Showing papers by "Humboldt University of Berlin published in 2012"

The oyster genome reveals stress adaptation and complexity of shell formation

Abstract: The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.

Review of AdS/CFT Integrability: An Overview

Abstract: This is the introductory chapter of a review collection on integrability in the context of the AdS/CFT correspondence. In the collection we present an overview of the achievements and the status of this subject as of the year 2010.

Process Mining Manifesto

Abstract: Process mining techniques are able to extract knowledge from event logs commonly available in today’s information systems. These techniques provide new means to discover, monitor, and improve processes in a variety of application domains. There are two main drivers for the growing interest in process mining. On the one hand, more and more events are being recorded, thus, providing detailed information about the history of processes. On the other hand, there is a need to improve and support business processes in competitive and rapidly changing environments. This manifesto is created by the IEEE Task Force on Process Mining and aims to promote the topic of process mining. Moreover, by defining a set of guiding principles and listing important challenges, this manifesto hopes to serve as a guide for software developers, scientists, consultants, business managers, and end-users. The goal is to increase the maturity of process mining as a new tool to improve the (re)design, control, and support of operational business processes.

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

Abstract: We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.

Catalysis by metallic nanoparticles in aqueous solution: model reactions.

Abstract: Catalysis by metallic nanoparticles is certainly among the most intensely studied problems in modern nanoscience. However, reliable tests for catalytic performance of such nanoparticles are often poorly defined, which makes comparison and benchmarking rather difficult. We tackle in this tutorial review a subset of well-studied reactions that take place in aqueous phase and for which a comprehensive kinetic analysis is available. Two of these catalytic model reactions are under consideration here, namely the reduction of (i) p-nitrophenol and (ii) hexacyanoferrate (III), both by borohydride ions. Both reactions take place at the surface of noble metal nanoparticles at room temperature and can be accurately monitored by UV-vis spectroscopy. Moreover, the total surface area of the nanoparticles in solution can be known with high precision and thus can be directly used for the kinetic analysis. Hence, these model reactions represent cases of heterogeneous catalysis that can be modelled with the accuracy typically available for homogeneous catalysis. Both model reactions allow us to discuss a number of important concepts and questions, namely the dependence of catalytic activity on the size of the nanoparticles, electrochemistry of nanoparticles, surface restructuring, the use of carrier systems and the role of diffusion control.

Multivalency as a chemical organization and action principle.

Abstract: Multivalent interactions can be applied universally for a targeted strengthening of an interaction between different interfaces or molecules. The binding partners form cooperative, multiple receptor-ligand interactions that are based on individually weak, noncovalent bonds and are thus generally reversible. Hence, multi- and polyvalent interactions play a decisive role in biological systems for recognition, adhesion, and signal processes. The scientific and practical realization of this principle will be demonstrated by the development of simple artificial and theoretical models, from natural systems to functional, application-oriented systems. In a systematic review of scaffold architectures, the underlying effects and control options will be demonstrated, and suggestions will be given for designing effective multivalent binding systems, as well as for polyvalent therapeutics.

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

Abstract: Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.

Still a Host of Hosts for Wolbachia : Analysis of Recent Data Suggests That 40% of Terrestrial Arthropod Species Are Infected

Abstract: Wolbachia are intracellular bacteria that manipulate the reproduction of their arthropod hosts in remarkable ways. They are predominantly transmitted vertically from mother to offspring but also occasionally horizontally between species. In doing so, they infect a huge range of arthropod species worldwide. Recently, a statistical analysis estimated the infection frequency of Wolbachia among arthropod hosts to be 66%. At the same time, the authors of this analysis highlighted some weaknesses of the underlying data and concluded that in order to improve the estimate, a larger number of individuals per species should be assayed and species be chosen more randomly. Here we apply the statistical approach to a more appropriate data set from a recent survey that tested both a broad range of species and a sufficient number of individuals per species. Indeed, we find a substantially different infection frequency: We now estimate the proportion of Wolbachia-infected species to be around 40% which is lower than the previous estimate but still points to a surprisingly high number of arthropods harboring the bacteria. Notwithstanding this difference, we confirm the previous result that, within a given species, typically most or only a few individuals are infected. Moreover, we extend our analysis to include several reproductive parasites other than Wolbachia that were also screened for in the aforementioned empirical survey. For these symbionts we find a large variation in estimated infection frequencies and corroborate the finding that Wolbachia are the most abundant endosymbionts among arthropod species.

