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We measured memory span for assembly instructions involving objects with handles oriented to the left or right side. Right-handed participants remembered more instructions when objects' handles were spatially congruent with the hand used in forthcoming assembly actions. No such affordance-based memory benefit was found for left-handed participants. These results are discussed in terms of motor simulation as an embodied rehearsal mechanism.
Program behavior that relies on contextual information, such as physical location or network accessibility, is common in today's applications, yet its representation is not sufficiently supported by programming languages. With context-oriented programming (COP), such context-dependent behavioral variations can be explicitly modularized and dynamically activated. In general, COP could be used to manage any context-specific behavior. However, its contemporary realizations limit the control of dynamic adaptation. This, in turn, limits the interaction of COP's adaptation mechanisms with widely used architectures, such as event-based, mobile, and distributed programming. The JCop programming language extends Java with language constructs for context-oriented programming and additionally provides a domain-specific aspect language for declarative control over runtime adaptations. As a result, these redesigned implementations are more concise and better modularized than their counterparts using plain COP. JCop's main features have been described in our previous publications. However, a complete language specification has not been presented so far. This report presents the entire JCop language including the syntax and semantics of its new language constructs.
The tricarboxylic acid (TCA) cycle is a crucial component of respiratory metabolism in both photosynthetic and heterotrophic plant organs. All of the major genes of the tomato TCA cycle have been cloned recently, allowing the generation of a suite of transgenic plants in which the majority of the enzymes in the pathway are progressively decreased. Investigations of these plants have provided an almost complete view of the distribution of control in this important pathway. Our studies suggest that citrate synthase, aconitase, isocitrate dehydrogenase, succinyl CoA ligase, succinate dehydrogenase, fumarase and malate dehydrogenase have control coefficients flux for respiration of -0.4, 0.964, -0.123, 0.0008, 0.289, 0.601 and 1.76, respectively; while 2-oxoglutarate dehydrogenase is estimated to have a control coefficient of 0.786 in potato tubers. These results thus indicate that the control of this pathway is distributed among malate dehydrogenase, aconitase, fumarase, succinate dehydrogenase and 2-oxoglutarate dehydrogenase. The unusual distribution of control estimated here is consistent with specific non-cyclic flux mode and cytosolic bypasses that operate in illuminated leaves. These observations are discussed in the context of known regulatory properties of the enzymes and some illustrative examples of how the pathway responds to environmental change are given.
Observations of radio halos and relics in galaxy clusters indicate efficient electron acceleration. Protons should likewise be accelerated and, on account of weak energy losses, can accumulate, suggesting that clusters may also be sources of very high energy (VHE; E > 100 GeV) gamma-ray emission. We report here on VHE gamma-ray observations of the Coma galaxy cluster with the VERITAS array of imaging Cerenkov telescopes, with complementing Fermi Large Area Telescope observations at GeV energies. No significant gamma-ray emission from the Coma Cluster was detected. Integral flux upper limits at the 99% confidence level were measured to be on the order of (2-5) x 10(-8) photonsm(-2) s(-1) (VERITAS, >220 GeV) and similar to 2 x 10(-6) photonsm(-2) s(-1) (Fermi, 1-3GeV), respectively. We use the gamma-ray upper limits to constrain cosmic rays (CRs) and magnetic fields in Coma. Using an analytical approach, the CR-to-thermal pressure ratio is constrained to be < 16% from VERITAS data and <1.7% from Fermi data (averaged within the virial radius). These upper limits are starting to constrain the CR physics in self-consistent cosmological cluster simulations and cap the maximum CR acceleration efficiency at structure formation shocks to be <50%. Alternatively, this may argue for non-negligible CR transport processes such as CR streaming and diffusion into the outer cluster regions. Assuming that the radio-emitting electrons of the Coma halo result from hadronic CR interactions, the observations imply a lower limit on the central magnetic field in Coma of similar to(2-5.5) mu G, depending on the radial magnetic field profile and on the gamma-ray spectral index. Since these values are below those inferred by Faraday rotation measurements in Coma (for most of the parameter space), this renders the hadronic model a very plausible explanation of the Coma radio halo. Finally, since galaxy clusters are dark matter (DM) dominated, the VERITAS upper limits have been used to place constraints on the thermally averaged product of the total self-annihilation cross section and the relative velocity of the DM particles, <sigma nu >.
Pioneered by Clark's microelectrode more than half a century ago, there has been substantial interest in developing new, miniaturized optical methods to detect molecular oxygen inside cells. While extensively used for animal tissue measurements, applications of intracellular optical oxygen biosensors are still scarce in plant science. A critical aspect is the strong autofluorescence of the green plant tissue that interferes with optical signals of commonly used oxygen probes. A recently developed dual-frequency phase modulation technique can overcome this limitation, offering new perspectives for plant research. This review gives an overview on the latest optical sensing techniques and methods based on phosphorescence quenching in diverse tissues and discusses the potential pitfalls for applications in plants. The most promising oxygen sensitive probes are reviewed plus different oxygen sensing structures ranging from micro-optodes to soluble nanoparticles. Moreover, the applicability of using heterologously expressed oxygen binding proteins and fluorescent proteins to determine changes in the cellular oxygen concentration are discussed as potential non-invasive cellular oxygen reporters.
The fluorescence response of a set of cyclam-triazole-dye ligands is controlled by the appended dye, but simple reversal of the triazole topology affords a novel probe for Zn2+ with a longer fluorescence lifetime and higher fluorescence quantum yield upon Zn2+ binding (<tau t > = 2.0 ns, Phi(f) = 0.76).
Companies have to adhere to compliance requirements. The compliance analysis of business operations is typically a joint effort of business experts and compliance experts. Those experts need to create a common understanding of business processes to effectively conduct compliance management. In this paper, we present a technique that aims at supporting this process. We argue that process templates generated out of compliance requirements provide a basis for negotiation among business and compliance experts. We introduce a semi-automated and iterative approach to the synthesis of such process templates from compliance requirements expressed in Linear Temporal Logic (LTL). We show how generic constraints related to business process execution are incorporated and present criteria that point at underspecification. Further, we outline how such underspecification may be resolved to iteratively build up a complete specification. For the synthesis, we leverage existing work on process mining and process restructuring. However, our approach is not limited to the control-flow perspective, but also considers direct and indirect data-flow dependencies. Finally, we elaborate on the application of the derived process templates and present an implementation of our approach. (C) 2012 Elsevier Ltd. All rights reserved.
