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Permanent genetic resources added to molecular ecology resources database 1 April 2011-31 May 2011
(2011)
This article documents the addition of 92 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anopheles minimus, An. sinensis, An. dirus, Calephelis mutica, Lutjanus kasmira, Murella muralis and Orchestia montagui. These loci were cross-tested on the following species: Calephelis arizonensi, Calephelis borealis, Calephelis nemesis, Calephelis virginiensis and Lutjanus bengalensis.
Parsability approaches of several grammar formalisms generating also non-context-free languages are explored. Chomsky grammars, Lindenmayer systems, grammars with controlled derivations, and grammar systems are treated. Formal properties of these mechanisms are investigated, when they are used as language acceptors. Furthermore, cooperating distributed grammar systems are restricted so that efficient deterministic parsing without backtracking becomes possible. For this class of grammar systems, the parsing algorithm is presented and the feature of leftmost derivations is investigated in detail.
We investigate the decidability of the operation problem for TOL languages and subclasses. Fix an operation on formal languages. Given languages from the family considered (OL languages, TOL languages, or their propagating variants), is the application of this operation to the given languages still a language that belongs to the same language family? Observe, that all the Lindenmayer language families in question are anti-AFLs, that is, they are not closed under homomorphisms, inverse homomorphisms, intersection with regular languages, union, concatenation, and Kleene closure. Besides these classical operations we also consider intersection and substitution, since the language families under consideration are not closed under these operations, too. We show that for all of the above mentioned language operations, except for the Kleene closure, the corresponding operation problems of OL and TOL languages and their propagating variants are not even semidecidable. The situation changes for unary OL languages. In this case we prove that the operation problems with respect to Kleene star, complementation, and intersection with regular sets are decidable.
Parallel communicating finite automata (PCFAs) are systems of several finite state automata which process a common input string in a parallel way and are able to communicate by sending their states upon request. We consider deterministic and nondeterministic variants and distinguish four working modes. It is known that these systems in the most general mode are as powerful as one-way multi-head finite automata. It is additionally known that the number of heads corresponds to the number of automata in PCFAs in a constructive way. Thus, undecidability results as well as results on the hierarchies induced by the number of heads carry over from multi-head finite automata to PCFAs in the most general mode. Here, we complement these undecidability and hierarchy results also for the remaining working modes. In particular, we show that classical decidability questions are not semi-decidable for any type of PCFAs under consideration. Moreover, it is proven that the number of automata in the system induces infinite hierarchies for deterministic and nondeterministic PCFAs in three working modes.
In response to stress small organic compounds termed osmolytes are ubiquitously accumulated in all cell types to regulate the intracellular solvent quality and to counteract the deleterious effect on the stability and function of cellular proteins. Given the evidence that destabilization of the native state of a protein either by mutation or by environmental changes triggers the aggregation in the neurodegenerative pathologies, the modulation of the intracellular solute composition with osmolytes is an attractive strategy to stabilize an aggregating protein. Here we report the effect of three natural osmolytes on the in vivo and in vitro aggregation landscape of huntingtin exon 1 implicated in the Huntington's disease. Trimethylamine N-oxide (TMAO) and proline redirect amyloid fibrillogenesis of the pathological huntingtin exon 1 to nonamyloidogenic amorphous assemblies via two dissimilar molecular mechanisms. TMAO causes a rapid formation of bulky amorphous aggregates with minimally exposed surface area, whereas proline solubilizes the monomer and suppresses the accumulation of early transient aggregates. Conversely, glycine betaine enhances fibrillization in a fashion reminiscent of the genesis of functional amyloids. Strikingly, none of the natural osmolytes can completely abrogate the aggregate formation; however, they redirect the amyloidogenesis into alternative, nontoxic aggregate species. Our study reveals new insights into the complex interactions of osmoprotectants with polyQaggregates.
Eye fixation durations during normal reading correlate with processing difficulty, but the specific cognitive mechanisms reflected in these measures are not well understood. This study finds support in German readers' eye fixations for two distinct difficulty metrics: surprisal, which reflects the change in probabilities across syntactic analyses as new words are integrated; and retrieval, which quantifies comprehension difficulty in terms of working memory constraints. We examine the predictions of both metrics using a family of dependency parsers indexed by an upper limit on the number of candidate syntactic analyses they retain at successive words. Surprisal models all fixation measures and regression probability. By contrast, retrieval does not model any measure in serial processing. As more candidate analyses are considered in parallel at each word, retrieval can account for the same measures as surprisal. This pattern suggests an important role for ranked parallelism in theories of sentence comprehension.
Eye fixation durations during normal reading correlate with processing difficulty, but the specific cognitive mechanisms reflected in these measures are not well understood. This study finds support in German readers' eye fixations for two distinct difficulty metrics: surprisal, which reflects the change in probabilities across syntactic analyses as new words are integrated; and retrieval, which quantifies comprehension difficulty in terms of working memory constraints. We examine the predictions of both metrics using a family of dependency parsers indexed by an upper limit on the number of candidate syntactic analyses they retain at successive words. Surprisal models all fixation measures and regression probability. By contrast, retrieval does not model any measure in serial processing. As more candidate analyses are considered in parallel at each word, retrieval can account for the same measures as surprisal. This pattern suggests an important role for ranked parallelism in theories of sentence comprehension.
Eye fixation durations during normal reading correlate with processing difficulty but the specific cognitive mechanisms reflected in these measures are not well understood. This study finds support in German readers’ eyefixations for two distinct difficulty metrics: surprisal, which reflects the change in probabilities across syntactic analyses as new words are integrated, and retrieval, which quantifies comprehension difficulty in terms of working memory constraints. We examine the predictions of both metrics using a family of dependency parsers indexed by an upper limit on the number of candidate syntactic analyses they retain at successive words. Surprisal models all fixation measures and regression probability. By contrast, retrieval does not model any measure in serial processing. As more candidate analyses are considered in parallel at each word, retrieval can account for the same measures as surprisal. This pattern suggests an important role for ranked parallelism in theories of sentence comprehension.
Dutch allows for variation as to whether the first position in the sentence is occupied by the subject or by some other constituent, such as the direct object. In particular situations, however, this commonly observed variation in word order is ‘frozen’ and only the subject appears in first position. We hypothesize that this partial freezing of word order in Dutch can be explained from the dependence of the speaker’s choice of word order on the hearer’s interpretation of this word order. A formal model of this interaction between the speaker’s perspective and the hearer’s perspective is presented in terms of bidirectional Optimality Theory. Empirical predictions of this model regarding the interaction between word order and definiteness are confirmed by a quantitative corpus study.
