Showing papers by "Bielefeld University published in 2014"

Equation of state in ( 2+1 )-flavor QCD

Abstract: We present results for the equation of state in ($2+1$)-flavor QCD using the highly improved staggered quark action and lattices with temporal extent ${N}_{\ensuremath{\tau}}=6$, 8, 10, and 12. We show that these data can be reliably extrapolated to the continuum limit and obtain a number of thermodynamic quantities and the speed of sound in the temperature range 130--400 MeV. We compare our results with previous calculations and provide an analytic parameterization of the pressure, from which other thermodynamic quantities can be calculated, for use in phenomenology. We show that the energy density in the crossover region, $145\text{ }\text{ }\mathrm{MeV}\ensuremath{\le}T\ensuremath{\le}163\text{ }\text{ }\mathrm{MeV}$, defined by the chiral transition, is ${\ensuremath{\epsilon}}_{c}=(0.18--0.5)\text{ }\text{ }\mathrm{GeV}/{\mathrm{fm}}^{3}$, i.e., $(1.2--3.1)\text{ }{\ensuremath{\epsilon}}_{\text{nuclear}}$. At high temperatures, we compare our results with resummed and dimensionally reduced perturbation theory calculations. As a byproduct of our analyses, we obtain the values of the scale parameters ${r}_{0}$ from the static quark potential and ${w}_{0}$ from the gradient flow.

Tolerance to drought and salt stress in plants: Unraveling the signaling networks.

Abstract: Tolerance of plants to abiotic stressors such as drought and salinity is triggered by complex multicomponent signaling pathways to restore cellular homeostasis and promote survival. Major plant transcription factor families such as bZIP, NAC, AP2/ERF, and MYB orchestrate regulatory networks underlying abiotic stress tolerance. Sucrose non-fermenting 1-related protein kinase 2 and mitogen-activated protein kinase pathways contribute to initiation of stress adaptive downstream responses and promote plant growth and development. As a convergent point of multiple abiotic cues, cellular effects of environmental stresses are not only imbalances of ionic and osmotic homeostasis but also impaired photosynthesis, cellular energy depletion, and redox imbalances. Recent evidence of regulatory systems that link sensing and signaling of environmental conditions and the intracellular redox status have shed light on interfaces of stress and energy signaling. ROS (reactive oxygen species) cause severe cellular damage by peroxidation and de-esterification of membrane-lipids, however, current models also define a pivotal signaling function of ROS in triggering tolerance against stress. Recent research advances suggest and support a regulatory role of ROS in the cross talks of stress triggered hormonal signaling such as the abscisic acid pathway and endogenously induced redox and metabolite signals. Here, we discuss and review the versatile molecular convergence in the abiotic stress responsive signaling networks in the context of ROS and lipid-derived signals and the specific role of stomatal signaling.

Choosing and using diversity indices: Insights for ecological applications from the German Biodiversity Exploratories

Abstract: Biodiversity, a multidimensional property of natural systems, is difficult to quantify partly because of the multitude of indices proposed for this purpose. Indices aim to describe general properties of communities that allow us to compare different regions, taxa, and trophic levels. Therefore, they are of fundamental importance for environmental monitoring and conservation, although there is no consensus about which indices are more appropriate and informative. We tested several common diversity indices in a range of simple to complex statistical analyses in order to determine whether some were better suited for certain analyses than others. We used data collected around the focal plant Plantago lanceolata on 60 temperate grassland plots embedded in an agricultural landscape to explore relationships between the common diversity indices of species richness (S), Shannon's diversity (H'), Simpson's diversity (D-1), Simpson's dominance (D-2), Simpson's evenness (E), and Berger-Parker dominance (BP). We calculated each of these indices for herbaceous plants, arbuscular mycorrhizal fungi, aboveground arthropods, belowground insect larvae, and P.lanceolata molecular and chemical diversity. Including these trait-based measures of diversity allowed us to test whether or not they behaved similarly to the better studied species diversity. We used path analysis to determine whether compound indices detected more relationships between diversities of different organisms and traits than more basic indices. In the path models, more paths were significant when using H', even though all models except that with E were equally reliable. This demonstrates that while common diversity indices may appear interchangeable in simple analyses, when considering complex interactions, the choice of index can profoundly alter the interpretation of results. Data mining in order to identify the index producing the most significant results should be avoided, but simultaneously considering analyses using multiple indices can provide greater insight into the interactions in a system.

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Abstract: Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.

