantom{\rule{0.3em}{0ex}}\mathrm{fm}/c$) or for too high transverse momentum (${p}_{T}\ensuremath{\lesssim}1$ GeV) in the final state, the expected dissipative corrections are too large for a fluid description to be reliable. Moreover, viscosity-induced modifications of hadronic transverse momentum spectra can be accommodated to a significant degree in an ideal fluid description by modifications of the decoupling stage. We argue that these conclusions, drawn from model studies, can also be expected to arise in significantly more complex, realistic fluid dynamics simulations of heavy ion collisions.

Perspectives and advances of biological H2 production in microorganisms.

Abstract: The rapid development of clean fuels for the future is a critically important global challenge for two main reasons. First, new fuels are needed to supplement and ultimately replace depleting oil reserves. Second, fuels capable of zero CO2 emissions are needed to slow the impact of global warming. This review summarizes the development of solar powered bio-H2 production processes based on the conversion of photosynthetic products by fermentative bacteria, as well as using photoheterotrophic and photoautrophic organisms. The use of advanced bioreactor systems and their potential and limitations in terms of process design, efficiency, and cost are also briefly reviewed.

The unstable glasma

Abstract: We discuss results from $3+1$-D numerical simulations of SU(2) Yang-Mills equations for an unstable glasma expanding into the vacuum after a high energy heavy-ion collision. We expand on our earlier work on a non-Abelian Weibel instability in such a system and study the behavior of the instability in greater detail on significantly larger lattices than previously. We establish the time scale for the onset of the instability and demonstrate that the growth rate is robust as one approaches the continuum limit. For large violations of boost invariance, non-Abelian effects cause the growth of soft modes to saturate. At late times, we observe significant creation of longitudinal pressure and a systematic trend towards isotropy. These time scales however are significantly larger than those required for early thermalization in heavy-ion collisions. We discuss additional effects in the produced glasma that may speed up thermalization.