Objectives: Today, the doping attitudes of athletes can either be measured by asking athletes directly or with the help of indirect attitude measurement procedures as for example the implicit association test (IAT). Using indirect measures may be helpful for example when psychological effects of doping prevention programs shall be evaluated. In the present study we have analyzed and compared measurement properties of two recently published IATs.
Design: The IATs "doping substance vs. tea blend" and "doping substance vs. legal nutritional supplement" were presented to two randomly assigned independent samples of 102 athletes (44 male, 58 female; mean age 23.6 years) from different sports. Both IATs were complemented by a control IAT "word vs. non-word".
Methods: In order to test central measurement properties of both IATs, distributions of measured values, correlations with the control IAT, reliability analyses, and analyses of error rates were performed.
Results: Results pointed to a rather negative doping attitude in most athletes. Especially the fact that in the "doping vs. supplement" IAT error rates (12%) and adaptational learning effects across test blocks were substantial (eta(2) = .22), indicating that participants had difficulties correctly assigning the word stimuli to the respective category, we see slight advantages for the "doping vs. tea" IAT (e.g. satisfactory internal scale consistency Cronbach's-alpha = .78 among athletes reporting to be regularly involved in competitions).
Conclusion: The less satisfactory measurement properties of the "doping vs. supplement" IAT can possibly be explained by the fact that the boundaries between (legal) supplements and (illegal) doping substances have been shifted from time to time so that athletes were not sure whether substances were legal or not.
Entangled inputs can enhance the capacity of quantum channels, this being one of the consequences of the celebrated result showing the nonadditivity of several quantities relevant for quantum information science. In this work, we answer the converse question (whether entangled inputs can ever render noisy quantum channels to have maximum capacity) to the negative: No sophisticated entangled input of any quantum channel can ever enhance the capacity to the maximum possible value, a result that holds true for all channels both for the classical as well as the quantum capacity. This result can hence be seen as a bound as to how "nonadditive quantum information can be.'' As a main result, we find first practical and remarkably simple computable single-shot bounds to capacities, related to entanglement measures. As examples, we discuss the qubit amplitude damping and identify the first meaningful bound for its classical capacity.
Background: The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions.
Results: For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures.
Conclusions: The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element.
Background: The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions.
Results: For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures.
Conclusions: The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element.
Phase behaviour and the mesoscopic structure of zwitanionic surfactant mixtures based on the zwitterionic tetradecyldimethylamine oxide (TDMAO) and anionic lithium perfluoroalkyl carboxylates have been investigated for various chain lengths of the perfluoro surfactant with an emphasis on spontaneously forming vesicles. These mixtures were studied at a constant total concentration of 50 mM and characterised by means of dynamic light scattering (DLS), electric conductivity, small-angle neutron scattering (SANS), viscosity, and cryo-scanning electron microscopy (Cryo-SEM). No vesicles are formed for relatively short perfluoro surfactants. The extension of the vesicle phase becomes substantially larger with increasing chain length of the perfluoro surfactant, while at the same time the size of these vesicles increases. Head group interactions in these systems play a central role in the ability to form vesicles, as already protonating 10 mol% of the TDMAO largely enhances the propensity for vesicle formation. The range of vesicle formation in the phase diagram is not only substantially enlarged but also extends to shorter perfluoro surfactants, where without protonation no vesicles would be formed. The size and polydispersity of the vesicles are related to the chain length of the perfluoro surfactant, the vesicles becoming smaller and more monodisperse with increasing perfluoro surfactant chain length. The ability of the mixed systems to form well-defined unilamellar vesicles accordingly can be controlled by the length of the alkyl chain of the perfluorinated surfactant and depends strongly on the charge conditions, which can be tuned easily by pH-variation.
The aim of this study was to investigate the supralaryngeal control of the production of the Korean three-way contrast in velar stops. First, an EMA-experiment with three Korean speakers was carried out, and the kinematic properties of the tongue back were analyzed (length of the deceleration phase of the movement, peak velocity, peak acceleration, amplitude and duration of the looping movement during consonantal closure, and angle of incidence between tongue and palate at contact onset). To understand the potential motor control mechanisms underlying the production of the three-way contrast, the target hypothesis, which suggests that articulator movements in stops are directed towards a target at or beyond the palate, was evaluated by comparing its predictions with our experimental findings. Evidence was found in support of this hypothesis. Hence, the hypothesis was further explored in a modeling study. The results suggest that variability in the articulatory parameters can be explained by a single control parameter, namely the target position of the tongue. In a third step the Korean velar stops were simulated by varying the target position. The results show that the main trends of the simulated consonants are in good agreement with the experimental findings.
Purpose: The aim of this study was to relate speakers' auditory acuity for the sibilant contrast, their use of motor equivalent trading relationships in producing the sibilant /integral/, and their produced acoustic distance between the sibilants /s/ and /integral/. Specifically, the study tested the hypotheses that during adaptation to a perturbation of vocal-tract shape, high-acuity speakers use motor equivalence strategies to a greater extent than do low-acuity speakers in order to reach their smaller phonemic goal regions, and that high-acuity speakers produce greater acoustic distance between 2 sibilant phonemes than do low-acuity speakers.
Method: Articulographic data from 7 German speakers adapting to a perturbation were analyzed for the use of motor equivalence. The speakers' produced acoustic distance between /s/ and /integral/ was calculated. Auditory acuity was assessed for the same speakers.
Results: High-acuity speakers used motor equivalence to a greater extent when adapting to a perturbation than did low-acuity speakers. Additionally, high-acuity speakers produced greater acoustic contrasts than did low-acuity-speakers. It was observed that speech rate had an influence on the use of motor equivalence: Slow speakers used motor equivalence to a lesser degree than did fast speakers.
Conclusion: These results provide support for the mutual interdependence of speech perception and production.
The purpose of this work is to investigate the role of three articulatory parameters (tongue position, jaw position and tongue grooving) in the production of /s/. Six normal speakers' speech was perturbed by a palatal prosthesis. The fricative was recorded acoustically and through electromagnetic articulography in four conditions: (1) unperturbed, (2) perturbed with auditory feedback masked, (3) perturbed with auditory feedback available and (4) perturbed after a 2-week adaptation period. At the end of the adaptation, speakers produced more high-frequency noise while either having a higher jaw position or more grooving of the tongue or both. We discuss the potential clinical implications of the results with regard to the role of jaw height and tongue grooving in the treatment of impaired /s/.
