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From the roots of the African plant Bulbine frutescens (Asphodelaceae), two unprecedented novel dimeric phenylanthraquinones, named joziknipholones A and B, possessing axial and centrochirality, were isolated, together with six known compounds. Structural elucidation of the new metabolites was achieved by spectroscopic and chiroptical methods, by reductive cleavage of the central bond between the monomeric phenylanthraquinone and -anthrone portions with sodium dithionite, and by quantum chemical CD calculations. Based on the recently revised absolute axial configuration of the parent phenylanthraquinones, knipholone and knipholone anthrone, the new dimers were attributed to possess the P- configuration (i.e., with the acetyl portions below the anthraquinone plane) at both axes in the case of joziknipholone A, whereas in joziknipholone B, the knipholone part was found to be M-configured. Joziknipholones A and B are active against the chloroquine resistant strain K1 of the malaria pathogen, Plasmodium falciparum, and show moderate activity against murine leukemic lymphoma L5178y cells.
The introduction of a new powdery mildew disease on Rhus hirta in various parts of Germany (Brandenburg, Rhine- Westphalia, Sachsen-Anhalt and Saxony) is reported. The anamorph found on this host agrees well with the North American Podosphaera pruinosa. Although the teleomorph has not yet been found in Germany and a molecular study has not yet been possible due to the lack of fresh North American material for a comparison, there is little doubt that the European outbreak of the Rhus powdery mildew disease may be referred to as Podosphaera pruinosa. Morphology, taxonomy and distribution of Podosphaera species on Rhus and other hosts of the Anacardiaceae are discussed in detail.
We prove a local in time existence and uniqueness theorem of classical solutions of the coupled Einstein{Euler system, and therefore establish the well posedness of this system. We use the condition that the energy density might vanish or tends to zero at infinity and that the pressure is a certain function of the energy density, conditions which are used to describe simplified stellar models. In order to achieve our goals we are enforced, by the complexity of the problem, to deal with these equations in a new type of weighted Sobolev spaces of fractional order. Beside their construction, we develop tools for PDEs and techniques for hyperbolic and elliptic equations in these spaces. The well posedness is obtained in these spaces.
Parsing costs as predictors of reading difficulty : an evaluation using the Potsdam Sentence Corpus
(2008)
Parsing costs as predictors of reading difficulty: An evaluation using the Potsdam Sentence Corpus
(2008)
The surprisal of a word on a probabilistic grammar constitutes a promising complexity metric for human sentence comprehension difficulty. Using two different grammar types, surprisal is shown to have an effect on fixation durations and regression probabilities in a sample of German readers’ eye movements, the Potsdam Sentence Corpus. A linear mixed-effects model was used to quantify the effect of surprisal while taking into account unigram and bigram frequency, word length, and empirically-derived word predictability; the so-called “early” and “late” measures of processing difficulty both showed an effect of surprisal. Surprisal is also shown to have a small but statistically non-significant effect on empirically-derived predictability itself. This work thus demonstrates the importance of including parsing costs as a predictor of comprehension difficulty in models of reading, and suggests that a simple identification of syntactic parsing costs with early measures and late measures with durations of post-syntactic events may be difficult to uphold.
Finite state methods for natural language processing often require the construction and the intersection of several automata. In this paper, we investigate the question of determining the best order in which these intersections should be performed. We take as an example lexical disambiguation in polarity grammars. We show that there is no efficient way to minimize the state complexity of these intersections.
Jesper Juul has convincingly argued that the conflict over the proper object of study has shifted from “rules or story” to “player or game.” But a key component of digital games is still missing from either of these oppositions: that of the computer itself. This paper offers a way of thinking about the phenomenology of the videogame from the perspective of the computer rather than the game or the player.