A series of new heteroleptic MN2S2 transition metal complexes with M = Cu2+ for EPR measurements and as diamagnetic hosts Ni2+, Zn2+, and Pd2+ were synthesized and characterized. The ligands are N2 = 4, 4'-bis(tert-butyl)-2, 2'-bipyridine (tBu2bpy) and S2 =1, 2-dithiooxalate, (dto), 1, 2-dithiosquarate, (dtsq), maleonitrile-1, 2-dithiolate, or 1, 2-dicyanoethene-1, 2-dithiolate, (mnt). The CuII complexes were studied by EPR in solution and as powders, diamagnetically diluted in the isostructural planar [NiII(tBu2bpy)(S2)] or[PdII(tBu2bpy)(S2)] as well as in tetrahedrally coordinated[ZnII(tBu2bpy)(S2)] host structures to put steric stress on the coordination geometry of the central CuN2S2 unit. The spin density contributions for different geometries calculated from experimental parameters are compared with the electronic situation in the frontier orbital, namely in the semi-occupied molecular orbital (SOMO) of the copper complex, derived from quantum chemical calculations on different levels (EHT and DFT). One of the hosts, [NiII(tBu2bpy)(mnt)], is characterized by X-ray structure analysis to prove the coordination geometry. The complex crystallizes in a square-planar coordination mode in the monoclinic space group P21/a with Z = 4 and the unit cell parameters a = 10.4508(10) angstrom, b = 18.266(2) angstrom, c = 12.6566(12) angstrom, beta = 112.095(7)degrees. Oxidation and reductions potentials of one of the host complexes, [Ni(tBu2bpy)(mnt)], were obtained by cyclovoltammetric measurements.
MHC genes encode proteins that are responsible for the recognition of foreign antigens and the triggering of a subsequent, adequate immune response of the organism. Thus they hold a key position in the immune system of vertebrates. It is believed that the extraordinary genetic diversity of MHC genes is shaped by adaptive selectional processes in response to the reoccurring adaptations of parasites and pathogens. A large number of MHC studies were performed in a wide range of wildlife species aiming to understand the role of immune gene diversity in parasite resistance under natural selection conditions. Methodically, most of this work with very few exceptions has focussed only upon the structural, i.e. sequence diversity of regions responsible for antigen binding and presentation. Most of these studies found evidence that MHC gene variation did indeed underlie adaptive processes and that an individual’s allelic diversity explains parasite and pathogen resistance to a large extent. Nevertheless, our understanding of the effective mechanisms is incomplete. A neglected, but potentially highly relevant component concerns the transcriptional differences of MHC alleles. Indeed, differences in the expression levels MHC alleles and their potential functional importance have remained unstudied. The idea that also transcriptional differences might play an important role relies on the fact that lower MHC gene expression is tantamount with reduced induction of CD4+ T helper cells and thus with a reduced immune response. Hence, I studied the expression of MHC genes and of immune regulative cytokines as additional factors to reveal the functional importance of MHC diversity in two free-ranging rodent species (Delomys sublineatus, Apodemus flavicollis) in association with their gastrointestinal helminths under natural selection conditions. I established the method of relative quantification of mRNA on liver and spleen samples of both species in our laboratory. As there was no available information on nucleic sequences of potential reference genes in both species, PCR primer systems that were established in laboratory mice have to be tested and adapted for both non-model organisms. In the due course, sets of stable reference genes for both species were found and thus the preconditions for reliable measurements of mRNA levels established. For D. sublineatus it could be demonstrated that helminth infection elicits aspects of a typical Th2 immune response. Whereas mRNA levels of the cytokine interleukin Il4 increased with infection intensity by strongyle nematodes neither MHC nor cytokine expression played a significant role in D. sublineatus. For A. flavicollis I found a negative association between the parasitic nematode Heligmosomoides polygyrus and hepatic MHC mRNA levels. As a lower MHC expression entails a lower immune response, this could be evidence for an immune evasive strategy of the nematode, as it has been suggested for many micro-parasites. This implies that H. polygyrus is capable to interfere actively with the MHC transcription. Indeed, this parasite species has long been suspected to be immunosuppressive, e.g. by induction of regulatory T-helper cells that respond with a higher interleukin Il10 and tumor necrosis factor Tgfb production. Both cytokines in turn cause an abated MHC expression. By disabling recognition by the MHC molecule H. polygyrus might be able to prevent an activation of the immune system. Indeed, I found a strong tendency in animals carrying the allele Apfl-DRB*23 to have an increased infection intensity with H. polygyrus. Furthermore, I found positive and negative associations between specific MHC alleles and other helminth species, as well as typical signs of positive selection acting on the nucleic sequences of the MHC. The latter was evident by an elevated rate of non-synonymous to synonymous substitutions in the MHC sequences of exon 2 encoding the functionally important antigen binding sites whereas the first and third exons of the MHC DRB gene were highly conserved. In conclusion, the studies in this thesis demonstrate that valid procedures to quantify expression of immune relevant genes are also feasible in non-model wildlife organisms. In addition to structural MHC diversity, also MHC gene expression should be considered to obtain a more complete picture on host-pathogen coevolutionary selection processes. This is especially true if parasites are able to interfere with systemic MHC expression. In this case advantageous or disadvantageous effects of allelic binding motifs are abated. The studies could not define the role of MHC gene expression in antagonistic coevolution as such but the results suggest that it depends strongly on the specific parasite species that is involved.