An environmental bacterial taxon with a large and distinct metabolic repertoire

Abstract: Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such ‘talented’ producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus ‘Entotheonella’ with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. ‘Entotheonella’ spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum ‘Tectomicrobia’. The pronounced bioactivities and chemical uniqueness of ‘Entotheonella’ compounds provide significant opportunities for ecological studies and drug discovery.

The genome of the recently domesticated crop plant sugar beet ( Beta vulgaris )

Abstract: Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.

The environmental controls that govern the end product of bacterial nitrate respiration

Abstract: In the biogeochemical nitrogen cycle, microbial respiration processes compete for nitrate as an electron acceptor. Denitrification converts nitrate into nitrogenous gas and thus removes fixed nitrogen from the biosphere, whereas ammonification converts nitrate into ammonium, which is directly reusable by primary producers. We combined multiple parallel long-term incubations of marine microbial nitrate-respiring communities with isotope labeling and metagenomics to unravel how specific environmental conditions select for either process. Microbial generation time, supply of nitrite relative to nitrate, and the carbon/nitrogen ratio were identified as key environmental controls that determine whether nitrite will be reduced to nitrogenous gas or ammonium. Our results define the microbial ecophysiology of a biogeochemical feedback loop that is key to global change, eutrophication, and wastewater treatment.

Neuromorphic Electronic Circuits for Building Autonomous Cognitive Systems

Abstract: Several analog and digital brain-inspired electronic systems have been recently proposed as dedicated solutions for fast simulations of spiking neural networks. While these architectures are useful for exploring the computational properties of large-scale models of the nervous system, the challenge of building low-power compact physical artifacts that can behave intelligently in the real world and exhibit cognitive abilities still remains open. In this paper, we propose a set of neuromorphic engineering solutions to address this challenge. In particular, we review neuromorphic circuits for emulating neural and synaptic dynamics in real time and discuss the role of biophysically realistic temporal dynamics in hardware neural processing architectures; we review the challenges of realizing spike-based plasticity mechanisms in real physical systems and present examples of analog electronic circuits that implement them;we describe the computational properties of recurrent neural networks and show how neuromorphic winner-take-all circuits can implement working-memory and decision-making mechanisms. We validate the neuromorphic approach proposed with experimental results obtained from our own circuits and systems, and argue how the circuits and networks presented in this work represent a useful set of components for efficiently and elegantly implementing neuromorphic cognition.

Measuring underreporting and under-ascertainment in infectious disease datasets: a comparison of methods

Abstract: Background: Efficient and reliable surveillance and notification systems are vital for monitoring public health and disease outbreaks. However, most surveillance and notification systems are affected by a degree of underestimation (UE) and therefore uncertainty surrounds the ‘true’ incidence of disease affecting morbidity and mortality rates. Surveillance systems fail to capture cases at two distinct levels of the surveillance pyramid: from the community since not all cases seek healthcare (under-ascertainment), and at the healthcare-level, representing a failure to adequately report symptomatic cases that have sought medical advice (underreporting). There are several methods to estimate the extent of under-ascertainment and underreporting. Methods: Within the context of the ECDC-funded Burden of Communicable Diseases in Europe (BCoDE)-project, an extensive literature review was conducted to identify studies that estimate ascertainment or reporting rates for salmonellosis and campylobacteriosis in European Union Member States (MS) plus European Free Trade Area (EFTA) countries Iceland, Norway and Switzerland and four other OECD countries (USA, Canada, Australia and Japan). Multiplication factors (MFs), a measure of the magnitude of underestimation, were taken directly from the literature or derived (where the proportion of underestimated, under-ascertained, or underreported cases was known) and compared for the two pathogens. Results: MFs varied between and within diseases and countries, representing a need to carefully select the most appropriate MFs and methods for calculating them. The most appropriate MFs are often disease-, country-, age-, and sex-specific. Conclusions: When routine data are used to make decisions on resource allocation or to estimate epidemiological parameters in populations, it becomes important to understand when, where and to what extent these data represent the true picture of disease, and in some instances (such as priority setting) it is necessary to adjust for underestimation. MFs can be used to adjust notification and surveillance data to provide more realistic estimates of incidence.

Physiological aspects of raffinose family oligosaccharides in plants: protection against abiotic stress.