Streamflow dynamics in mountainous environments are controlled by runoff generation processes in the basin upstream. Runoff generation processes are thus a major control of the terrestrial part of the water cycle, influencing both, water quality and water quantity as well as their dynamics. The understanding of these processes becomes especially important for the prediction of floods, erosion, and dangerous mass movements, in particular as hydrological systems often show threshold behavior. In case of extensive environmental changes, be it in climate or in landuse, the understanding of runoff generation processes will allow us to better anticipate the consequences and can thus lead to a more responsible management of resources as well as risks. In this study the runoff generation processes in a small undisturbed catchment in the Chilean Andes were investigated. The research area is characterized by steep hillslopes, volcanic ash soils, undisturbed old growth forest and high rainfall amounts. The investigation of runoff generation processes in this data scarce area is of special interest as a) little is known on the hydrological functioning of the young volcanic ash soils, which are characterized by extremely high porosities and hydraulic conductivities, b) no process studies have been carried out in this area at either slope or catchment scale, and c) understanding the hydrological processes in undisturbed catchments will provide a basis to improve our understanding of disturbed systems, the shift in processes that followed the disturbance and maybe also future process evolution necessary for the achievement of a new steady state. The here studied catchment has thus the potential to serve as a reference catchment for future investigations. As no long term data of rainfall and runoff exists, it was necessary to replace long time series of data with a multitude of experimental methods, using the so called "multi-method approach". These methods cover as many aspects of runoff generation as possible and include not only the measurement of time series such as discharge, rainfall, soil water dynamics and groundwater dynamics, but also various short term measurements and experiments such as determination of throughfall amounts and variability, water chemistry, soil physical parameters, soil mineralogy, geo-electrical soundings and tracer techniques. Assembling the results like pieces of a puzzle produces a maybe not complete but nevertheless useful picture of the dynamic ensemble of runoff generation processes in this catchment. The employed methods were then evaluated for their usefulness vs. expenditures (labour and financial costs). Finally, the hypotheses - the perceptual model of runoff generation generated from the experimental findings - were tested with the physically based model Catflow. Additionally the process-based model Wasim-ETH was used to investigate the influence of landuse on runoff generation at the catchment scale. An initial assessment of hydrologic response of the catchment was achieved with a linear statistical model for the prediction of event runoff coefficients. The parameters identified as best predictors give a first indication of important processes. Various results acquired with the "multi-method approach" show that response to rainfall is generally fast. Preferential vertical flow is of major importance and is reinforced by hydrophobicity during the summer months. Rapid lateral water transport is necessary to produce the fast response signal, however, while lateral subsurface flow was observed at several soil moisture profiles, the location and type of structures causing fast lateral flow on the hillslope scale is still not clear and needs to be investigated in more detail. Surface runoff has not been observed and is unlikely due to the high hydraulic conductivities of the volcanic ash soils. Additionally, a large subsurface storage retains most of the incident rainfall amount during events (>90%, often even >95%) and produces streamflow even after several weeks of drought. Several findings suggest a shift in processes from summer to winter causing changes in flow patterns, changes in response of stream chemistry to rainfall events and also in groundwater-surface water interactions. The results of the modelling study confirm the importance of rapid and preferential flow processes. However, due to the limited knowledge on subsurface structures the model still does not fully capture runoff response. Investigating the importance of landuse on runoff generation showed that while peak runoff generally increased with deforested area, the location of these areas also had an effect. Overall, the "multi-method approach" of replacing long time series with a multitude of experimental methods was successful in the identification of dominant hydrological processes and thus proved its applicability for data scarce catchments under the constraint of limited resources.
Monitoring animal populations in changing environments is crucial to wildlife conservation and management, but restrictions in resources are a recurring problem for wildlife managers and researchers throughout Africa. Land-use- induced shrub encroachment in Kalahari savannah rangelands has led to fragmentation of the landscape. Mammalian carnivores are particularly vulnerable to local extinction in fragmented landscapes, but their low numbers and their often nocturnal and secretive habits make them difficult to monitor. In this study, we tested the applicability of a passive tracking method and compared two measurement methods and index calculations for monitoring small carnivores across a grazing gradient in the southern Kalahari. During the four years of monitoring in a five-year period, we used the knowledge of indigenous Khoisan Bushmen for the identification of carnivore tracks on 640 sand transects (5 m x 250 m). Our results showed that this simple and inexpensive observation method enabled detailed monitoring of 10 small carnivore species across the grazing gradient. A binary index calculated an index based on presence/absence of a species' tracks on each transect, whereas the track intrusion index used the number of track intrusions to each transect for each species in its calculations. For less common species, the two indices were similar in trend and magnitude, because the number of intrusions to each transect was typically 1 or 0. Usually, the two indices showed relatively strong correlations. However, species with patchy distributions of higher numbers presented difficulties for the binary index to monitor trends, but not for the track intrusion index.