Mid-infrared optical properties of thin films of aluminum oxide, titanium dioxide, silicon dioxide, aluminum nitride, and silicon nitride

Abstract: The complex refractive index components, n and k, have been studied for thin films of several common dielectric materials with a low to medium refractive index as functions of wavelength and stoichiometry for mid-infrared (MIR) wavelengths within the range 1.54–14.29 μm (700–6500 cm−1). The materials silicon oxide, silicon nitride, aluminum oxide, aluminum nitride, and titanium oxide are prepared using room temperature reactive sputter deposition and are characterized using MIR variable angle spectroscopic ellipsometry. The investigation shows how sensitive the refractive index functions are to the O2 and N2 flow rates, and for which growth conditions the materials deposit homogeneously. It also allows conclusions to be drawn on the degree of amorphousness and roughness. To facilitate comparison of the materials deposited in this work with others, the index of refraction was also determined and provided for the near-IR and visible ranges of the spectrum. The results presented here should serve as a useful information base for designing optical coatings for the MIR part of the electromagnetic spectrum. The results are parameterized to allow them to be easily used for coating design.

Urban land teleconnections and sustainability

Abstract: This paper introduces urban land teleconnections as a conceptual framework that explicitly links land changes to underlying urbanization dynamics. We illustrate how three key themes that are currently addressed separately in the urban sustainability and land change literatures can lead to incorrect conclusions and misleading results when they are not examined jointly: the traditional system of land classification that is based on discrete categories and reinforces the false idea of a rural–urban dichotomy; the spatial quantification of land change that is based on place-based relationships, ignoring the connections between distant places, especially between urban functions and rural land uses; and the implicit assumptions about path dependency and sequential land changes that underlie current conceptualizations of land transitions. We then examine several environmental “grand challenges” and discuss how urban land teleconnections could help research communities frame scientific inquiries. Finally, we point to existing analytical approaches that can be used to advance development and application of the concept.

Evidence for an excess of B̄→D( *)τ -ν ̄τ decays

Abstract: Based on the full BaBar data sample, we report improved measurements of the ratios R(D(*)) = B(B -> D(*) Tau Nu)/B(B -> D(*) l Nu), where l is either e or mu. These ratios are sensitive to new physics contributions in the form of a charged Higgs boson. We measure R(D) = 0.440 +- 0.058 +- 0.042 and R(D*) = 0.332 +- 0.024 +- 0.018, which exceed the Standard Model expectations by 2.0 sigma and 2.7 sigma, respectively. Taken together, our results disagree with these expectations at the 3.4 sigma level. This excess cannot be explained by a charged Higgs boson in the type II two-Higgs-doublet model. We also report the observation of the decay B -> D Tau Nu, with a significance of 6.8 sigma.

Best practices for justifying fossil calibrations

Abstract: At this time, no abstract is available. SciVerse Scopus has content delivery agreements in place with each publisher and currently contains 30 million records with an abstract. An abstract may not be present due to incomplete data, as supplied by the publisher, or is still in the process of being indexed.

o-Fluoroazobenzenes as Readily Synthesized Photoswitches Offering Nearly Quantitative Two-Way Isomerization with Visible Light

Abstract: Azobenzene functionalized with ortho-fluorine atoms has a lower energy of the n-orbital of the Z-isomer, resulting in a separation of the E and Z isomers' n→π* absorption bands. Introducing para-substituents allows for further tuning of the absorption spectra of o-fluoroazobenzenes. In particular, electron-withdrawing ester groups give rise to a 50 nm separation of the n→π* transitions. Green and blue light can therefore be used to induce E→Z and Z→E isomerizations, respectively. The o-fluoroazobenzene scaffold is readily synthesized and can be inserted into larger structures via its aryl termini. These new azobenzene derivatives can be switched in both ways with high photoconversions, and their Z-isomers display a remarkably long thermal half-life.

Can farmers’ adaptation to climate change be explained by socio-economic household-level variables?