Abstract: Abiotic stresses resulting from water deficit, high salinity or periods of drought adversely affect plant growth and development and represent major selective forces during plant evolution. The raffinose family oligosaccharides (RFOs) are synthesised from sucrose by the subsequent addition of activated galactinol moieties donated by galactinol. RFOs are characterised as compatible solutes involved in stress tolerance defence mechanisms, although evidence also suggests that they act as antioxidants, are part of carbon partitioning strategies and may serve as signals in response to stress. The key enzyme and regulatory point in RFO biosynthesis is galactinol synthase (GolS), and an increase of GolS in expression and activity is often associated with abiotic stress. It has also been shown that different GolS isoforms are expressed in response to different types of abiotic stress, suggesting that the timing and accumulation of RFOs are controlled for each abiotic stress. However, the accumulation of RFOs in response to stress is not universal and other functional roles have been suggested for RFOs, such as being part of a carbon storage mechanism. Transgenic Arabidopsis plants with increased galactinol and raffinose concentrations had better ROS scavenging capacity, while many sugars have been shown in vitro to have antioxidant activity, suggesting that RFOs may also act as antioxidants. The RFO pathway also interacts with other carbohydrate pathways, such as that of O-methyl inositol (OMI), which shows that the functional relevance of RFOs must not be seen in isolation to overall carbon re-allocation during stress responses.

High-throughput sequencing reveals inbreeding depression in a natural population.

Abstract: Proxy measures of genome-wide heterozygosity based on approximately 10 microsatellites have been used to uncover heterozygosity fitness correlations (HFCs) for a wealth of important fitness traits in natural populations. However, effect sizes are typically very small and the underlying mechanisms remain contentious, as a handful of markers usually provides little power to detect inbreeding. We therefore used restriction site associated DNA (RAD) sequencing to accurately estimate genome-wide heterozygosity, an approach transferrable to any organism. As a proof of concept, we first RAD sequenced oldfield mice (Peromyscus polionotus) from a known pedigree, finding strong concordance between the inbreeding coefficient and heterozygosity measured at 13,198 single-nucleotide polymorphisms (SNPs). When applied to a natural population of harbor seals (Phoca vitulina), a weak HFC for parasite infection based on 27 microsatellites strengthened considerably with 14,585 SNPs, the deviance explained by heterozygosity increasing almost fivefold to a remarkable 49%. These findings arguably provide the strongest evidence to date of an HFC being due to inbreeding depression in a natural population lacking a pedigree. They also suggest that under some circumstances heterozygosity may explain far more variation in fitness than previously envisaged.

What Drives Adult Personality Development? A Comparison of Theoretical Perspectives and Empirical Evidence:

Abstract: Increasing numbers of empirical studies provide compelling evidence that personality traits change across the entire lifespan. What initiates this continuing personality development and how does th...

Eye Movement Control

Abstract: is well-known that eye movements are central to visual perception [1]. Visual acuity decreases dramatically in the periphery of vision, and precise eye movements to specific locations are vital to foveate objects of interest and identify them with high accuracy [1–4]. Given the importance of eye movements for visual perception, there has been a surge of interest in the topic, with numerous studies being conducted to clarify the variables that determine our eye movements (for a historical review see [5]). In fact, Google Scholar shows that eye movements are discussed in over a million publications, and a Web of Science search reveals 17,000 publications with eye movement in the title or abstract. As shown in Figure 1, the number of publications with eye movement in the title or abstract has also steadily increased over years, culminating in about 200 papers published in 2013. Figure 1 The number of publications with the “eye movement” in the title or abstract, according to a Web of Science search 2014. Despite the surge of interest in eye movements, many questions remain unresolved. This is also reflected in this special issue on eye movement control. First, there are a variety of different eye movements [2, 4]. Among the most widely known eye movements are the fast, ballistic saccades (including superfast express saccades) (e.g., B. de Gelder et al., this issue), smooth-pursuit eye movements (J. N. van der Geest et al., this issue), and vergence eye movements (e.g., P. M. Grove et al., this issue) required to fixate objects at different depths. Less well-known and yet intensely researched are microsaccades, tremor, slow drift, and vestibuloocular and optokinetic eye movements that stabilize gaze during motions of the head and motions of large regions of the image on the retina [2, 4]. Secondly and more importantly for the current special issue, eye movements are also controlled by a variety of different factors [1, 4]. Apart from being subject to diverse muscular and ocular constraints, successful voluntary control over eye movements critically depends on the quality of the visual input, which in turn depends on a variety of internal and external factors [1, 6, 7]. The contributions to the present special issue clarify key elements of both internal and external factors in eye movement control (G. W. Alpers et al., U. Ansorge et al., B. de Gelder et al., P. M. Grove et al., D. R. Hardwick et al., W. E. Huddlestone et al., J. Kassubek et al., A. Khan et al., A. Piras et al., N. D. Smith et al., J. N. van der Geest et al., and D. Venini et al., this issue). In the present contributions, eye movements have also been used to provide new insights into ocular and neurological disorders (J. Kassubek et al., N. D. Smith et al., this issue) and shed new light on the relationship between covert attention and eye movements (e.g., G. W. Alpers et al., U. Ansorge et al., D. R. Hardwick et al., and A. Khan et al., this issue; see also [6–9]). Together, the papers in this special issue provide a timely update on eye movement control that reflects current hot topics in the field, spanning the range from cognitive science over applied psychology to clinical psychology and neuroscience. Stefanie I. Becker Gernot Horstmann Arvid Herwig