Seasonal differences in spatial distribution of small carnivores in fragmented savannah landscapes
(2008)
Since Harris’ parser in the late 50s, multiword units have been progressively integrated in parsers. Nevertheless, in the most part, they are still restricted to compound words, that are more stable and less numerous. Actually, language is full of semi-fixed expressions that also form basic semantic units: semi-fixed adverbial expressions (e.g. time), collocations. Like compounds, the identification of these structures limits the combinatorial complexity induced by lexical ambiguity. In this paper, we detail an experiment that largely integrates these notions in a finite-state procedure of segmentation into super-chunks, preliminary to a parser.We show that the chunker, developped for French, reaches 92.9% precision and 98.7% recall. Moreover, multiword units realize 36.6% of the attachments within nominal and prepositional phrases.
A chemotaxonomic evaluation using hplc profiling was undertaken to resolve the infrageneric and intergeneric affinities of over 150 strains of Xylariaceae. Daldinia placentiformis, Hypoxylon nicaraguense, H. polyporus, and Phylacia sagrana were found to contain 8-methoxy-1-naphthol, which is apparently absent in Annulohypoxylon, Hypoxylon, and related genera with bipartite stromata. D. placentiformis and other species of Daldinia and Entonaema produced this naphthol, 5-hydroxy-2-methylchromone, isosclerone derivatives, and 'AB-5046' phytotoxins. Phylacia sagrana differed from most Daldinia spp., except for D. caldariorum, by producing eutypine derivatives in addition to the above compounds. indolylquinones were observed in H. nicaraguense and H. polyporus. Isosclerones were also identified in the A. multiforme complex, but Hypoxylon and other Annulohypoxylon and most Hypoxylon spp. studied Annulohypoxylon spp. contained S-methylmellein as the major metabolite of their cultures. Based on the occurrence of the above metabolites, further mellein-type dihydroisocoumarins, teleomorphic and anamorphic Xylariaceae with Nodulisporium-like anamorphs ('Hypoxyloideae') were divided into various chemotypes. A comparison of their 5.8S/ ITS nuc-rDNA sequences agreed in some important aspects with the above results: H. nicaraguense and H. polyporus appeared basal to a clade comprising Daldinia, Entonaema, and Ph. sagrana. The latter species appeared allied to D. caldariorum, but was distantly related to Pyrenomyxa morganii and Hypoxylon s. str. (C) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.
This work analyzes the saving and consumption behavior of agents faced with the possibility of unemployment in a dynamic and stochastic life cycle model. The intertemporal optimization is based on Dynamic Programming with a backward recursion algorithm. The implemented uncertainty is not based on income shocks as it is done in traditional life cycle models but uses Markov probabilities where the probability for the next employment status of the agent depends on the current status. The utility function used is a CRRA function (constant relative risk aversion), combined with a CES function (constant elasticity of substitution) and has several consumption goods, a subsistence level, money and a bequest function.
One of the main problems in machine learning is to train a predictive model from training data and to make predictions on test data. Most predictive models are constructed under the assumption that the training data is governed by the exact same distribution which the model will later be exposed to. In practice, control over the data collection process is often imperfect. A typical scenario is when labels are collected by questionnaires and one does not have access to the test population. For example, parts of the test population are underrepresented in the survey, out of reach, or do not return the questionnaire. In many applications training data from the test distribution are scarce because they are difficult to obtain or very expensive. Data from auxiliary sources drawn from similar distributions are often cheaply available. This thesis centers around learning under differing training and test distributions and covers several problem settings with different assumptions on the relationship between training and test distributions-including multi-task learning and learning under covariate shift and sample selection bias. Several new models are derived that directly characterize the divergence between training and test distributions, without the intermediate step of estimating training and test distributions separately. The integral part of these models are rescaling weights that match the rescaled or resampled training distribution to the test distribution. Integrated models are studied where only one optimization problem needs to be solved for learning under differing distributions. With a two-step approximation to the integrated models almost any supervised learning algorithm can be adopted to biased training data. In case studies on spam filtering, HIV therapy screening, targeted advertising, and other applications the performance of the new models is compared to state-of-the-art reference methods.