Abstract: A better understanding of processes that shape farmers’ adaptation to climate change is critical to identify vulnerable entities and to develop well-targeted adaptation policies. However, it is currently poorly understood what determines farmers’ adaptation and how to measure it. In this study, we develop an activity-based adaptation index (AAI) and explore the relationship between socioeconomic variables and farmers’ adaptation behavior by means of an explanatory factor analysis and a multiple linear regression model using latent variables. The model was tested in six villages situated in two administrative wards in the Morogoro region of Tanzania. The Mlali ward represents a system of relatively high agricultural potential, whereas the Gairo ward represents a system of low agricultural potential. A household survey, a rapid rural appraisal and, a stakeholder workshop were used for data collection. The data were analyzed using factor analysis, multiple linear regression, descriptive statistical methods and qualitative content analysis. The empirical results are discussed in the context of theoretical concepts of adaptation and the sustainable livelihood approach. We found that public investment in rural infrastructure, in the availability and technically efficient use of inputs, in a good education system that provides equal chances for women, and in the strengthening of social capital, agricultural extension and, microcredit services are the best means of improving the adaptation of the farmers from the six villages in Gairo and Mlali. We conclude that the newly developed AAI is a simple but promising way to capture the complexity of adaptation processes that addresses a number of shortcomings of previous index studies.

Experimental observation of chimeras in coupled-map lattices

Abstract: In systems of oscillators, phase-locking behaviour can, in theory, coexist with incoherent dynamics—invoking the fabled chimera state. Now, experimental realization of a coupled-map lattice reveals dynamical states displaying coexisting spatial domains of coherence and incoherence.

Electron performance measurements with the ATLAS detector using the 2010 LHC proton-proton collision data

Abstract: Detailed measurements of the electron performance of the ATLAS detector at the LHC are reported, using decays of the Z, W and J/psi particles. Data collected in 2010 at root s = 7 TeV are used, corresponding to an integrated luminosity of almost 40 pb(-1). The inter-alignment of the inner detector and the electromagnetic calorimeter, the determination of the electron energy scale and resolution, and the performance in terms of response uniformity and linearity are discussed. The electron identification, reconstruction and trigger efficiencies, as well as the charge misidentification probability, are also presented.

Controlling on-surface polymerization by hierarchical and substrate-directed growth

Abstract: A key challenge in the field of nanotechnology, in particular in the design of molecular machines, novel materials or molecular electronics, is the bottom-up construction of covalently bound molecular architectures in a well-defined arrangement. To date, only rather simple structures have been obtained because of the limitation of one-step connection processes. Indeed, for the formation of sophisticated structures, step-by-step connection of molecules is required. Here, we present a strategy for the covalent connection of molecules in a hierarchical manner by the selective and sequential activation of specific sites, thereby generating species with a programmed reactivity. This approach leads to improved network quality and enables the fabrication of heterogeneous architectures with high selectivity. Furthermore, substrate-directed growth and a preferred orientation of the molecular nanostructures are achieved on an anisotropic surface. The demonstrated control over reactivity and diffusion during covalent bond formation constitutes a promising route towards the creation of sophisticated multi-component molecular nanostructures.

Models of anomalous diffusion in crowded environments

Abstract: A particle's motion in crowded environments often exhibits anomalous diffusion, whose nature depends on the situation at hand and is formalized within different physical models. Thus, such environments may contain traps, labyrinthine paths or macromolecular structures, which the particles may be attached to. Physical assumptions are translated into mathematical models which often come with nice mathematical instruments for their description, e.g. fractional diffusion equations. The beauty of the instrument sometimes seduces an investigator to use it without any connection to the physical model. The author hopes that the present discussion will reduce the danger of such inappropriate use.

Measurement of the azimuthal anisotropy for charged particle production in √ sNN = 2.76 TeV lead-lead collisions with the ATLAS detector