This study examined the effects of competing speech on auditory semantic comprehension using a dichotic sentence-word priming paradigm. Lexical decision performance for target words presented in spoken sentences was compared in strongly and weakly biasing semantic contexts. Targets were either congruent or incongruent with the sentential bias. Sentences were presented to one auditory channel (right or left), either in isolation or with competing speech produced by a single talker of the same gender presented simultaneously. The competing speech signal was either presented in the same auditory channel as the sentence context, or in a different auditory channel, and was either meaningful (played forward) or unintelligible (time-reversed).
Biasing contexts presented in isolation facilitated responses to congruent targets and inhibited responses to incongruent targets, relative to a neutral baseline. Facilitation priming was reduced or eliminated by competing speech presented in the same auditory channel, supporting previous findings that semantic activation is highly sensitive to the intelligibility of the context signal. Competing speech presented in a different auditory channel affected facilitation priming differentially depending upon ear of presentation, suggesting hemispheric differences in the processing of the attended and competing signals. Results were consistent with previous claims of a right ear advantage for meaningful speech, as well as with visual word recognition findings implicating the left hemisphere in the generation of semantic predictions and the right hemisphere in the integration of newly encountered words into the sentence-level meaning. Unlike facilitation priming, inhibition was relatively robust to the energetic and informational masking effects of competing speech and was not influenced by the strength of the contextual bias or the meaningfulness of the competing signal, supporting a two-process model of sentence priming in which inhibition reflects later-stage, expectancy-driven strategic processes that may benefit from perceptual reanalysis after initial semantic activation.
Developing Critical Thinking
(2012)
Developing critical thinking
(2012)
Experimental and quantitative research in the field of human language processing and production strongly depends on the quality of the underlying language material: beside its size, representativeness, variety and balance have been discussed as important factors which influence design, analysis and interpretation of experiments and their results. This volume brings together creators and users of both general purpose and specialized lexical resources which are used in psychology, psycholinguistics, neurolinguistics and cognitive research. It aims to be a forum to report experiences and results, review problems and discuss perspectives of any linguistic data used in the field.
We present a toy-model for an ensemble of adhering mesoscopic constituents in order to estimate the effect of the granular temperature on the sizes of embedded aggregates. The major goal is to illustrate the relation between the mean aggregate size and the granular temperature in dense planetary rings. For sake of simplicity we describe the collective behavior of the ensemble by means of equilibrium statistical mechanics, motivated by the stationary temperature established by the balance between a Kepler-shear driven viscous heating and inelastic cooling in these cosmic granular disks. The ensemble consists of N' equal constituents which can form cluster(s) or move like a gas-or both phases may coexist-depending on the (granular) temperature of the system. We assume the binding energy levels of a cluster E-c = -N-c gamma a to be determined by a certain contact number N-c, given by the configuration of N constituents of the aggregate (energy per contact: -gamma a). By applying canonical and grand-canonical ensembles, we show that the granular temperature T of a gas of constituents (their mean kinetic energy) controls the size distribution of the aggregates. They are the smaller the higher the granular temperature T is. A mere gas of single constituents is sustained for T >> gamma a. In the case of large clusters (low temperatures T << gamma a) the size distribution becomes a Poissonian.
Glycolate oxidase (GO) catalyses the oxidation of glycolate to glyoxylate, thereby consuming O-2 and producing H2O2. In this work, Arabidopsis thaliana plants expressing GO in the chloroplasts (GO plants) were used to assess the expressional behavior of reactive oxygen species (ROS)-responsive genes and transcription factors (TFs) after metabolic induction of H2O2 formation in chloroplasts. In this organelle, GO uses the glycolate derived from the oxygenase activity of RubisCO. Here, to identify genes responding to an abrupt production of H2O2 in chloroplasts we used quantitative real-time PCR (qRT-PCR) to test the expression of 187 ROS-responsive genes and 1880 TFs after transferring GO and wild-type (WT) plants grown at high CO2 levels to ambient CO2 concentration. Our data revealed coordinated expression changes of genes of specific functional networks 0.5 h after metabolic induction of H2O2 production in GO plants, including the induction of indole glucosinolate and camalexin biosynthesis genes. Comparative analysis using available microarray data suggests that signals for the induction of these genes through H2O2 may originate in the chloroplast. The TF profiling indicated an up-regulation in GO plants of a group of genes involved in the regulation of proanthocyanidin and anthocyanin biosynthesis. Moreover, the upregulation of expression of IF and IF interacting proteins affecting development (e.g., cell division, stem branching, flowering time, flower development) would impact growth and reproductive capacity, resulting in altered development under conditions that promote the formation of H2O2.
The minima on the potential energy surface of 1,2-bis(o-carboxyphenoxy)ethane (CPE) molecule in its electronic ground state were searched by a molecular dynamics simulation performed with MM2 force field. For each of the found minimum-energy conformers, the corresponding equilibrium geometry, charge distribution, HOMO-LUMO energy gap, force field, vibrational normal modes and associated IR and Raman spectral data were determined by means of the density functional theory (DFT) based electronic structure calculations carried out by using B3LYP method and various Pople-style basis sets. The obtained theoretical data confirmed the significant effects of the intra- and inter-molecular hydrogen bonding interactions on the conformational structure, force field, and group vibrations of the molecule. The same data have also revealed that two of the determined stable conformers, both of which exhibit pseudo-crown structure, are considerably more favorable in energy to the others and accordingly provide the major contribution to the experimental spectra of CPE. In the light of the improved vibrational spectral data obtained within the "SQM FF" methodology and "Dual Scale Factors" approach for the monomer and dimer forms of these two conformers, a reliable assignment of the fundamental bands observed in the experimental room-temperature IR and Raman spectra of the molecule was given, and the sensitivities of its group vibrations to conformation, substitution and dimerization were discussed.