Natural auditory scene statistics shapes human spatial hearing

Abstract: Human perception, cognition, and action are laced with seemingly arbitrary mappings. In particular, sound has a strong spatial connotation: Sounds are high and low, melodies rise and fall, and pitch systematically biases perceived sound elevation. The origins of such mappings are unknown. Are they the result of physiological constraints, do they reflect natural environmental statistics, or are they truly arbitrary? We recorded natural sounds from the environment, analyzed the elevation-dependent filtering of the outer ear, and measured frequency-dependent biases in human sound localization. We find that auditory scene statistics reveals a clear mapping between frequency and elevation. Perhaps more interestingly, this natural statistical mapping is tightly mirrored in both ear-filtering properties and in perceived sound location. This suggests that both sound localization behavior and ear anatomy are fine-tuned to the statistics of natural auditory scenes, likely providing the basis for the spatial connotation of human hearing.

Additional strange hadrons from QCD thermodynamics and strangeness freezeout in heavy ion collisions.

Abstract: We compare lattice QCD results for appropriate combinations of net strangeness fluctuations and their correlations with net baryon number fluctuations with predictions from two hadron resonance gas (HRG) models having different strange hadron content. The conventionally used HRG model based on experimentally established strange hadrons fails to describe the lattice QCD results in the hadronic phase close to the QCD crossover. Supplementing the conventional HRG with additional, experimentally uncharted strange hadrons predicted by quark model calculations and observed in lattice QCD spectrum calculations leads to good descriptions of strange hadron thermodynamics below the QCD crossover. We show that the thermodynamic presence of these additional states gets imprinted in the yields of the ground-state strange hadrons leading to a systematic 5-8 MeV decrease of the chemical freeze-out temperatures of ground-state strange baryons.

Studying Changes in Life Circumstances and Personality: It's About Time

Abstract: Most theories of personality development posit that changes in life circumstances (e.g. due to major life events) can lead to changes in personality, but few studies have examined the exact time course of these changes. In this article, we argue that time needs to be considered explicitly in theories and empirical studies on personality development. We discuss six notions on the role of time in personality development. First, people can differ before the event. Second, change can be non-linear and discontinuous. Third, change can be reversible. Fourth, change can occur before the event. Fifth, control groups are needed to disentangle age-related and event-related changes. Sixth, we need to move beyond examining single major life events and study the effects of non-normative events, non-events, multiple events, and minor events on personality. We conclude by summarizing the methodological and theoretical implications of these notions.

Fast Retrograde Signaling in Response to High Light Involves Metabolite Export, MITOGEN-ACTIVATED PROTEIN KINASE6, and AP2/ERF Transcription Factors in Arabidopsis

Abstract: Regulation of the expression of nuclear genes encoding chloroplast proteins allows for metabolic adjustment in response to changing environmental conditions. This regulation is linked to retrograde signals that transmit information on the metabolic state of the chloroplast to the nucleus. Transcripts of several APETALA2/ETHYLENE RESPONSE FACTOR transcription factors (AP2/ERF-TFs) were found to respond within 10 min after transfer of low-light-acclimated Arabidopsis thaliana plants to high light. Initiation of this transcriptional response was completed within 1 min after transfer to high light. The fast responses of four AP2/ERF genes, ERF6, RRTF1, ERF104, and ERF105, were entirely deregulated in triose phosphate/phosphate translocator (tpt) mutants. Similarly, activation of MITOGEN-ACTIVATED PROTEIN KINASE6 (MPK6) was upregulated after 1 min in the wild type but not in the tpt mutant. Based on this, together with altered transcript regulation in mpk6 and erf6 mutants, a retrograde signal transmission model is proposed starting with metabolite export through the triose phosphate/phosphate translocator with subsequent MPK6 activation leading to initiation of AP2/ERF-TF gene expression and other downstream gene targets. The results show that operational retrograde signaling in response to high light involves a metabolite-linked pathway in addition to previously described redox and hormonal pathways.