The selective infrared (IR) excitation of molecular vibrations is a powerful tool to control the photoreactivity prior to electronic excitation in the ultraviolet / visible (UV/Vis) light regime ("vibrationally mediated chemistry"). For adsorbates on surfaces it has been theoretically predicted that IR preexcitation will lead to higher UV/Vis photodesorption yields and larger cross sections for other photoreactions. In a recent experiment, IR-mediated desorption of molecular hydrogen from a Si(111) surface on which atomic hydrogen and deuterium were co-adsorbed was achieved, following a vibrational mechanism as indicated by the isotope-selectivity. In the present work, selective vibrational IR excitation of adsorbate molecules, treated as multi-dimensional oscillators on dissipative surfaces, has been simulated within the framework of open-system density matrix theory. Not only potential-mediated, inter-mode coupling poses an obstacle to selective excitation but also the coupling of the adsorbate ("system") modes to the electronic and phononic degrees of freedom of the surface ("bath") does. Vibrational relaxation thereby takes place, depending on the availabilty of energetically fitting electron-hole (e/h) pairs and/or phonons (lattice vibrations) in the surface, on time-scales ranging from milliseconds to several hundreds of femtoseconds. On metal surfaces, where the relaxation process of the adsorbate via the e/h pair mechanism dominates, vibrational lifetimes are usually shorter than on insulator or semiconductor surfaces, in the range of picoseconds, being also the timescale of the IR pulses used here. Further inhibiting factors for selectivity can be the harmonicity of a mode and weak dipole activities ("dark modes") rendering vibrational excitation with moderate field intensities difficult. In addition to simple analytical pulses, optimal control theory (OCT) has been employed here to generate a suitable electric field to populate the target state/mode maximally. The complex OCT fields were analyzed by Husimi transformation, resolving the control field in time and energy. The adsorbate/surface systems investigated were CO/Cu(100), H/Si(100) and 2H/Ru(0001). These systems proved to be suitable models to study the above mentioned effects. Further, effects of temperature, pure dephasing (elastic scattering processes), pulse duration and dimensionality (up to four degrees of freedom) were studied. It was possible to selectively excite single vibrational modes, often even state-selective. Special processes like hot-band excitation, vibrationally mediated desorption and the excitation of "dark modes" were simulated. Finally, a novel OCT algorithm in density matrix representation has been developed which allows for time-dependent target operators and thus enables to control the excitation mechanism instead of only the final state. The algorithm is based on a combination of global (iterative) and local (non-iterative) OCT schemes, such that short, globally controlled time-intervals are coupled locally in time. Its numerical performance and accuracy were tested and verified and it was successfully applied to stabilize a two-state linear-combination and to enforce a successive "ladder climbing" in a rather harmonic system, where monochromatic, analytical pulses simultaneously excited several states, leading to a population loss in the target state.
Competition is a key process in plant populations and communities. We thus need, if we are to predict the responses of ecological systems to environmental change, a comprehensive and mechanistic understanding of plant competition. Considering competition, however, only at the population level is not sufficient because plant individuals usually are different, interact locally, and can adapt their behaviour to the current state of themselves and of their biotic and abiotic environment. Therefore, simulation models that are individual-based and spatially explicit are increasingly used for studying competition in plant systems. Many different individual-based modelling approaches exist to represent competition, but it is not clear how good they are in reflecting essential aspects of plant competition. We therefore first summarize current concepts and theories addressing plant competition. Then, we review individual-based approaches for modelling competition among plants. We distinguish between approaches that are used for more than 10 years and more recent ones. We identify three major gaps that need to be addressed more in the future: the effects of plants on their local environment, adaptive behaviour, and below-ground competition. To fill these gaps, the representation of plants and their interactions have to be more mechanistic than most existing approaches. Developing such new approaches is a challenge because they are likely to be more complex and to require more detailed knowledge and data on individual-level processes underlying competition. We thus need a more integrated research strategy for the future, where empirical and theoretical ecologists as well as computer scientists work together on formulating, implementing, parameterization, testing, comparing, and selecting the new approaches. (c) 2008 Rubel Foundation, ETH Zurich. Published by Elsevier GmbH. All rights reserved.