Sedimentological, provenance, and detrital thermochronological results for basin fill at the modern deformation front of the northern Andes (6 degrees N latitude) provide a long-term, Eocene to Pliocene record of foreland-basin sedimentation along the Eastern Cordillera !Janos basin boundary in Colombia. Lithofacies assemblages and paleocurrent orientations in the upward-coarsening, 5-km-thick succession of the Nunchia syncline reveal a systematic shift from craton-derived, shallow-marine distal foreland (back-bulge) accumulation in the Mirador Formation, to orogen-sourced, deltaic, and coastalinfluenced sedimentation of the distal to medial foreland (foredeep) in the Carbonera and Leon Formations, to anastomosing fluvial and distributive braided fluvial megafan systems of the proximal foreland (foredeep to wedge-top) basin in the lower and upper Guayabo Formation. These changes in depositional processes and sediment dispersal are supported by up-section variations in detrital zircon U-Pb and (U-Th)/He ages that record exhumation of evolving, compartmentalized sediment source areas in the Eastern Cordillera. The data are interpreted in terms of a progressive eastward advance in foldand-thrust deformation, with late Eocene Oligocene deformation in the axial zone of the Eastern Cordillera along the western edge of Floresta basin (Soapaga thrust), early Miocene reactivation (inversion) of the eastern margin of the Mesozoic rift system (Pajarito and Guaicaramo thrusts), and middle late Miocene propagation of a footwall shortcut fault (Vopal thrust) that created the Nunchia syncline in a wedge-top (piggyback) setting of the eastern foothills along the transition from the Eastern Cordillera to Harms foreland basin. Collectively, the data presented here for the frontal Eastern Cordillera define a general in-sequence pattern of eastwardadvancing fold-and-thrust deformation during Cenozoic east-west shortening in the Colombian Andes.
The time-dependent approach to electronic spectroscopy, as popularized by Heller and co-workers in the 1980s, is applied here in conjunction with linear-response, time-dependent density functional theory to study vibronic absorption and resonance Raman spectra of beta-carotene, with and without a solvent. Two-state models, the harmonic and the Condon approximations are used in order to do so. A new code has been developed which includes excited state displacements, vibrational frequency shifts, and Duschinsky rotation, i.e., mode mixing, for both non-adiabatic spectroscopies. It is shown that Duschinsky rotation has a pronounced effect on the resonance Raman spectra of beta-carotene. In particular, it can explain a recently found anomalous behaviour of the so-called nu(1) peak in resonance Raman spectra [N. Tschirner, M. Schenderlein, K. Brose, E. Schlodder, M. A. Mroginski, C. Thomsen, and P. Hildebrandt, Phys. Chem. Chem. Phys. 11, 11471 (2009)], which shifts with the change in excitation wavelength.
Whereas the US President signed the Kyoto Protocol, the failure of the US Congress to ratify it seriously hampered subsequent international climate cooperation. This recent US trend, of signing environmental treaties but failing to ratify them, could thwart attempts to come to a future climate agreement. Two complementary explanations of this trend are proposed. First, the political system of the US has distinct institutional features that make it difficult for presidents to predict whether the Senate will give its advice and consent to multilateral environmental agreements (MEAs) and whether Congress will pass the required enabling legislation. Second, elected for a fixed term, US presidents might benefit politically from supporting MEAs even when knowing that legislative support is not forthcoming. Four policy implications are explored, concerning the scope for unilateral presidential action, the potential for bipartisan congressional support, the effectiveness of a treaty without the US, and the prospects for a deep, new climate treaty.
Policy relevance
Why does the failure of US ratification of multilateral environmental treaties occur? This article analyses the domestic political mechanisms involved in cases of failed US ratification. US non-participation in global environmental institutions often has serious ramifications. For example, it sharply limited Kyoto's effectiveness and seriously hampered international climate negotiations for years. Although at COP 17 in Durban the parties agreed to negotiate a new agreement by 2015, a new global climate treaty may well trigger a situation resembling the one President Clinton faced in 1997 when he signed Kyoto but never obtained support for it in the Senate. US failure to ratify could thwart future climate agreements.
Density Functional Calculations of the Anisotropic Effects of Borazine and 1,3,2,4-Diazadiboretidine
(2012)
On the basis of the nucleus-independent chemical shift (NICS) concept, the anisotropic effects of two inorganic rings, namely, borazine and planar 1,3,2,4-diazadiboretidine, are quantitatively calculated and visualized as isochemical shielding surfaces (ICSSs). Dissection of magnetic shielding values along the three Cartesian axes into contributions from s and p bonds by the natural chemical shieldingnatural bond orbital (NCSNBO) method revealed that their appearance is not a simple reflection of the extent of (anti)aromaticity.
Based on the nucleus-independent chemical shift (NICS) concept, isotropic magnetic shielding values have been computed along the three Cartesian axes for ethene, cyclobutadiene, benzene, naphthalene, and benzocyclobutadiene, starting from the molecular/ring center up to 10 angstrom away. These through-space NMR spectroscopic shielding (TSNMRS) values, which reflect the anisotropic effects, have been broken down into contributions from localized- and canonical molecular orbitals (LMOs and CMOs); these contributions revealed that the proton NMR spectroscopic chemical shifts of nuclei that are spatially close to the C?C double bond or the aromatic ring should not be explained in terms of the conventionally accepted p-electron shielding/deshielding effects. In fact, these effects followed the predictions only for the antiaromatic cyclobutadiene ring.
Impact of the carbazole derivative wiskostatin on mechanical stability
and dynamics of motile cells
(2012)
Many essential functions in eukaryotic cells like phagocytosis, division, and motility rely on the dynamical properties of the actin cytoskeleton. A central player in the actin system is the Arp2/3 complex. Its activity is controlled by members of the WASP (Wiskott-Aldrich syndrome protein) family. In this work, we investigated the effect of the carbazole derivative wiskostatin, a recently identified N-WASP inhibitor, on actin-driven processes in motile cells of the social ameba . Drug-treated cells exhibited an altered morphology and strongly reduced pseudopod formation. However, TIRF microscopy images revealed that the overall cortical network structure remained intact. We probed the mechanical stability of wiskostatin-treated cells using a microfluidic device. While the total amount of F-actin in the cells remained constant, their stiffness was strongly reduced. Furthermore, wiskostatin treatment enhanced the resistance to fluid shear stress, while spontaneous motility as well as chemotactic motion in gradients of cAMP were reduced. Our results suggest that wiskostatin affects the mechanical integrity of the actin cortex so that its rigidity is reduced and actin-driven force generation is impaired.