Understanding and predicting the composition and spatial structure of communities is a central challenge in ecology. An important structural property of animal communities is the distribution of individual home ranges. Home range formation is controlled by resource heterogeneity, the physiology and behaviour of individual animals, and their intra- and interspecific interactions. However, a quantitative mechanistic understanding of how home range formation influences community composition is still lacking. To explore the link between home range formation and community composition in heterogeneous landscapes we combine allometric relationships for physiological properties with an algorithm that selects optimal home ranges given locomotion costs, resource depletion and competition in a spatially-explicit individual-based modelling framework. From a spatial distribution of resources and an input distribution of animal body mass, our model predicts the size and location of individual home ranges as well as the individual size distribution (ISD) in an animal community. For a broad range of body mass input distributions, including empirical body mass distributions of North American and Australian mammals, our model predictions agree with independent data on the body mass scaling of home range size and individual abundance in terrestrial mammals. Model predictions are also robust against variation in habitat productivity and landscape heterogeneity. The combination of allometric relationships for locomotion costs and resource needs with resource competition in an optimal foraging framework enables us to scale from individual properties to the structure of animal communities in heterogeneous landscapes. The proposed spatially-explicit modelling concept not only allows for detailed investigation of landscape effects on animal communities, but also provides novel insights into the mechanisms by which resource competition in space shapes animal communities.
A thermosensitive statistical copolymer based on oligo(ethylene glycol) methacrylates incorporating biotin was synthesized by free radical copolymerisation. The influence of added avidin on its thermoresponsive behaviour was investigated. The specific binding of avidin to the biotinylated copolymers provoked a marked increase of the lower critical solution temperature.
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.
We consider the nonlinear extension of the Kuramoto model of globally coupled phase oscillators where the phase shift in the coupling function depends on the order parameter. A bifurcation analysis of the transition from fully synchronous state to partial synchrony is performed. We demonstrate that for small ensembles it is typically mediated by stable cluster states, that disappear with creation of heteroclinic cycles, while for a larger number of oscillators a direct transition from full synchrony to a periodic or a quasiperiodic regime occurs.
The use of nano zerovalent iron (nZVI) for environmental remediation is a promising new technique for in situ remediation. Due to its high surface area and high reactivity, nZVI is able to dechlorinate organic contaminants and render them harmless. Limited mobility, due to fast aggregation and sedimentation of nZVI, limits the capability for source and plume remediation. Carbo-Iron is a newly developed material consisting of activated carbon particles (d50 = 0,8 µm) that are plated with nZVI particles. These particles combine the mobility of activated carbon and the reactivity of nZVI. This paper presents the first results of the transport experiments.
In this paper, we propose a derivative-free method for recovering symmetric and non-symmetric potential functions of inverse Sturm-Liouville problems from the knowledge of eigenvalues. A class of boundary value methods obtained as an extension of Numerov's method is the major tool for approximating the eigenvalues in each Broyden iteration step. Numerical examples demonstrate that the method is able to reduce the number of iteration steps, in particular for non-symmetric potentials, without accuracy loss.
Public debate about energy relations between the EU and Russia is distorted. These distortions present considerable obstacles to the development of true partnership. At the core of the conflict is a struggle for resource rents between energy producing, energy consuming and transit countries. Supposed secondary aspects, however, are also of great importance. They comprise of geopolitics, market access, economic development and state sovereignty. The European Union, having engaged in energy market liberalisation, faces a widening gap between declining domestic resources and continuously growing energy demand. Diverse interests inside the EU prevent the definition of a coherent and respected energy policy. Russia, for its part, is no longer willing to subsidise its neighbouring economies by cheap energy exports. The Russian government engages in assertive policies pursuing Russian interests. In so far, it opts for a different globalisation approach, refusing the role of mere energy exporter. In view of the intensifying struggle for global resources, Russia, with its large energy potential, appears to be a very favourable option for European energy supplies, if not the best one. However, several outcomes of the strategic game between the two partners can be imagined. Engaging in non-cooperative strategies will in the end leave all stakeholders worse-off. The European Union should therefore concentrate on securing its partnership with Russia instead of damaging it. Stable cooperation would need the acceptance that the partner may pursue his own goals, which might be different from one’s own interests. The question is, how can a sustainable compromise be found? This thesis finds that a mix of continued dialogue, a tit for tat approach bolstered by an international institutional framework and increased integration efforts appears as a preferable solution.
In many architectures for fault-tolerant quantum computing universality is achieved by a combination of Clifford group unitary operators and preparation of suitable nonstabilizer states, the so-called magic states. Universality is possible even for some fairly noisy nonstabilizer states, as distillation can convert many noisy copies into fewer purer magic states. Here we propose protocols that exploit multiple species of magic states in surprising ways. These protocols provide examples of previously unobserved phenomena that are analogous to catalysis and activation well known in entanglement theory.
Well-preserved primary contact relationships between a Late Proterozoic metasedimentary and the metagranitic core and Palaeozoic cover series of the Menderes Massif have been recognized in the eastern part of the Cine submassif on a regional-scale. Metaconglomerates occur as laterally discontinuous channel-fill bodies close the base of the metaquartzarenite directly above the basement. The pebbles in the metaconglomerates consist mainly of different types of tourmaline-rich leucocratic granitoids, tourmalinite and schist in a sandy matrix. Petrographic features, geochemical compositions and zircon radiometric ages (549.6 +/- 3.7-552.3 +/- 3.1 Ma) of the diagnostic clasts of the metaconglomerates (e.g. leucocratic granitoids and tourmalinites) show excellent agreement with their in situ equivalents (549.0 +/- 5.4 Ma) occurring in the Pan-African basement as stocks and veins.
The correlation between clasts in the metaconglomerates and granitoids of the basement suggests that the primary contact between the basement and cover series is a regional unconformity (supra-Pan-African Unconformity) representing deep erosion of the Pan-African basement followed by the deposition of the cover series. Hence the usage of 'core-cover' terminology in the Menderes Massif is valid. Consequently, these new data preclude the views that the granitic precursors of the leucocratic orthogneisses are Tertiary intrusions.
How much is too much? - a case report of nutritional supplement use of a high-performance athlete
(2011)
Although dietary nutrient intake is often adequate, nutritional supplement use is common among elite athletes. However, high-dose supplements or the use of multiple supplements may exceed the recommended daily allowance (RDA) of particular nutrients or even result in a daily intake above tolerable upper limits (UL). The present case report presents nutritional intake data and supplement use of a highly trained male swimmer competing at international level. Habitual energy and micronutrient intake were analysed by 3 d dietary reports. Supplement use and dosage were assessed, and total amount of nutrient supply was calculated. Micronutrient intake was evaluated based on RDA and UL as presented by the European Scientific Committee on Food, and maximum permitted levels in supplements (MPL) are given. The athlete's diet provided adequate micronutrient content well above RDA except for vitamin D. Simultaneous use of ten different supplements was reported, resulting in excess intake above tolerable UL for folate, vitamin E and Zn. Additionally, daily supplement dosage was considerably above MPL for nine micronutrients consumed as artificial products. Risks and possible side effects of exceeding UL by the athlete are discussed. Athletes with high energy intake may be at risk of exceeding UL of particular nutrients if multiple supplements are added. Therefore, dietary counselling of athletes should include assessment of habitual diet and nutritional supplement intake. Educating athletes to balance their diets instead of taking supplements might be prudent to prevent health risks that may occur with long-term excess nutrient intake.