* 1. Large female insects usually have high potential fecundity. Therefore selection should favour an increase in body size given that these females get opportunities to realize their potential advantage by maturing and laying more eggs. However, ectotherm physiology is strongly temperature-dependent, and activities are carried out sufficiently only within certain temperature ranges. Thus it remains unclear if the fecundity advantage of a large size is fully realized in natural environments, where thermal conditions are limiting. * 2. Insect fecundity might be limited by temperature at two levels; first eggs need to mature, and then the female needs time for strategic ovipositing of the egg. Since a female cannot foresee the number of oviposition opportunities that she will encounter on a given day, the optimal rate of egg maturation will be governed by trade-offs associated with egg- and time-limited oviposition. As females of different sizes will have different amounts of body reserves, size-dependent allocation trade-offs between the mother"s condition and her egg production might be expected. * 3. In the temperate butterfly Pararge aegeria, the time and temperature dependence of oviposition and egg maturation, and the interrelatedness of these two processes were investigated in a series of laboratory experiments, allowing a decoupling of the time budgets for the respective processes. * 4. The results show that realized fecundity of this species can be limited by both the temperature dependence of egg maturation and oviposition under certain thermal regimes. Furthermore, rates of oviposition and egg maturation seemed to have regulatory effects upon each other. Early reproductive output was correlated with short life span, indicating a cost of reproduction. Finally, large females matured more eggs than small females when deprived of oviposition opportunities. Thus, the optimal allocation of resources to egg production seems dependent on female size. * 5. This study highlights the complexity of processes underlying rates of egg maturation and oviposition in ectotherms under natural conditions. We further discuss the importance of temperature variation for egg- vs. time-limited fecundity and the consequences for the evolution of female body size in insects.
Objective To demonstrate that children homozygous for the 10-repeat allele of the common dopamine transporter (DAT1) polymorphism who were exposed to maternal prenatal smoke exhibited significantly higher hyperactivity-impulsivity than children without these environmental or genetic risks. Study design We performed a prospective longitudinal study from birth into early adulthood monitoring the long-term outcome of early risk factors. Maternal prenatal smoking was determined during a standardized interview with the mother when the child was 3 months old. At age 15 years, 305 adolescents participated in genotyping for the DAT1 40 base pair variable number of tandem repeats polymorphism and assessment of inattention, hyperactivity-impulsivity, and oppositional defiant/conduct disorder symptoms with die Kiddie- Sads-Present and Lifetime Version. Results There was no bivariate association between DAT1 genotype, prenatal smoke exposure and symptoms of attention deficit hyperactivity disorder. However, a significant interaction between DAT1 genotype and prenatal smoke exposure emerged (P =.012), indicating that males with prenatal smoke exposure who were homozygous for the DAT1 10r allele had higher hyperactivity-impulsivity than males from all other groups. In females, no significant main effects of DAT1 genotype or prenatal smoke exposure or interaction effects on any symptoms were evident (all P >.25). Conclusions This study provides further evidence for the multifactorial nature of attention deficit hyperactivity disorder and the importance of studying both genetic and environmental factors and their interaction.
One of the informal properties often used to describe a new virtual world is its degree of openness. Yet what is an “open” virtual world? Does the phrase mean generally the same thing to different people? What distinguishes an open world from a less open world? Why does openness matter anyway? The answers to these questions cast light on an important, but shadowy, and uneasy, topic for virtual worlds: the relationship between those who construct the virtual, and those who use these constructions.
This paper describes a two-level formalism where feature structures are used in contextual rules. Whereas usual two-level grammars describe rational sets over symbol pairs, this new formalism uses tree structured regular expressions. They allow an explicit and precise definition of the scope of feature structures. A given surface form may be described using several feature structures. Feature unification is expressed in contextual rules using variables, like in a unification grammar. Grammars are compiled in finite state multi-tape transducers.