Sperm proteins of the marine sessile mussels of the Mytilus edulis species complex are models to investigate reproductive isolation and speciation. This study aimed at identifying sperm proteins and their corresponding genes. This was aided by the use of monoclonal antibodies that preferentially bind to yet unknown sperm molecules. By identifying their target molecules, this approach identified proteins with relevance to Mytilus sperm function. This procedure identified 16 proteins, for example, enkurin, laminin, porin and heat shock proteins. The potential use of these proteins as genetic markers to study reproductive isolation is exemplified by analysing the enkurin locus. Enkurin evolution is driven by purifying selection, the locus displays high levels of intraspecific variation and species-specific alleles group in distinct phylogenetic clusters. These findings characterize enkurin as informative candidate biomarker for analyses of clinal variation and differential introgression in hybrid zones, for example, to understand determinants of reproductive isolation in Baltic Mytilus populations.
The SP-PLP-EPR technique is used to carry out a detailed investigation of the radical termination kinetics of 1H, 1H, 2H, 2H-tridecafluorooctyl methacrylate (TDFOMA) in bulk at relatively low conversion. Composite-model behavior for chain-length-dependent termination rate coefficients, kti,i, is observed. It is found that for TDFOMA, ic approximate to 60 independent of temperature, and as approximate to 0.65 and al approximate to 0.2 at 80 degrees C and above. However, at lower temperatures the situation is strikingly different, with the significantly higher average values of as = 0.89 +/- 0.15 and al = 0.32 +/- 0.10 being obtained at 50 degrees C and below. This makes TDFOMA the first monomer to be found that exhibits clearly different exponent values, as and al, at lower and higher temperature, and that has both a high as, like an acrylate, and a high ic, like a methacrylate.
We consider open many-body systems governed by a time-dependent quantum master equation with short-range interactions. With a generalized Lieb-Robinson bound, we show that the evolution in this very generic framework is quasilocal; i.e., the evolution of observables can be approximated by implementing the dynamics only in a vicinity of the observables' support. The precision increases exponentially with the diameter of the considered subsystem. Hence, time evolution can be simulated on classical computers with a cost that is independent of the system size. Providing error bounds for Trotter decompositions, we conclude that the simulation on a quantum computer is additionally efficient in time. For experiments and simulations in the Schrodinger picture, our result can be used to rigorously bound finite-size effects.
Complex networks have been successfully employed to represent different levels of biological systems, ranging from gene regulation to protein-protein interactions and metabolism. Network-based research has mainly focused on identifying unifying structural properties, including small average path length, large clustering coefficient, heavy-tail degree distribution, and hierarchical organization, viewed as requirements for efficient and robust system architectures. Existing studies estimate the significance of network properties using a generic randomization scheme - a Markov-chain switching algorithm - which generates unrealistic reactions in metabolic networks, as it does not account for the physical principles underlying metabolism. Therefore, it is unclear whether the properties identified with this generic approach are related to the functions of metabolic networks. Within this doctoral thesis, I have developed an algorithm for mass-balanced randomization of metabolic networks, which runs in polynomial time and samples networks almost uniformly at random. The properties of biological systems result from two fundamental origins: ubiquitous physical principles and a complex history of evolutionary pressure. The latter determines the cellular functions and abilities required for an organism’s survival. Consequently, the functionally important properties of biological systems result from evolutionary pressure. By employing randomization under physical constraints, the salient structural properties, i.e., the smallworld property, degree distributions, and biosynthetic capabilities of six metabolic networks from all kingdoms of life are shown to be independent of physical constraints, and thus likely to be related to evolution and functional organization of metabolism. This stands in stark contrast to the results obtained from the commonly applied switching algorithm. In addition, a novel network property is devised to quantify the importance of reactions by simulating the impact of their knockout. The relevance of the identified reactions is verified by the findings of existing experimental studies demonstrating the severity of the respective knockouts. The results suggest that the novel property may be used to determine the reactions important for viability of organisms. Next, the algorithm is employed to analyze the dependence between mass balance and thermodynamic properties of Escherichia coli metabolism. The thermodynamic landscape in the vicinity of the metabolic network reveals two regimes of randomized networks: those with thermodynamically favorable reactions, similar to the original network, and those with less favorable reactions. The results suggest that there is an intrinsic dependency between thermodynamic favorability and evolutionary optimization. The method is further extended to optimizing metabolic pathways by introducing novel chemically feasibly reactions. The results suggest that, in three organisms of biotechnological importance, introduction of the identified reactions may allow for optimizing their growth. The approach is general and allows identifying chemical reactions which modulate the performance with respect to any given objective function, such as the production of valuable compounds or the targeted suppression of pathway activity. These theoretical developments can find applications in metabolic engineering or disease treatment. The developed randomization method proposes a novel approach to measuring the significance of biological network properties, and establishes a connection between large-scale approaches and biological function. The results may provide important insights into the functional principles of metabolic networks, and open up new possibilities for their engineering.
Complex networks have been successfully employed to represent different levels of biological systems, ranging from gene regulation to protein-protein interactions and metabolism. Network-based research has mainly focused on identifying unifying structural properties, such as small average path length, large clustering coefficient, heavy-tail degree distribution and hierarchical organization, viewed as requirements for efficient and robust system architectures. However, for biological networks, it is unclear to what extent these properties reflect the evolutionary history of the represented systems. Here, we show that the salient structural properties of six metabolic networks from all kingdoms of life may be inherently related to the evolution and functional organization of metabolism by employing network randomization under mass balance constraints. Contrary to the results from the common Markov-chain switching algorithm, our findings suggest the evolutionary importance of the small-world hypothesis as a fundamental design principle of complex networks. The approach may help us to determine the biologically meaningful properties that result from evolutionary pressure imposed on metabolism, such as the global impact of local reaction knockouts. Moreover, the approach can be applied to test to what extent novel structural properties can be used to draw biologically meaningful hypothesis or predictions from structure alone.