Background: Athletes may differ in their resting metabolic rate (RMR) from the general population. However, to estimate the RMR in athletes, prediction equations that have not been validated in athletes are often used. The purpose of this study was therefore to verify the applicability of commonly used RMR predictions for use in athletes. Methods: The RMR was measured by indirect calorimetry in 17 highly trained rowers and canoeists of the German national teams (BMI 24 +/- 2 kg/m(2), fat-free mass 69 +/- 15 kg). In addition, the RMR was predicted using Cunningham (CUN) and Harris-Benedict (HB) equations. A two-way repeated measures ANOVA was calculated to test for differences between predicted and measured RMR (alpha = 0.05). The root mean square percentage error (RMSPE) was calculated and the Bland-Altman procedure was used to quantify the bias for each prediction. Results: Prediction equations significantly underestimated the RMR in males (p < 0.001). The RMSPE was calculated to be 18.4% (CUN) and 20.9% (HB) in the entire group. The bias was 133 kcal/24 h for CUN and 202 kcal/24 h for HB. Conclusions: Predictions significantly underestimate the RMR in male heavyweight endurance athletes but not in females. In athletes with a high fat-free mass, prediction equations might therefore not be applicable to estimate energy requirements. Instead, measurement of the resting energy expenditure or specific prediction equations might be needed for the individual heavyweight athlete.
Adequate energy intake in adolescent athletes is considered important. Total energy expenditure (TEE) can be calculated from resting energy expenditure (REE) and physical activity level (PAL). However, validated PAL recommendations are available for adult athletes only. Purpose was to comprise physical activity data in adolescent athletes and to establish PAL recommendations for this population. In 64 competitive athletes (15.3 +/- 1.5yr, 20.5 +/- 2.0kg/m(2)) and 14 controls (15.1 +/- 1.1yr, 21 +/- 2.1kg/m(2)) TEE was calculated using 7-day activity protocols validated against doubly-labeled water. REE was estimated by Schofield-HW equation, and PAL was calculated as TEE:REE. Observed PAL in adolescent athletes (1.90 +/- 0.35) did not differ compared with controls (1.84 +/- 0.32, p = .582) and was lower than recommended for adult athletes by the WHO. In conclusion, applicability of PAL values recommended for adult athletes to estimate energy requirements in adolescent athletes must be questioned. Instead, a PAL range of 1.75-2.05 is suggested.
Recent studies have shown that rhizosphere hydraulic properties may differ from those of the bulk soil. Specifically, mucilage at the root-soil interface may increase the rhizosphere water holding capacity and hydraulic conductivity during drying. The goal of this study was to point out the implications of such altered rhizosphere hydraulic properties for soil-plant water relations. We addressed this problem through modeling based on a steady-rate approach. We calculated the water flow toward a single root assuming that the rhizosphere and bulk soil were two concentric cylinders having different hydraulic properties. Based on our previous experimental results, we assumed that the rhizosphere had higher water holding capacity and unsaturated conductivity than the bulk soil. The results showed that the water potential gradients in the rhizosphere were much smaller than in the bulk soil. The consequence is that the rhizosphere attenuated and delayed the drop in water potential in the vicinity of the root surface when the soil dried. This led to increased water availability to plants, as well as to higher effective conductivity under unsaturated conditions. The reasons were two: (i) thanks to the high unsaturated conductivity of the rhizosphere, the radius of water uptake was extended from the root to the rhizosphere surface; and (ii) thanks to the high soil water capacity of the rhizosphere, the water depletion in the bulk soil was compensated by water depletion in the rhizosphere. We conclude that under the assumed conditions, the rhizosphere works as an optimal hydraulic conductor and as a reservoir of water that can be taken up when water in the bulk soil becomes limiting.
Genetic variation is crucial for the long-term survival of the species as it provides the potential for adaptive responses to environmental changes such as emerging diseases. The Major Histocompatibility Complex (MHC) is a gene family that plays a central role in the vertebrate’s immune system by triggering the adaptive immune response after exposure to pathogens. MHC genes have become highly suitable molecular markers of adaptive significance. They synthesize two primary cell surface molecules namely MHC class I and class II that recognize short fragments of proteins derived respectively from intracellular (e.g. viruses) and extracellular (e.g. bacteria, protozoa, arthropods) origins and present them to immune cells. High levels of MHC polymorphism frequently observed in natural populations are interpreted as an adaptation to detect and present a wide array of rapidly evolving pathogens. This variation appears to be largely maintained by positive selection driven mainly by pathogenic selective pressures. For my doctoral research I focused on MHC I and II variation in free-ranging cheetahs (Acinonyx jubatus) and leopards (Panthera pardus) on Namibian farmlands. Both felid species are sympatric thus subject to similar pathogenic pressures but differ in their evolutionary and demographic histories. The main aims were to investigate 1) the extent and patterns of MHC variation at the population level in both felids, 2) the association between levels of MHC variation and disease resistance in free-ranging cheetahs, and 3) the role of selection at different time scales in shaping MHC variation in both felids. Cheetahs and leopards represent the largest free-ranging carnivores in Namibia. They concentrate in unprotected areas on privately owned farmlands where domestic and other wild animals also occur and the risk of pathogen transmission is increased. Thus, knowledge on adaptive genetic variation involved in disease resistance may be pertinent to both felid species’ conservation. The cheetah has been used as a classic example in conservation genetics textbooks due to overall low levels of genetic variation. Reduced variation at MHC genes has been associated with high susceptibility to infectious diseases in cheetahs. However, increased disease susceptibility has only been observed in captive cheetahs whereas recent studies in free-ranging Namibian cheetahs revealed a good health status. This raised the question whether the diversity at MHC I and II genes in free-ranging cheetahs is higher than previously reported. In this study, a total of 10 MHC I alleles and four MHC II alleles were observed in 149 individuals throughout Namibia. All alleles but one likely belong to functional MHC genes as their expression was confirmed. The observed alleles belong to four MHC I and three MHC II genes in the species as revealed by phylogenetic analyses. Signatures of historical positive selection acting on specific sites that interact directly with pathogen-derived proteins were detected in both MHC classes. Furthermore, a high genetic differentiation at MHC I was observed between Namibian cheetahs from east-central and north-central regions known to differ substantially in exposure to feline-specific viral pathogens. This suggests that the patterns of MHC I variation in the current population mirrors different pathogenic selective pressure imposed by viruses. Cheetahs showed low levels of MHC diversity compared with other mammalian species including felids, but this does not seem to influence the current immunocompetence of free-ranging cheetahs in Namibia and contradicts the previous conclusion that the cheetah is a paradigm species of disease susceptibility. However, it cannot be ruled out that the low MHC variation might limit a prosperous immunocompetence in the case of an emerging disease scenario because none of the remaining alleles might be able to recognize a novel pathogen. In contrast to cheetahs, leopards occur in most parts of Africa being perhaps the most abundant big cat in the continent. Leopards seem to have escaped from large-scale declines due to epizootics in the past in contrast to some free-ranging large carnivore populations in Africa that have been afflicted by epizootics. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, I characterized genetic variation at MHC I and MHC II genes in free-ranging leopards from Namibia. A total of six MHC I and six MHC II sequences were detected in 25 individuals from the east-central region. The maximum number of sequences observed per individual suggests that they likely correspond to at least three MHC I and three MHC II genes. Hallmarks of MHC evolution were confirmed such as historical positive selection, recombination and trans-species polymorphism. The low MHC variation detected in Namibian leopards is not conclusive and further research is required to assess the extent of MHC variation in different areas of its geographic range. Results from this thesis will contribute to better understanding the evolutionary significance of MHC and conservation implications in free-ranging felids. Translocation of wildlife is an increasingly used management tool for conservation purposes that should be conducted carefully as it may affect the ability of the translocated animals to cope with different pathogenic selective pressures.