Soils play a crucial role in biogeochemical cycles as spatially distributed sources and sinks of nutrients. Any spatial patterns depend on soil forming processes, our understanding of which is still limited, especially in regards to tropical rainforests. The objective of our study was to investigate the effects of landscape properties, with an emphasis on the geometry of the land surface, on the spatial heterogeneity of soil chemical properties, and to test the suitability of soil-landscape modeling as an appropriate technique to predict the spatial variability of exchangeable K and Mg in a humid tropical forest in Panama. We used a design-based, stratified sampling scheme to collect soil samples at 108 sites on Barro Colorado Island, Panama. Stratifying variables are lithology, vegetation and topography. Topographic variables were generated from high-resolution digital elevation models with a grid size of 5 m. We took samples from five depths down to I m, and analyzed for total and exchangeable K and Mg. We used simple explorative data analysis techniques to elucidate the importance of lithology for soil total and exchangeable K and Mg. Classification and Regression Trees (CART) were adopted to investigate importance of topography, lithology and vegetation for the spatial distribution of exchangeable K and Mg and with the intention to develop models that regionalize the point observations using digital terrain data as explanatory variables. Our results suggest that topography and vegetation do not control the spatial distribution of the selected soil chemical properties at a landscape scale and lithology is important to some degree. Exchangeable K is distributed equally across the study area indicating that other than landscape processes, e.g. biogeochemical processes, are responsible for its spatial distribution. Lithology contributes to the spatial variation of exchangeable Mg but controlling variables could not be detected. The spatial variation of soil total K and Mg is mainly influenced by lithology.
Bacteriophage HK620 infects Escherichia coli H and is closely related to Shigella phage Sf6 and Salmonella phage P22. All three Podoviridae recognize and cleave their respective host cell receptor polysaccharide by homotrimeric tailspike proteins. The three proteins exhibit high sequence identity in the 110 residues of their N-terminal particle- binding domains, but no apparent sequence similarity in their major, receptor-binding parts. We have biochemically characterized the receptor-binding part of HK620 tailspike and determined its crystal structure to 1.38 Å resolution. Its major domain is a right-handed parallel ;-helix, as in Sf6 and P22 tailspikes. HK620 tailspike has endo-N- acetylglucosaminidase activity and produces hexasaccharides of an O18A1-type O-antigen. As indicated by the structure of a hexasaccharide complex determined at 1.6 Å resolution, the endoglycosidase-active sites are located intramolecularly, as in P22, and not between subunits, as in Sf6 tailspike. In contrast, the extreme C-terminal domain of HK620 tailspike forms a ;-sandwich, as in Sf6 and unlike P22 tailspike. Despite the different folds, structure-based sequence alignments of the C-termini reveal motifs conserved between the three proteins. We propose that the tailspike genes of P22, Sf6 and HK620 have a common precursor and are not mosaics of unrelated gene fragments.
This article describes a HMM-based word-alignment method that can selectively enforce a contiguity constraint. This method has a direct application in the extraction of a bilingual terminological lexicon from a parallel corpus, but can also be used as a preliminary step for the extraction of phrase pairs in a Phrase-Based Statistical Machine Translation system. Contiguous source words composing terms are aligned to contiguous target language words. The HMM is transformed into a Weighted Finite State Transducer (WFST) and contiguity constraints are enforced by specific multi-tape WFSTs. The proposed method is especially suited when basic linguistic resources (morphological analyzer, part-of-speech taggers and term extractors) are available for the source language only.
A new series of unsubstituted and substituted pyridinium salts bearing a 4-oxothiazolidinyl moiety has been prepared by an efficient rearrangement of 2-(1-bromoalkylidene)thiazolidin-4-ones. The process in based on three steps, namely carbon-bromine cleavage, bromine transfer, and substitution, each induced by pyridine or its derivatives, acting as base and reactant.
Choice-based Conjointanalyse
(2008)
Chitooligosaccharides are composed of glycosamin and N-acetylglycisamin residues. Gel permeations chromatography is employed for the separation of oligomers, cation exchange chromatography is used for the separation of homologes and isomers. Trideuterioacetylation of the chitooligosaccharides followed by MALDI-TOF mass spectrometry allowes for the quantitation of mixtures of homologes. vMALDI LTQ multiple-stage MS is employed for quantitative sequencing of complex mixtures of heterochitooligosaccharides. Pure homologes and isomers are applied to biological assays. Chitooligosaccahrides form high-affinity non-covalent complexes with HC gp-39 (human cartilage glycoprotein of 39 kDa). The affinity of the chitooligosaccharides depends on DP, FA and the sequence of glycosamin and N-acetylglycosamin moieties. (+)nanoESI Q TOF MS/MS is used for identification of a high-affinity binding chitooligosaccharide of a non-covalent chitinase B - chitooligosaccharide complex. DADAA is identified as the heterochitoisomer binding with highest affinity and biostability to HC gp-39. Fluorescence based enzyme assays confirm the results.