Background: Reconstruction of genome-scale metabolic networks has resulted in models capable of reproducing experimentally observed biomass yield/growth rates and predicting the effect of alterations in metabolism for biotechnological applications. The existing studies rely on modifying the metabolic network of an investigated organism by removing or inserting reactions taken either from evolutionary similar organisms or from databases of biochemical reactions (e.g., KEGG). A potential disadvantage of these knowledge-driven approaches is that the result is biased towards known reactions, as such approaches do not account for the possibility of including novel enzymes, together with the reactions they catalyze.
Results: Here, we explore the alternative of increasing biomass yield in three model organisms, namely Bacillus subtilis, Escherichia coil, and Hordeum vulgare, by applying small, chemically feasible network modifications. We use the predicted and experimentally confirmed growth rates of the wild-type networks as reference values and determine the effect of inserting mass-balanced, thermodynamically feasible reactions on predictions of growth rate by using flux balance analysis.
Conclusions: While many replacements of existing reactions naturally lead to a decrease or complete loss of biomass production ability, in all three investigated organisms we find feasible modifications which facilitate a significant increase in this biological function. We focus on modifications with feasible chemical properties and a significant increase in biomass yield. The results demonstrate that small modifications are sufficient to substantially alter biomass yield in the three organisms. The method can be used to predict the effect of targeted modifications on the yield of any set of metabolites (e.g., ethanol), thus providing a computational framework for synthetic metabolic engineering.
A lamin in lower eukaryotes?
(2012)
Lamins are the major components of the nuclear lamina and serve not only as a mechanical support, but are also involved in chromatin organization, epigenetic regulation, transcription and mitotic events. Despite these universal tasks, lamins have so far been found only in metazoans. Yet, recently we have identified Dictyostelium NE81 as the first lamin-like protein in a lower eukaryote. Based on the current knowledge, we draw a model for nuclear envelope organization in Dictyostelium in this Extra View and we review the experimental data that justified this classification. Furthermore we provide unpublished data underscoring the requirement of posttranslational CaaX-box processing for proper protein localization at the nuclear envelope. Sequence comparison of NE81 sequences from four Dictyostelia with bona fide lamins illustrates the evolutional relationship between these proteins. Under certain conditions these usually unicellular social amoebae congregate to form a multicellular body. We propose that the evolution of the lamin-like NE81 went along with the invention of multicellularity.
Data dependencies, or integrity constraints, are used to improve the quality of a database schema, to optimize queries, and to ensure consistency in a database. In the last years conditional dependencies have been introduced to analyze and improve data quality. In short, a conditional dependency is a dependency with a limited scope defined by conditions over one or more attributes. Only the matching part of the instance must adhere to the dependency. In this paper we focus on conditional inclusion dependencies (CINDs). We generalize the definition of CINDs, distinguishing covering and completeness conditions. We present a new use case for such CINDs showing their value for solving complex data quality tasks. Further, we define quality measures for conditions inspired by precision and recall. We propose efficient algorithms that identify covering and completeness conditions conforming to given quality thresholds. Our algorithms choose not only the condition values but also the condition attributes automatically. Finally, we show that our approach efficiently provides meaningful and helpful results for our use case.
Generalized facilitated diffusion model for DNA-binding proteins with search and recognition states
(2012)
Transcription factors (TFs) such as the lac repressor find their target sequence on DNA at remarkably high rates. In the established Berg-von Hippel model for this search process, the TF alternates between three-dimensional diffusion in the bulk solution and one-dimensional sliding along the DNA chain. To overcome the so-called speed-stability paradox, in similar models the TF was considered as being present in two conformations (search state and recognition state) between which it switches stochastically. Combining both the facilitated diffusion model and alternating states, we obtain a generalized model. We explicitly treat bulk excursions for rodlike chains arranged in parallel and consider a simplified model for coiled DNA. Compared to previously considered facilitated diffusion models, corresponding to limiting cases of our generalized model, we surprisingly find a reduced target search rate. Moreover, at optimal conditions there is no longer an equipartition between the time spent by the protein on and off the DNA chain.
The blowfly salivary gland - A model system for analyzing the regulation of plasma membrane V-ATPase
(2012)
Vacuolar H+-ATPases (V-ATPases) are heteromultimeric proteins that use the energy of ATP hydrolysis for the electrogenic transport of protons across membranes. They are common to all eukaryotic cells and are located in the plasma membrane or in membranes of acid organelles. In many insect epithelia, V-ATPase molecules reside in large numbers in the apical plasma membrane and create an electrochemical proton gradient that is used for the acidification or alkalinization of the extracellular space, the secretion or reabsorption of ions and fluids, the import of nutrients, and diverse other cellular activities. Here, we summarize our results on the functions and regulation of V-ATPase in the tubular salivary gland of the blowfly Calliphora vicina. In this gland, V-ATPase activity energizes the secretion of a KCl-rich saliva in response to the neurohormone serotonin (5-HT). Because of particular morphological and physiological features, the blowfly salivary glands are a superior and exemplary system for the analysis of the intracellular signaling pathways and mechanisms that modulate V-ATPase activity and solute transport in an insect epithelium.
Magnetotactic bacteria produce chains of magnetite nanoparticles, which are called magnetosomes and are used for navigational purposes. We use these cells as a biological template to prepare a hollow hybrid material based on silica and magnetite, and show that the synthetic route is nondestructive as the material conserves the cell morphology as well as the alignment of the magnetic particles. The hybrid material can be resuspended in aqueous solution, and can be shown to orient itself in an external magnetic field. We anticipate that chemical modification of the silica can be used to functionalize the material surface in order to obtain multifunctional materials with specialized applications, e.g. targeted drug delivery.
The paper presents a classification of the basic types of admissible solutions of the general Friedmann equation with non-vanishing cosmological constant and for the case that radiation and matter do not couple. There are four distinct types. The classification uses first the discriminant of a polynomial of the third degree, closely related to the right hand side of the Friedmann equation. The decisive term is then a critical radiation density which can be calculated explicitly.