Abstract: Differential measurements of charged particle azimuthal anisotropy are presented for lead-lead collisions at root sNN = 2.76 TeV with the ATLAS detector at the LHC, based on an integrated luminosity of approximately 8 mu b(-1). This anisotropy is characterized via a Fourier expansion of the distribution of charged particles in azimuthal angle relative to the reaction plane, with the coefficients v(n) denoting the magnitude of the anisotropy. Significant v(2)-v(6) values are obtained as a function of transverse momentum (0.5 = 3 are found to vary weakly with both eta and centrality, and their p(T) dependencies are found to follow an approximate scaling relation, v(n)(1/n)(p(T)) proportional to v(2)(1/2)(p(T)), except in the top 5% most central collisions. A Fourier analysis of the charged particle pair distribution in relative azimuthal angle (Delta phi = phi(a)-phi(b)) is performed to extract the coefficients v(n,n) = . For pairs of charged particles with a large pseudorapidity gap (|Delta eta = eta(a) - eta(b)| > 2) and one particle with p(T) < 3 GeV, the v(2,2)-v(6,6) values are found to factorize as v(n,n)(p(T)(a), p(T)(b)) approximate to v(n) (p(T)(a))v(n)(p(T)(b)) in central and midcentral events. Such factorization suggests that these values of v(2,2)-v(6,6) are primarily attributable to the response of the created matter to the fluctuations in the geometry of the initial state. A detailed study shows that the v(1,1)(p(T)(a), p(T)(b)) data are consistent with the combined contributions from a rapidity-even v(1) and global momentum conservation. A two-component fit is used to extract the v(1) contribution. The extracted v(1) isobserved to cross zero at pT approximate to 1.0 GeV, reaches a maximum at 4-5 GeV with a value comparable to that for v(3), and decreases at higher p(T).

Performance of the ATLAS Trigger System in 2010

Abstract: Proton-proton collisions at root s = 7 TeV and heavy ion collisions at root(NN)-N-s = 2.76 TeV were produced by the LHC and recorded using the ATLAS experiment's trigger system in 2010. The LHC is designed with a maximum bunch crossing rate of 40 MHz and the ATLAS trigger system is designed to record approximately 200 of these per second. The trigger system selects events by rapidly identifying signatures of muon, electron, photon, tau lepton, jet, and B meson candidates, as well as using global event signatures, such as missing transverse energy. An overview of the ATLAS trigger system, the evolution of the system during 2010 and the performance of the trigger system components and selections based on the 2010 collision data are shown. A brief outline of plans for the trigger system in 2011 is presented.

The biology and chemistry of high-valent iron–oxo and iron–nitrido complexes

Abstract: Selective functionalization of unactivated C-H bonds and ammonia production are extremely important industrial processes. A range of metalloenyzmes achieve these challenging tasks in biology by activating dioxygen and dinitrogen using cheap and abundant transition metals, such as iron, copper and manganese. High-valent iron-oxo and -nitrido complexes act as active intermediates in many of these processes. The generation of well-described model compounds can provide vital insights into the mechanism of such enzymatic reactions. Advances in the chemistry of model high-valent iron-oxo and -nitrido systems can be related to our understanding of the biological systems.

Fluorinated copolymer PCPDTBT with enhanced open-circuit voltage and reduced recombination for highly efficient polymer solar cells.

Abstract: A novel fluorinated copolymer (F-PCPDTBT) is introduced and shown to exhibit significantly higher power conversion efficiency in bulk heterojunction solar cells with PC(70)BM compared to the well-known low-band-gap polymer PCPDTBT. Fluorination lowers the polymer HOMO level, resulting in high open-circuit voltages well exceeding 0.7 V. Optical spectroscopy and morphological studies with energy-resolved transmission electron microscopy reveal that the fluorinated polymer aggregates more strongly in pristine and blended layers, with a smaller amount of additives needed to achieve optimum device performance. Time-delayed collection field and charge extraction by linearly increasing voltage are used to gain insight into the effect of fluorination on the field dependence of free charge-carrier generation and recombination. F-PCPDTBT is shown to exhibit a significantly weaker field dependence of free charge-carrier generation combined with an overall larger amount of free charges, meaning that geminate recombination is greatly reduced. Additionally, a 3-fold reduction in non-geminate recombination is measured compared to optimized PCPDTBT blends. As a consequence of reduced non-geminate recombination, the performance of optimized blends of fluorinated PCPDTBT with PC(70)BM is largely determined by the field dependence of free-carrier generation, and this field dependence is considerably weaker compared to that of blends comprising the non-fluorinated polymer. For these optimized blends, a short-circuit current of 14 mA/cm(2), an open-circuit voltage of 0.74 V, and a fill factor of 58% are achieved, giving a highest energy conversion efficiency of 6.16%. The superior device performance and the low band-gap render this new polymer highly promising for the construction of efficient polymer-based tandem solar cells.