Recent evidence suggests that metabolic changes play a pivotal role in the biology of cancer and in particular renal cell carcinoma (RCC). Here, a global metabolite profiling approach was applied to characterize the metabolite pool of RCC and normal renal tissue. Advanced decision tree models were applied to characterize the metabolic signature of RCC and to explore features of metastasized tumours. The findings were validated in a second independent dataset. Vitamin E derivates and metabolites of glucose, fatty acid, and inositol phosphate metabolism determined the metabolic profile of RCC. alpha-tocopherol, hippuric acid, myoinositol, fructose-1-phosphate and glucose-1-phosphate contributed most to the tumour/normal discrimination and all showed pronounced concentration changes in RCC. The identified metabolic profile was characterized by a low recognition error of only 5% for tumour versus normal samples. Data on metastasized tumours suggested a key role for metabolic pathways involving arachidonic acid, free fatty acids, proline, uracil and the tricarboxylic acid cycle. These results illustrate the potential of mass spectroscopy based metabolomics in conjunction with sophisticated data analysis methods to uncover the metabolic phenotype of cancer. Differentially regulated metabolites, such as vitamin E compounds, hippuric acid and myoinositol, provide leads for the characterization of novel pathways in RCC.
Biomarkers for the prediction of mortality and morbidity in patients with renal replacement therapy
(2011)
The mortality of end-stage renal disease (ESRD) patients on dialysis remains high despite great improvement of dialysis technologies in the past decades.
These patients die due to infectious diseases (mainly sepsis), cardiovascular diseases such as myocardial infarction, heart failure, stroke, and, in particular, sudden cardiac death. End stage renal disease is a complex condition, where the failure of kidney function is accompanied by numerous metabolic changes affecting almost all organ systems of the human body. Many of the biomarker characteristics of the individually affected organ systems have been associated with adverse outcomes. These biomarkers are different in patients with ESRD compared to the general population in the prediction of morbidity and mortality. Biomarker research in this field should aim to identify patients at risk for the different disease entities.
Traditional biomarkers such as CRP, BNP, and troponins as well as new biomarkers such as fetuin, CD 154, and relaxin were analyzed in patients on dialysis. We will include observational as well as prospective clinical trials in this review. Furthermore, we will also discuss proteomics biomarker studies. The article assess the potential diagnostic value of different biomarkers in daily clinical practice as well as their usefulness for clinical drug development in end stage renal disease patients.
Background: Uremic cardiomyopathy contributes substantially to mortality in chronic kidney disease (CKD) patients. Glucagon-like peptide-1 (GLP-1) may improve cardiac function, but is mainly degraded by dipeptidyl peptidase-4 (DPP-4).
Methodology/Principal Findings: In a rat model of chronic renal failure, 5/6-nephrectomized [5/6N] rats were treated orally with DPP-4 inhibitors (linagliptin, sitagliptin, alogliptin) or placebo once daily for 4 days from 8 weeks after surgery, to identify the most appropriate treatment for cardiac dysfunction associated with CKD. Linagliptin showed no significant change in blood level AUC(0-infinity) in 5/6N rats, but sitagliptin and alogliptin had significantly higher AUC(0-infinity) values; 41% and 28% (p=0.0001 and p=0.0324), respectively. No correlation of markers of renal tubular and glomerular function with AUC was observed for linagliptin, which required no dose adjustment in uremic rats. Linagliptin 7 mu mol/kg caused a 2-fold increase in GLP-1 (AUC 201.0 ng/l*h) in 5/6N rats compared with sham-treated rats (AUC 108.6 ng/l*h) (p=0.01). The mRNA levels of heart tissue fibrosis markers were all significantly increased in 5/6N vs control rats and reduced/normalized by linagliptin.
Conclusions/Significance: DPP-4 inhibition increases plasma GLP-1 levels, particularly in uremia, and reduces expression of cardiac mRNA levels of matrix proteins and B-type natriuretic peptides (BNP). Linagliptin may offer a unique approach for treating uremic cardiomyopathy in CKD patients, with no need for dose-adjustment.
In this paper, we describe tools and resources for the study of African languages developed at the Collaborative Research Centre 632 "Information Structure". These include deeply annotated data collections of 25 sub-Saharan languages that are described together with their annotation scheme, as well as the corpus tool ANNIS, which provides unified access to a broad variety of annotations created with a range of different tools. With the application of ANNIS to several African data collections, we illustrate its suitability for the purpose of language documentation, distributed access, and the creation of data archives.