Neuromuscular activity of the lower leg is dependent on the task performed, speed of movement and gender. Whether training volume influences neuromuscular activity is not known. The EMG of physically active persons differing in running mileage was analysed to investigate this. 55 volunteers were allocated to a low (LM: < 30 km), intermediate (IM: > 30 km & < 45 km) or high mileage (HM: > 45 km) group according to their weekly running volume. Neuromuscular activity of the lower leg was measured during running (3.33 m.s(-1)). Mean amplitude values for preactivation, weight acceptance and push-off were calculated and normalised to the mean activity of the entire gait cycle. Higher activity in the gastrocnemius group was observed in weight acceptance in LM compared to IM (+30%) and HM (+25%) but lower activity was present in the push-off for LM compared to IM and HM. For the peroneal muscle, differences were present in the push-off where HM showed increased activity compared to IM (+24%) and LM (+60%). The tibial muscle revealed slightly lower activity during preactivation for the high mileage runners. Neuromuscular activity differs during stance between the high and intermediate group compared to low mileage runners. Slight adaptations in neuromuscular activation indicate a more target-oriented activation strategy possibly due to repetitive training in runners with higher weekly mileage.
Contemporary cosmological conceptions suggest that the dark matter in haloes of galaxies and galaxy clusters has most likely a clumpy structure. If a stream of gas penetrates through it, a small-scale gravitational field created by the clumps disturbs the flow resulting in momentum exchange between the stream and the dark matter. In this article, we perform an analysis of this effect, based on the hierarchical halo model of the dark matter structure and Navarro-Frenk-White density profiles. We consider the clumps of various masses, from the smallest up to the highest ones M = 10(9) M circle dot. It has been found that in any event the effect grows with the mass of the clump: not only the drag force F acting on the clump but also its acceleration w = F/M increases.
We discuss various astrophysical systems. The mechanism proved to be ineffective in the case of galaxy or galaxy cluster collisions. On the other hand, it played an important role during the process of galaxy formation. As a result, the dark matter should have formed a more compact, oblate and faster rotating substructure in the halo of our Galaxy. We have shown that this thick disc should be more clumpy than the halo. This fact is very important for the indirect detection experiments since it is the clumps that give the main contribution to the annihilation signal. Our calculations show that the mechanism of momentum exchange between the dark and baryon matter is ineffective on the outskirts of the galactic halo. It means that the clumps from there were not transported to the thick disc, and this region should be more clumpy than the halo on the average.
The indirect detection of dark matter requires that dark matter annihilation products be discriminated from conventional astrophysical backgrounds. Here, we re-analyze GeV-band gamma-ray observations of the prominent Milky Way dwarf satellite galaxy Segue 1, for which the expected astrophysical background is minimal. We explicitly account for the angular extent of the conservatively expected gamma-ray signal and keep the uncertainty in the dark-matter profile external to the likelihood analysis of the gamma-ray data.
Ground-motion prediction equations (GMPE) are essential in probabilistic seismic hazard studies for estimating the ground motions generated by the seismic sources. In low-seismicity regions, only weak motions are available during the lifetime of accelerometric networks, and the equations selected for the probabilistic studies are usually models established from foreign data. Although most GMPEs have been developed for magnitudes 5 and above, the minimum magnitude often used in probabilistic studies in low-seismicity regions is smaller. Disaggregations have shown that, at return periods of engineering interest, magnitudes less than 5 may be contributing to the hazard. This paper presents the testing of several GMPEs selected in current international and national probabilistic projects against weak motions recorded in France (191 recordings with source-site distances up to 300 km, 3:8 <= M-w <= 4:5). The method is based on the log-likelihood value proposed by Scherbaum et al. (2009). The best-fitting models (approximately 2:5 <= LLH <= 3:5) over the whole frequency range are the Cauzzi and Faccioli (2008), Akkar and Bommer (2010), and Abrahamson and Silva (2008) models. No significant regional variation of ground motions is highlighted, and the magnitude scaling could be the predominant factor in the control of ground-motion amplitudes. Furthermore, we take advantage of a rich Japanese dataset to run tests on randomly selected low-magnitude subsets, and confirm that a dataset of similar to 190 observations, the same size as the French dataset, is large enough to obtain stable LLH estimates. Additionally we perform the tests against larger magnitudes (5-7) from the Japanese dataset. The ranking of models is partially modified, indicating a magnitude scaling effect for some of the models, and showing that extrapolating testing results obtained from low-magnitude ranges to higher magnitude ranges is not straightforward.
Micronutrient deficiencies are widespread in developing countries, particularly in remote communities such as mobile pastoralists. The nutritional and vitamin A status of this population is not well-documented in Chad. This study assessed serum retinol levels among women and children under five-year-old in nomadic and semi-nomadic pastoralist and rural-settled communities, who are similarly exposed to risk factors such as gastrointestinal parasitic infection, anaemia and emaciation. The novel method of portable fluorometry was used for the first time to measure beta-carotene and retinol levels in a pastoral nomadic area. Moderate level blood retinol deficiency (< 0.7 mu mol/L) was observed in 5% (CI 1-11) of nomadic, 29% (CI 13-45) of semi-nomadic and 22% (CI 8-35) of sedentary women. In children, 1% (CI 0.1-4), 17% (CI 9-25) and 28% (CI 18-39), respectively, had moderate level blood retinol deficiency. In nomadic communities, women and children had blood retinol levels close to normal. Deficiency of retinol was strongly linked with lifestyle (nomadic, semi-nomadic and settled) among women and lifestyle and age among children. The results support an ecological linkage between human retinol levels and livestock milk retinol. This study shows the feasibility of portable retinol and beta-carotene measurement in human blood as well as human and animal milk under remote field conditions, but the approach requires further validation.