Inhibition of IL-12/IL-23 signaling reduces Alzheimer's disease–like pathology and cognitive decline

Abstract: The pathology of Alzheimer's disease has an inflammatory component that is characterized by upregulation of proinflammatory cytokines, particularly in response to amyloid-β (Aβ). Using the APPPS1 Alzheimer's disease mouse model, we found increased production of the common interleukin-12 (IL-12) and IL-23 subunit p40 by microglia. Genetic ablation of the IL-12/IL-23 signaling molecules p40, p35 or p19, in which deficiency of p40 or its receptor complex had the strongest effect, resulted in decreased cerebral amyloid load. Although deletion of IL-12/IL-23 signaling from the radiation-resistant glial compartment of the brain was most efficient in mitigating cerebral amyloidosis, peripheral administration of a neutralizing p40-specific antibody likewise resulted in a reduction of cerebral amyloid load in APPPS1 mice. Furthermore, intracerebroventricular delivery of antibodies to p40 significantly reduced the concentration of soluble Aβ species and reversed cognitive deficits in aged APPPS1 mice. The concentration of p40 was also increased in the cerebrospinal fluid of subjects with Alzheimer's disease, which suggests that inhibition of the IL-12/IL-23 pathway may attenuate Alzheimer's disease pathology and cognitive deficits.

Intended and Unintended Consequences of Mandatory IFRS Adoption: A Review of Extant Evidence and Suggestions for Future Research

Abstract: This paper discusses empirical evidence on the economic consequences of mandatory IFRS adoption in the European Union and provides suggestions on how future research can add to our understanding of these effects. Based on the stated objectives of the EU’s so-called ‘IAS Regulation,’ we distinguish between intended and unintended consequences of mandatory IFRS adoption. Empirical research on the intended consequences generally fails to document an increase in the comparability or transparency of financial statements. In contrast, there is rich and almost unanimous evidence of positive effects on capital markets and at the macroeconomic level. We argue that certain research design issues are likely to contribute to this apparent mismatch in findings. The literature investigating unintended consequences of mandatory IFRS adoption is still in its infancy. However, extant empirical evidence and insights from non-IFRS settings suggest that mandatory IFRS adoption has the potential to materially affect contractual outcomes. We conclude that both the intended and the unintended consequences deserve further scrutiny to assess the costs and benefits of mandatory IFRS adoption and provide specific guidance for future research.

Thermosensitive Au-PNIPA yolk-shell nanoparticles with tunable selectivity for catalysis.

Abstract: Metallic nanoparticles have been the subject of intense research recently because of their catalytic properties, which may differ considerably from the bulk metal. As the free nanoparticles tend to aggregate and are difficult to handle in catalytic applications, colloidal carrier systems have been developed that encapsulate and stabilize the particles. 5] More recently, so-called smart carrier systems, such as thermosensitive microgels, have become the focus of research. These hybrids react on external stimuli and allow the catalytic properties to be altered accordingly. Thus, thermosensitive polystyrene (PS)-poly(N-isopropylacrylamide) (PNIPA) core–shell microgels were applied as the active nanoreactor for the immobilization of metal nanoparticles. The catalytic activity of immobilized metal nanoparticles can be tuned by the swelling and shrinking of the microgels. Liz-Marz n et al. have developed a AuPNIPA core–shell colloidal system. They found that the thermoresponsive PNIPA shell with limited cross-linking allows for particularly efficient control of the catalysis of encapsulated Au nanoparticles. Recently, yolk–shell structures that consist of a single metal nanoparticle within an inorganic or polymeric shell 19] have become the subject of intense research. These systems can be used to tune the catalytic activity of the enclosed nanoparticle by a suitable architecture of the shell. Yolk–shell structures have the clear advantages in that individual metal nanoparticles are enclosed in a compartment that prevents aggregation with other nanoparticles. Furthermore, the embedded gold nanoparticle has a free surface that is not blocked by any surface group or polymer compared to the Au-PNIPA core–shell system. Moreover, the permeability of the shell may be tuned to a certain extent. Therefore, yolk– shell systems may be regarded as true nanoreactors that allow the catalytic activity of single nanoparticles to be studied in a defined environment. Herein we present a thermosensitive yolk–shell system that uses temperature as a trigger for reaction. Figure 1a shows the underlying principle of these systems: A single Au nanoparticle is encapsulated in a hollow thermosensitive PNIPA shell. The porosity and the hydrophobicity of this shell can be tuned in a well-defined manner by temperature while the colloidal stability of the entire hybrid is fully maintained. We show this by monitoring the reduction of hydrophilic 4-