High vitamin A ingestion or high serum retinol have been postulated to increase the risk of fractures and osteoporosis by reduced bone mineral density (BMD). Retinol is carried and transported to the tissues bound to retinol binding protein 4 (RBP4) and transthyretin (TTR). The relationships between retinol, retinol transport protein, retinol binding protein 4 (RBP4) and transthyretin (TTR) and BMD and osteoporosis are unclear. To examine the association between retinol and RBP4 and TTR and osteoporosis, 73 osteoporotic and 71 normal Thai postmenopausal women were studied. RBP4 and retinol levels did not differ between the groups. Serum TTR was significantly higher in control than osteoporotic subjects (89.47 and 144.53 mu g/ml, respectively, p=0.003, Mann-Whitney U test). TTR was positively correlated with BMD at several sites, such as the total radius bone (r=0.172, p=0.008, Spearman rank test). Osteoporosis risk was analyzed with binary logistic regression. Lean elderly Thais with lower TTR levels had a higher risk of osteoporosis. RBP4 and retinol levels had no relationship with disease status among Thai post-menopausal women. These results suggest calcium, minerals, vitamins and the retinol transport protein, transthyretin may be involved in the pathogenesis of osteoporosis.
We introduce hierarchical kFOIL as a simple extension of the multitask kFOIL learning algorithm. The algorithm first learns a core logic representation common to all tasks, and then refines it by specialization on a per-task basis. The approach can be easily generalized to a deeper hierarchy of tasks. A task clustering algorithm is also proposed in order to automatically generate the task hierarchy. The approach is validated on problems of drug-resistance mutation prediction and protein structural classification. Experimental results show the advantage of the hierarchical version over both single and multi task alternatives and its potential usefulness in providing explanatory features for the domain. Task clustering allows to further improve performance when a deeper hierarchy is considered.
The role of bedrock fractures and rock mass strength is often considered a primary influence on the efficiency of surface processes and the morphology of landscapes. Quantifying bedrock characteristics at hillslope scales, however, has proven difficult. Here, we present a new field-based method for quantifying the depth and apparent density of bedrock fractures within the shallow subsurface based on seismic refraction surveys. We examine variations in subsurface fracture patterns in both Fiordland and the Southern Alps of New Zealand to better constrain the influence of bedrock properties in governing rates and patterns of landslides, as well as the morphology of threshold landscapes. We argue that intense tectonic deformation produces uniform bedrock fracturing with depth, whereas geomorphic processes produce strong fracture gradients focused within the shallow subsurface. Additionally, we argue that hillslope strength and stability are functions of both the intact rock strength and the density of bedrock fractures, such that for a given intact rock strength, a threshold fracture-density exists that delineates between stable and unstable rock masses. In the Southern Alps, tectonic forces have pervasively fractured intrinsically weak rock to the verge of instability, such that the entire rock mass is susceptible to failure and landslides can potentially extend to great depths. Conversely, in Fiordland, tectonic fracturing of the strong intact rock has produced fracture densities less than the regional stability threshold. Therefore, bedrock failure in Fiordland generally occurs only after geomorphic fracturing has further reduced the rock mass strength. This dependence on geomorphic fracturing limits the depths of bedrock landslides to within this geomorphically weakened zone.
Alcohol abuse and dependence have proven to be complex genetic traits that are influenced by environmental factors. Primate and human studies have shown that early life stress increases the propensity for alcohol abuse in later life. The reinforcing properties of alcohol are mediated by dopaminergic signaling; however, there is little evidence to indicate how stress alters alcohol reinforcement. KCNJ6 (the gene encoding G-protein-coupled inwardly rectifying potassium channel 2 (GIRK2)) is a brain expressed potassium channel with inhibitory effects on dopaminergic tone. The properties of GIRK2 have been shown to be enhanced by the stress peptide corticotrophin-releasing hormone. Therefore, we sought to examine the role of KCNJ6 polymorphisms in adult alcohol dependence and stress-related alcohol abuse in adolescents. We selected 11 SNPs in the promoter region of KCNJ6, which were genotyped in 1152 adult alcohol dependents and 1203 controls. One SNP, rs2836016, was found to be associated with alcohol dependence (p = 0.01, false discovery rate). We then assessed rs2836016 in an adolescent sample of 261 subjects, which were characterized for early life stress and adolescent hazardous drinking, defined using the Alcohol Use Disorders Identification Test (AUDIT), to examine gene-environment interactions. In the adolescent sample, the risk genotype of rs2836016 was significantly associated with increased AUDIT scores, but only in those individuals exposed to high levels of psychosocial stress in early life (p = 0.01). Our findings show that KCNJ6 is associated with alcohol dependence and may moderate the effect of early psychosocial stress on risky alcohol drinking in adolescents. We have identified a candidate gene for future studies investigating a possible functional link between the response to stress and alcohol reinforcement.
Free Radical Copolymerization Kinetics of gamma-Methyl-alpha-methylene-gamma-butyrolactone (MeMBL)
(2011)
The propagation kinetics and copolymerization behavior of the biorenewable monomer gamma-methyl-alpha-methylene-gamma-butyrolactone (MeMBL) are studied using the Pulsed laser polymerization (PLP)/size exclusion chromatography (SEC) technique. The propagation rate coefficent for MeMBL is 15% higher than that of its structural analogue, methyl methacrylate (MMA), with a similar activation energy of 21.8 kJ . mol(-1). When compared to MMA, MeMBL is preferentially incorporated into copolymers when reacted with styrene (ST), MMA, and n-butyl acrylate (BA); the monomer reactivity ratios fit from bulk MeMBL/ST, MeMBL/MMA, and MeMBL/BA copolymerizations are r(MeMBL) = 0.80 +/- 0.04 and r(ST) = 0.34 +/- 0.04, r(MeMBL), = 3.0 +/- 0.3 and r(MMA) = 0.33 +/- 0.01, and r(MeMBL) = 7.0 +/- 2.0 and r(BA) = 0.16 +/- 0.03, respectively. In all cases, no significant variation with temperature was found between 50 and 90 degrees C. The implicit penultimate unit effect (IPUE) model was found to adequately fit the composition-averaged copolymerization propagation rate coefficient, k(p,cop), for the three systems.
We analyze the equilibrium properties of a weakly interacting, trapped quasi-one-dimensional Bose gas at finite temperatures and compare different theoretical approaches. We focus in particular on two stochastic theories: a number-conserving Bogoliubov (NCB) approach and a stochastic Gross-Pitaevskii equation (SGPE) that have been extensively used in numerical simulations. Equilibrium properties like density profiles, correlation functions, and the condensate statistics are compared to predictions based upon a number of alternative theories. We find that due to thermal phase fluctuations, and the corresponding condensate depletion, the NCB approach loses its validity at relatively low temperatures. This can be attributed to the change in the Bogoliubov spectrum, as the condensate gets thermally depleted, and to large fluctuations beyond perturbation theory. Although the two stochastic theories are built on different thermodynamic ensembles (NCB, canonical; SGPE, grand-canonical), they yield the correct condensate statistics in a large Bose-Einstein condensate (BEC) (strong enough particle interactions). For smaller systems, the SGPE results are prone to anomalously large number fluctuations, well known for the grand-canonical, ideal Bose gas. Based on the comparison of the above theories to the modified Popov approach, we propose a simple procedure for approximately extracting the Penrose-Onsager condensate from first-and second-order correlation functions that is both computationally convenient and of potential use to experimentalists. This also clarifies the link between condensate and quasicondensate in the Popov theory of low-dimensional systems.