QuantPrime
(2008)
Background
Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays.
Results
Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96%.
Conclusion
QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays.
The boundary paradigm (Rayner, 1975) with a novel preview manipulation was used to examine the extent of parafoveal processing of words to the right of fixation. Words n + 1 and n + 2 had either correct or incorrect previews prior to fixation (prior to crossing the boundary location). In addition, the manipulation utilized either a high or low frequency word in word n + 1 location on the assumption that it would be more likely that n + 2 preview effects could be obtained when word n + 1 was high frequency. The primary findings were that there was no evidence for a preview benefit for word n + 2 and no evidence for parafoveal-on-foveal effects when word n + 1 is at least four letters long. We discuss implications for models of eye-movement control in reading.
The boundary paradigm (Rayner, 1975) with a novel preview manipulation was used to examine the extent of parafoveal processing of words to the right of fixation. Words n+1 and n+2 had either correct or incorrect previews prior to fixation (prior to crossing the boundary location). In addition, the manipulation utilized either a high or low frequency word in word n+1 location on the assumption that it would be more likely that n+2 preview effects could be obtained when word n+1 was high frequency. The primary findings were that there was no evidence for a preview benefit for word n+2 and no evidence for parafoveal-on-foveal effects when word n+1 is at least four letters long. We discuss implications for models of eye-movement control in reading.
We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with increasing heterozygosity—a known phenomenon in the literature.
Oidium pedaliacearum sp. nov. (; O. sesami, nom. inval.) and Podosphaera macrospora comb. et stat. nov. (; Sphaerotheca alpina f. macrospora) are introduced, and the taxonomy and distribution of Erysiphe celosiae is discussed. New host species and new collections of Erysiphe cruciferarum (on Cleome hassleriana), E. flexuosa (on Aesculus hippocastanum), E. hedwigii (on Viburnum carlesii), E. heraclei (on Tinguarra montana), E. cf. macleayae (on Macleaya cordata), E. prunastri (on Prunus cerasifera), E. sedi (on Sedum aff. spectabilis), E. trifolii (on Trigonella caerulea), Golovinomyces cichoracearum (on Argyranthemum pinnatifidum subsp. succulentum), G. cf. hydrophyllacearum (on Nemophila menziesii), G. orontii (on Nolana spp.), G. cf. orontii (on Tiarella cordifolia), Neoerysiphe cumminsiana (on Bidens cf. ferulifolia), Oidium clitoriae (on Clitoria ternatea), O. cf. hortensiae (on Philadelphus coronarius), O. pedilanthi (on Pedilanthus tithymaloides), Oidium (Pseudoidium) sp. (on Utricularia alpina), Podosphaera sp. (on Bergia capensis), Sawadaea bicornis (on Acer platanoides) and S. tulasnei (on Acer ginnala and A. tatarica) are recorded from France, Germany, Greece and Mexico.
The aim of the present study was to investigate the test-retest reliability of the olfactory detection threshold subtest of the Sniffin" Sticks test battery, if administered repeatedly on 4 time points. The detection threshold test was repeatedly conducted in 64 healthy subjects. On the first testing session, the threshold test was accomplished 3 times (T(1) = 0 min, T(2) = 35 min, and T(3) = 105 min), representing a short-term testing. A fourth threshold test was conducted on a second testing session (T(4) = 35.1 days after the first testing session), representing a long-term testing. The average scores for olfactory detection threshold for n-butanol did not differ significantly across the 4 points of time. The test-retest reliability (Pearson"s r) between the 4 time points of threshold testing were in a range of 0.43-0.85 (P < 0.01). These results support the notion that the olfactory detection threshold test is a highly reliable method for repeated olfactory testing, even if the test is repeated more than once per day and over a long-term period. It is concluded that the olfactory detection threshold test of the Sniffin" Sticks is suitable for repeated testing during experimental or clinical studies.