Over the last two decades, macroecology the analysis of large-scale, multi-species ecological patterns and processes has established itself as a major line of biological research. Analyses of statistical links between environmental variables and biotic responses have long and successfully been employed as a main approach, but new developments are due to be utilized. Scanning the horizon of macroecology, we identified four challenges that will probably play a major role in the future. We support our claims by examples and bibliographic analyses. 1) Integrating the past into macroecological analyses, e.g. by using paleontological or phylogenetic information or by applying methods from historical biogeography, will sharpen our understanding of the underlying reasons for contemporary patterns. 2) Explicit consideration of the local processes that lead to the observed larger-scale patterns is necessary to understand the fine-grain variability found in nature, and will enable better prediction of future patterns (e.g. under environmental change conditions). 3) Macroecology is dependent on large-scale, high quality data from a broad spectrum of taxa and regions. More available data sources need to be tapped and new, small-grain large-extent data need to be collected. 4) Although macroecology already lead to mainstreaming cutting-edge statistical analysis techniques, we find that more sophisticated methods are needed to account for the biases inherent to sampling at large scale. Bayesian methods may be particularly suitable to address these challenges. To continue the vigorous development of the macroecological research agenda, it is time to address these challenges and to avoid becoming too complacent with current achievements.
Cyber-physical systems achieve sophisticated system behavior exploring the tight interconnection of physical coupling present in classical engineering systems and information technology based coupling. A particular challenging case are systems where these cyber-physical systems are formed ad hoc according to the specific local topology, the available networking capabilities, and the goals and constraints of the subsystems captured by the information processing part. In this paper we present a formalism that permits to model the sketched class of cyber-physical systems. The ad hoc formation of tightly coupled subsystems of arbitrary size are specified using a UML-based graph transformation system approach. Differential equations are employed to define the resulting tightly coupled behavior. Together, both form hybrid graph transformation systems where the graph transformation rules define the discrete steps where the topology or modes may change, while the differential equations capture the continuous behavior in between such discrete changes. In addition, we demonstrate that automated analysis techniques known for timed graph transformation systems for inductive invariants can be extended to also cover the hybrid case for an expressive case of hybrid models where the formed tightly coupled subsystems are restricted to smaller local networks.
Prior research has shown that quantity of schooling affects the development of intelligence in childhood and adolescence. However, it is still debated whether other aspects of schooling-such as ability tracking or, more generally, school quality-can also influence intelligence. In this study, the authors analyzed intelligence gains in academic- and vocational-track schools in Germany, testing for differential effects of school quality (academic vs. vocational track) on psychometric intelligence. Longitudinal data were obtained from a sample of N = 1,038 Grade 7 and 10 students in 49 schools. A nonverbal reasoning test was used as an indicator of general psychometric intelligence, and relevant psychological and social background variables were included in the analyses. Propensity score matching was used to control for selection bias. Results showed a positive effect of attending the academic track.
Honey bees (Apis mellifera) are well known for their excellent learning abilities. Although most age groups learn quickly to associate an odor with a sucrose reward, newly emerged bees and old foragers often perform poorly. For a long time, the reason for the poor learning performance of these age groups was unclear. We show that reduced sensitivity for sucrose is the cause for poor associative learning in newly emerged bees but not in old foragers. By increasing the sensitivity for sucrose through octopamine, we selectively improved the learning performance of insensitive newly emerged bees. Interestingly, the learning performance of foragers experiencing the same treatment remained low, despite the observed increase in sensitivity for the reward. We thus demonstrate that increasing sensitivity for the reward can improve the associative learning performance of bees when they are young but not when they had foraged for a long time. Importantly, octopamine can have very different effects on bees, depending on their initial sensory sensitivity. These differential effects of octopamine have important consequences for interpreting the action of biogenic amines on insect behavior.
The global warming potential of nitrous oxide (N2O) and its long atmospheric lifetime mean its presence in the atmosphere is of major concern, and that methods are required to measure and reduce emissions. Large spatial and temporal variations means, however, that simple extrapolation of measured data is inappropriate, and that other methods of quantification are required. Although process-based models have been developed to simulate these emissions, they often require a large amount of input data that is not available at a regional scale, making regional and global emission estimates difficult to achieve. The spatial extent of organic soils means that quantification of emissions from these soil types is also required, but will not be achievable using a process-based model that has not been developed to simulate soil water contents above field capacity or organic soils. The ECOSSE model was developed to overcome these limitations, and with a requirement for only input data that is readily available at a regional scale, it can be used to quantify regional emissions and directly inform land-use change decisions. ECOSSE includes the major processes of nitrogen (N) turnover, with material being exchanged between pools of SOM at rates modified by temperature, soil moisture, soil pH and crop cover. Evaluation of its performance at site-scale is presented to demonstrate its ability to adequately simulate soil N contents and N2O emissions from cropland soils in Europe. Mitigation scenarios and sensitivity analyses are also presented to demonstrate how ECOSSE can be used to estimate the impact of future climate and land-use change on N2O emissions.
Aims. We aim at analysing systematically the distribution and physical properties of neutral and mildly ionised gas in the Milky Way halo, based on a large absorption-selected data set.
Methods. Multi-wavelength studies were performed combining optical absorption line data of Ca II and Na I with follow-up H I 21-cm emission line observations along 408 sight lines towards low-and high-redshift QSOs. We made use of archival optical spectra obtained with UVES/VLT. H I data were extracted from the Effelsberg-Bonn H I survey and the Galactic All-Sky survey. For selected sight lines we obtained deeper follow-up observations using the Effelsberg 100-m telescope.
Results. Ca II (Na I) halo absorbers at intermediate and high radial velocities are present in 40-55% (20-35%) of the sightlines, depending on the column density threshold chosen. Many halo absorbers show multi-component absorption lines, indicating the presence of sub-structure. In 65% of the cases, absorption is associated with H I 21-cm emission. The Ca II (Na I) column density distribution function follows a power-law with a slope of beta approximate to -2.2 (-1.4).
Conclusions. Our absorption-selected survey confirms our previous results that the Milky Way halo is filled with a large number of neutral gas structures whose high column density tail represents the population of common H I high-and intermediate-velocity clouds seen in 21-cm observations. We find that Na I/Ca II column density ratios in the halo absorbers are typically smaller than those in the Milky Way disc, in the gas in the Magellanic Clouds, and in damped Lyman a systems. The small ratios (prominent in particular in high-velocity components) indicate a lower level of Ca depletion onto dust grains in Milky Way halo absorbers compared to gas in discs and inner regions of galaxies.