Synthesis and conformational analysis of new naphth[1,2-e][1,3]oxazino[3,4-c]quinazoline derivatives
(2011)
A new highly functionalized aminonaphthol derivative, 1-(amino(2-aminophenyl)methyl)-2-naphthol (4), was synthesized by the reaction of 2-naphthol, 2-nitrobenzaldehyde and tert-butyl carbamate or benzyl carbamate, followed by reduction and/or removal of the protecting group. The aminonaphthol derivative thus obtained was converted in ring-closure reactions with formaldehyde. benzaldehyde and/or phosgene to the corresponding naphth[1,2-e][1,3]oxazino[3,4-c]quinazoline derivatives. The conformational analysis of some derivatives by NMR spectroscopy and accompanying molecular modelling are also reported.
Synthesis and conformational analysis of new naphth[1,2-e][1,3]oxazino[3,4-c]quinazoline derivatives
(2011)
The loss of species from ecological communities can unleash a cascade of secondary extinctions, the risk and extent of which are likely to depend on the traits of the species that are lost from the community. To identify species traits that have the greatest impact on food web robustness to species loss we here subject allometrically scaled, dynamical food web models to several deletion sequences based on species' connectivity, generality, vulnerability or body mass. Further, to evaluate the relative importance of dynamical to topological effects we compare robustness between dynamical and purely topological models. This comparison reveals that the topological approach overestimates robustness in general and for certain sequences in particular. Top-down directed sequences have no or very low impact on robustness in topological analyses, while the dynamical analysis reveals that they may be as important as high-impact bottom-up directed sequences. Moreover, there are no deletion sequences that result, on average, in no or very few secondary extinctions in the dynamical approach. Instead, the least detrimental sequence in the dynamical approach yields an average robustness similar to the most detrimental (non-basal) deletion sequence in the topological approach. Hence, a topological analysis may lead to erroneous conclusions concerning both the relative and the absolute importance of different species traits for robustness. The dynamical sequential deletion analysis shows that food webs are least robust to the loss of species that have many trophic links or that occupy low trophic levels. In contrast to previous studies we can infer, albeit indirectly, that secondary extinctions were triggered by both bottom-up and top-down cascades.
Novel fluorescent nanosensors, based on a naphthyridine receptor, have been developed for the detection of guanosine nucleotides, and both their sensitivity and selectivity to various nucleotides were evaluated. The nanosensors were constructed from polystyrene nanoparticles functionalized by (N-(7-((3-aminophenyl) ethynyl)-1,8-naphthyridin- 2-yl) acetamide) via carbodiimide ester activation. We show that this naphthyridine nanosensor binds guanosine nucleotides preferentially over adenine, cytosine, and thymidine nucleotides. Upon interaction with nucleotides, the fluorescence of the nanosensor is gradually quenched yielding Stern-Volmer constants in the range of 2.1 to 35.9mM(-1). For all the studied quenchers, limits of detection (LOD) and tolerance levels for the nanosensors were also determined. The lowest (3 sigma) LOD was found for guanosine 3',5'-cyclic monophosphate (cGMP) and it was as low as 150 ng/ml. In addition, we demonstrated that the spatial arrangement of bound analytes on the nanosensors' surfaces is what is responsible for their selectivity to different guanosine nucleotides. We found a correlation between the changes of the fluorescence signal and the number of phosphate groups of a nucleotide. Results of molecular modeling and zeta-potential measurements confirm that the arrangement of analytes on the surface provides for the selectivity of the nanosensors. These fluorescent nanosensors have the potential to be applied in multi-analyte, array-based detection platforms, as well as in multiplexed microfluidic systems.
Continent-ocean-transition across a trans-tensional margin segment: off Bear Island, Barents Sea
(2011)
P>A 410 km long Ocean Bottom Seismometer profile spanning from the Bear Island, Barents Sea to oceanic crust formed along the Mohns Ridge has been modelled by use of ray-tracing with regard to observed P-waves. The northeastern part of the model represents typical continental crust, thinned from ca. 30 km thickness beneath the Bear Island to ca. 13 km within the Continent-Ocean-Transition. Between the Hornsund FZ and the Kn circle divide legga Fault, a 3-4 km thick sedimentary basin, dominantly of Permian/Carboniferous age, is modelled beneath the ca. 1.5 km thick layer of volcanics (Vestbakken Volcanic Province). The P-wave velocity in the 3-4 km thick lowermost continental crust is significantly higher than normal (ca. 7.5 km s-1). We interpret this layer as a mixture of mafic intrusions and continental crystalline blocks, dominantly related to the Paleocene-Early Eocene rifting event. The crystalline portion of the crust within the south-western part of the COT consists of a ca. 30 km wide and ca. 6 km thick high-velocity (7.3 km s-1) body. We interpret the body as a ridge of serpentinized peridotites. The magmatic portion of the ocean crust accreted along the Knipovich Ridge from continental break-up at ca. 35 Ma until ca. 20 Ma is 3-5 km thicker than normal. We interpret the increased magmatism as a passive response to the bending of this southernmost part of the Knipovich Ridge. The thickness of the magmatic portion of the crust formed along the Mohns Ridge at ca. 20 Ma decreases to ca. 3 km, which is normal for ultra slow spreading ridges.
Background: In Moco biosynthesis, sulfur is transferred from L-cysteine to MPT synthase, catalyzing the conversion of cPMP to MPT.
Results: The rhodanese-like protein YnjE is a novel protein involved in Moco biosynthesis.
Conclusion: YnjE enhances the rate of conversion of cPMP to MPT and interacts with MoeB and IscS. S
ignificance: To understand the mechanism of sulfur transfer and the role of rhodaneses in the cell.
Functional aspects of water soluble chlorophyll-binding protein (WSCP) in plants were investigated during the courses of leaf senescence, chlorophyll biogenesis, stress response and photoprotection. The cDNA sequence encoding WSCP from cauliflower was cloned into a binary vector to facilitate Agrobacterium tumefaciens mediated transformation of Nicotiana tabacum. The resultant transgenic tobacco plants overexpressed the CauWSCP gene under the control of a 35S-promoter. Analyses of protein and pigment contents indicate that WSCP overexpression does not enhance chlorophyll catabolism in vivo, thus rendering a role of WSCP in Chl degradation unlikely. Accumulation of higher levels of protochlorophyllide in WSCP overexpressor plants corroborates a proposed temporary storage and carrier function of WSCP for chlorophyll and late precursors. Although WSCP overexpressor plants did not show significant differences in non-photochemical quenching of chlorophyll fluorescence, they are characterized by significantly lower zeaxanthin accumulation and peroxidase activity at different light intensities, even at high light intensities of 700-900 mu mol photons m(-2) s(-1). These results suggest a photoprotective function of the functional chlorophyll binding-WSCP tetramer by shielding of chlorophylls from molecular oxygen.