Ermittlung standardisierter Bewertungssätze aus gesellschaftlicher Perspektive für die gesundheitsökonomische Evaluation

Abstract: Ziel: Aufgrund der demografischen Alterung gewinnen gesundheitsokonomische Evaluationen von Gesundheitsleistungen fur Altere an Bedeutung. Deshalb wurde ein Fragebogen fur die Ermittlung des gesundheitsbezogenen Ressourcenkonsums entwickelt. Die monetare Bewertung der im Fragebogen erfassten Einheiten stellt einen wichtigen Schritt zur Ermittlung der Kosten dar. Ziel dieser Arbeit ist es, Bewertungssatze fur die im Fragebogen erhobenen Einheiten von Gesundheitsleitungen aus gesellschaftlicher Perspektive zu ermitteln. Methodik: Die Bewertungssatze werden anhand regelmasig erscheinender offentlicher Quellen auf pragmatische Weise berechnet. Eine einfache Aktualisierung wird dadurch gewahrleistet. Ergebnisse: Der Beitrag stellt fur den ambulant-arztlichen Sektor, Heil-, Hilfs- und Arzneimittel, Krankenhauser, informelle und formelle Pflegeleistungen und Rehabilitationen gesellschaftliche Bewertungssatze fur Deutschland vor. Schlussfolgerungen: Neben der Bereitstellung von Bewertungssatzen fur die Inhalte des genannten Fragebogens konnen die kalkulierten Bewertungssatze zugleich als Referenzfall bei gesundheitsokonomischen Evaluationen dienen und so deren Vergleichbarkeit erhohen.

Toward plasmonics with nanometer precision: nonlinear optics of helium-ion milled gold nanoantennas.

Abstract: Plasmonic nanoantennas are versatile tools for coherently controlling and directing light on the nanoscale. For these antennas, current fabrication techniques such as electron beam lithography (EBL) or focused ion beam (FIB) milling with Ga(+)-ions routinely achieve feature sizes in the 10 nm range. However, they suffer increasingly from inherent limitations when a precision of single nanometers down to atomic length scales is required, where exciting quantum mechanical effects are expected to affect the nanoantenna optics. Here, we demonstrate that a combined approach of Ga(+)-FIB and milling-based He(+)-ion lithography (HIL) for the fabrication of nanoantennas offers to readily overcome some of these limitations. Gold bowtie antennas with 6 nm gap size were fabricated with single-nanometer accuracy and high reproducibility. Using third harmonic (TH) spectroscopy, we find a substantial enhancement of the nonlinear emission intensity of single HIL-antennas compared to those produced by state-of-the-art gallium-based milling. Moreover, HIL-antennas show a vastly improved polarization contrast. This superior nonlinear performance of HIL-derived plasmonic structures is an excellent testimonial to the application of He(+)-ion beam milling for ultrahigh precision nanofabrication, which in turn can be viewed as a stepping stone to mastering quantum optical investigations in the near-field.

Core and Surface Characteristics for the Description and Theory of Personality Differences and Development

Abstract: Individual differences in personality are often described on the basis of a small set of dimensional core characteristics that are commonly defined as largely consistent patterns of thoughts, feeli...

Efficient Exploratory Learning of Inverse Kinematics on a Bionic Elephant Trunk

Abstract: We present an approach to learn the inverse kinematics of the “bionic handling assistant”—an elephant trunk robot. This task comprises substantial challenges including high dimensionality, restrictive and unknown actuation ranges, and nonstationary system behavior. We use a recent exploration scheme, online goal babbling, which deals with these challenges by bootstrapping and adapting the inverse kinematics on the fly. We show the success of the method in extensive real-world experiments on the nonstationary robot, including a novel combination of learning and traditional feedback control. Simulations further investigate the impact of nonstationary actuation ranges, drifting sensors, and morphological changes. The experiments provide the first substantial quantitative real-world evidence for the success of goal-directed bootstrapping schemes, moreover with the challenge of nonstationary system behavior. We thereby provide the first functioning control concept for this challenging robot platform.