We establish elements of a new approch to ellipticity and parametrices within operator algebras on a manifold with higher singularities, only based on some general axiomatic requirements on parameter-dependent operators in suitable scales of spaces. The idea is to model an iterative process with new generations of parameter-dependent operator theories, together with new scales of spaces that satisfy analogous requirements as the original ones, now on a corresponding higher level. The “full” calculus is voluminous; so we content ourselves here with some typical aspects such as symbols in terms of order reducing families, classes of relevant examples, and operators near the conical exit to infinity.
DFT-GIAO-NBO and 13C NMR study of the delta-syn-axial effect in 2,4-disubstituted adamantanes
(2008)
Six groups of diastereomeric 2,4-disubstituted adamantanes were studied with DFT-GIAO-NBO (natural orbital analysis) methods. The calculated 13C chemical shifts reproduce well the experimental data. It was found that among all diastereomers, those bearing substituents in -syn-axial positions showed the largest overall deshielding, i.e. the sum of all 13C chemical shifts [;;(13C)] was the greatest and also had the highest delocalization contribution to the molecular energy evaluated with NBO. The higher delocalization energy is proposed to be the origin of the deshielding -syn-axial effect
Proceedings of the 2nd International Workshop on e-learning and Virtual and Remote Laboratories
(2008)
Through the ring closures of tetrahydroisoquinoline 1,3-amino alcohols bearing a phenyl group in the side- chain, diastereomers of novel 1- or 2-phenyl-substituted 1,3,2-oxazaphosphino[4,3-a]isoquinoline 4-oxides, and 1,2,3- oxathiazino[4,3-a]isoquinoline 4-oxides and 4,4-dioxides were prepared. NMR analysis and DFT calculations on the prepared tetrahydroisoquinoline-condensed 1,2,3-heterocycles revealed that their conformational equilibria of cis1-trans-cis2 type are influenced by the relative configuration of P-4 in the 1,3,2-oxazaphosphinanes, and by the position of the phenyl group in the 1,2,3-oxathiazines.
Interdisciplinary studies on information structure : ISIS ; Working papers of the SFB 632. - Vol. 10
(2008)
The 10th volume of the working paper series contains two papers contributed by SFB-members. The first paper “Single prosodic phrase sentences” by Caroline Féry (A1) and Heiner Drenhaus (C6, University of Potsdam) investigates the prosody of Wide Focus Partial Fronting in a series of production and perception experiments. The second paper “Focus Asymmetries in Bura” by Katharina Hartmann, Peggy Jacob (B2, Humboldt University Berlin) and Malte Zimmermann (A5, University of Potsdam) explores the strategies of marking focus in Bura (Chadic).
Contents 1. Styling for Service-Based 3D Geovisualization Benjamin Hagedorn 2. The Windows Monitoring Kernel Michael Schöbel 3. A Resource-Oriented Information Network Platform for Global Design Processes Matthias Uflacker 4. Federation in SOA – Secure Service Invocation across Trust Domains Michael Menzel 5. KStruct: A Language for Kernel Runtime Inspection Alexander Schmidt 6. Deconstructing Resources Hagen Overdick 7. FMC-QE – Case Studies Stephan Kluth 8. A Matter of Trust Rehab Al-Nemr 9. From Semi-automated Service Composition to Semantic Conformance Harald Meyer
It is a widespread idea that the roots of the Christian sermon can be found in the Jewish derasha. But the story of the interrelation of the two homiletical traditions, Jewish and Christian, from New Testament times to the present day is still untold. Can homiletical encounters be registered? Is there a common homiletical history - not only in the modern era, but also in rabbinic times and in the Middle Ages? Which current developments affect Jewish and Christian preaching today, in the 21st century? And, most important, what consequences may result from this mutual perception of Jewish and Christian homiletics for homiletical research and the practice of preaching? This book offers the papers of the first international conference (Bamberg, Germany, 6th to 8th March 2007) which brought together Jewish and Christian scholars to discuss Jewish and Christian homiletics in their historical development and relationship and to sketch out common homiletical projects.