Competition between water uptake and ice nucleation by glassy organic aerosol particles

Abstract: . Organic aerosol particles play a key role in climate by serving as nuclei for clouds and precipitation. Their sources and composition are highly variable, and their phase state ranges from liquid to solid under atmospheric conditions, affecting the pathway of activation to cloud droplets and ice crystals. Due to slow diffusion of water in the particle phase, organic particles may deviate in phase and morphology from their thermodynamic equilibrium state, hampering the prediction of their influence on cloud formation. We overcome this problem by combining a novel semi-empirical method for estimation of water diffusivity with a kinetic flux model that explicitly treats water diffusion. We estimate timescales for particle deliquescence as well as various ice nucleation pathways for a wide variety of organic substances, including secondary organic aerosol (SOA) from the oxidation of isoprene, α-pinene, naphthalene, and dodecane. The simulations show that, in typical atmospheric updrafts, glassy states and solid/liquid core-shell morphologies can persist for long enough that heterogeneous ice nucleation in the deposition and immersion mode can dominate over homogeneous ice nucleation. Such competition depends strongly on ambient temperature and relative humidity as well as humidification rate and particle size. Due to differences in glass transition temperature, hygroscopicity and atomic O / C ratio of the different SOA, naphthalene SOA particles have the highest potential to act as heterogeneous ice nuclei. Our findings demonstrate that kinetic limitations of water diffusion into organic aerosol particles are likely to be encountered under atmospheric conditions and can strongly affect ice nucleation pathways. For the incorporation of ice nucleation by organic aerosol particles into atmospheric models, our results demonstrate a demand for model formalisms that account for the effects of molecular diffusion and not only describe ice nucleation onsets as a function of temperature and relative humidity but also include updraft velocity, particle size and composition.

Question Answering over Linked Data (QALD-4)

Abstract: With the increasing amount of semantic data available on the web there is a strong need for systems that allow common web users to access this body of knowledge. Especially question answering systems have received wide attention, as they allow users to express arbitrarily complex information needs in an easy and intuitive fashion (for an overview see [4]). The key challenge lies in translating the users' information needs into a form such that they can be evaluated using standard Semantic Web query processing and inferencing techniques. Over the past years, a range of approaches have been developed to address this challenge, showing signicant advances towards answering natural language questions with respect to large, heterogeneous sets of structured data. However, only few systems yet address the fact that the structured data available nowadays is distributed among a large collection of interconnected datasets, and that answers to questions can often only be provided if information from several sources are combined. In addition, a lot of information is still available only in textual form, both on the web and in the form of labels and abstracts in linked data sources. Therefore approaches are needed that can not only deal with the specific character of structured data but also with finding information in several sources, processing both structured and unstructured information, and combining such gathered information into one answer. The main objective of the open challenge on question answering over linked data (QALD) is to provide up-to-date, demanding benchmarks that establish a standard against which question answering systems over structured data can be evaluated and compared. QALD-4 is the fourth instalment of the QALD open challenge, comprising three tasks: multilingual question answering, biomedical question answering over interlinked data, and hybrid question answering.

Gd(III)-PyMTA Label Is Suitable for In-Cell EPR

Abstract: Distance measurement in the nanometer range by electron paramagnetic resonance spectroscopy (EPR) in combination with site-directed spin labeling is a very powerful tool to monitor the structure and dynamics of biomacromolecules in their natural environment. However, in-cell application is hampered by the short lifetime of the commonly used nitroxide spin labels in the reducing milieu inside a cell. Here, we demonstrate that the Gd(III) based spin label Gd-PyMTA is suitable for in-cell EPR. Gd-PyMTA turned out to be cell compatible and was proven to be inert in in-cell extracts of Xenopus laevis oocytes at 18 °C for more than 24 h. The proline rich peptide H-AP10CP10CP10-NH2 was site-directedly spin labeled with Gd-PyMTA at both cysteine moieties. The resulting peptide, H-AP10C(Gd-PyMTA)P10C(Gd-PyMTA)P10-NH2, as well as the model compound Gd-spacer-Gd, which consists of a spacer of well-known stiffness, were microinjected into Xenopus laevis oocytes, and the Gd(III)-Gd(III) distances were determined by double electron-electron resonance (DEER) spectroscopy. To analyze the intracellular peptide conformation, a rotamer library was set up to take the conformational flexibility of the tether between the Gd(III) ion and the Cα of the cysteine moiety into account. The results suggest that the spin labeled peptide H-AP10C(Gd-PyMTA)P10C(Gd-PyMTA)P10-NH2 is inserted into cell membranes, coinciding with a conformational change of the oligoproline from a PPII into a PPI helix.