We study changes in effective stress (normal stress minus pore pressure) that occurred in the French Alps during the 2003-2004 Ubaye earthquake swarm. Two complementary data sets are used. First, a set of 974 relocated events allows us to finely characterize the shape of the seismogenic area and the spatial migration of seismicity during the crisis. Relocations are performed by a double-difference algorithm. We compute differences in travel times at stations both from absolute picking times and from cross-correlation delays of multiplets. The resulting catalog reveals a swarm alignment along a single planar structure striking N130 degrees E and dipping 80 degrees W. This relocated activity displays migration properties consistent with a triggering by a diffusive fluid overpressure front. This observation argues in favor of a deep-seated fluid circulation responsible for a significant part of the seismic activity in Ubaye. Second, we analyze time series of earthquake detections at a single seismological station located just above the swarm. This time series forms a dense chronicle of +16,000 events. We use it to estimate the history of effective stress changes during this sequence. For this purpose we model the rate of events by a stochastic epidemic-type aftershock sequence model with a nonstationary background seismic rate lambda(0)(t). This background rate is estimated in discrete time windows. Window lengths are determined optimally according to a new change-point method on the basis of the interevent times distribution. We propose that background events are triggered directly by a transient fluid circulation at depth. Then, using rate-and-state constitutive friction laws, we estimate changes in effective stress for the observed rate of background events. We assume that changes in effective stress occurred under constant shear stressing rate conditions. We finally obtain a maximum change in effective stress close to -8 MPa, which corresponds to a maximum fluid overpressure of about 8 MPa under constant normal stress conditions. This estimate is in good agreement with values obtained from numerical modeling of fluid flow at depth, or with direct measurements reported from fluid injection experiments.
Cross-coupling reactions, such as Buchwald-Hartwig arylamination and direct intramolecular biaryl coupling by C-H activation, were carried out using various Palladium-N-heterocyclic carbenes (Pd-NHC) as catalysts. The yields were good to excellent. The latter strategy was adopted to transform two dibenzylbutane lignans, isolated from the leaves of Ocotea macrophylla (Lauraceae), into the corresponding dibenzocyclooctane lignans in good overall yields. Supplemental materials are available for this article. Go to the publisher's online edition of Synthetic Communications (R) to view the free supplemental file.
Background: Flux coupling analysis (FCA) is a useful method for finding dependencies between fluxes of a metabolic network at steady-state. FCA classifies reactions into subsets (called coupled reaction sets) in which activity of one reaction implies activity of another reaction. Several approaches for FCA have been proposed in the literature.
Results: We introduce a new FCA algorithm, FFCA (Feasibility-based Flux Coupling Analysis), which is based on checking the feasibility of a system of linear inequalities. We show on a set of benchmarks that for genome-scale networks FFCA is faster than other existing FCA methods.
Conclusions: We present FFCA as a new method for flux coupling analysis and prove it to be faster than existing approaches. A corresponding software tool is freely available for non-commercial use at http://www.bioinformatics.org/ffca/.
Vertical flow filters and vertical flow constructed wetlands are established wastewater treatment systems and have also been proposed for the treatment of contaminated groundwater. This study investigates the removal processes of volatile organic compounds in a pilot-scale vertical flow filter. The filter is intermittently irrigated with contaminated groundwater containing benzene, MTBE and ammonium as the main contaminants. The system is characterized by unsaturated conditions and high contaminant removal efficiency. The aim of the present study is to evaluate the contribution of biodegradation and volatilization to the overall removal of benzene and MTBE. Tracer tests and flow rate measurements showed a highly transient flow and heterogeneous transport regime. Radon-222, naturally occurring in the treated groundwater, was used as a gas tracer and indicated a high volatilization potential. Radon-222 behavior was reproduced by numerical simulations and extrapolated for benzene and MTBE, and indicated these compounds also have a high volatilization potential. In contrast, passive sampler measurements on top of the filter detected only low benzene and MTBE concentrations. Biodegradation potential was evaluated by the analysis of catabolic genes involved in organic compound degradation and a quantitative estimation of biodegradation was derived from stable isotope fractionation analysis. Results suggest that despite the high volatilization potential, biodegradation is the predominant mass removal process in the filter system, which indicates that the volatilized fraction of the contaminants is still subject to subsequent biodegradation. In particular, the upper filter layer located between the injection tubes and the surface of the system might also contribute to biodegradation, and might play a crucial role in avoiding the emission of volatilized contaminants into the atmosphere.
Control over molecular architectures obtained via ADMET polymerization is limited by the step-growth nature of this technique. A new approach to this polycondensation method is described allowing for the synthesis of diblock and star-shaped polymers with molecular weight control by using the selectivity of olefin cross-metathesis between acrylates and terminal olefins.
The nutrient concentration in seeds determines many aspects of potential success of the sexual reproductive phase of plants, including the seed predation probability, efficiency of seed dispersal and seedling performance. Despite considerable research interest in latitudinal gradients of foliar nutrients, a similar gradient for seeds remains unexplored. We investigated a potential latitudinal gradient in seed nutrient concentrations within the widespread European understorey forest herb Anemone nemorosa L. We sampled seeds of A. nemorosa in 15 populations along a 1900-km long latitudinal gradient at three to seven seed collection dates post-anthesis and investigated the relative effects of growing degree-hours > 5 degrees C, soil characteristics and latitude on seed nutrient concentrations. Seed nitrogen, nitrogen:phosphorus ratio and calcium concentration decreased towards northern latitudes, while carbon:nitrogen ratios increased. When taking differences in growing degree-hours and measured soil characteristics into account and only considering the most mature seeds, the latitudinal decline remained particularly significant for seed nitrogen concentration. We argue that the decline in seed nitrogen concentration can be attributed to northward decreasing seed provisioning due to lower soil nitrogen availability or greater investment in clonal reproduction. This pattern may have large implications for the reproductive performance of this forest herb as the degree of seed provisioning ultimately co-determines seedling survival and reproductive success.
1. Worldwide, the floristic composition of temperate forests bears the imprint of past land use for decades to centuries as forests regrow on agricultural land. Many species, however, display significant interregional variation in their ability to (re)colonize post-agricultural forests. This variation in colonization across regions and the underlying factors remain largely unexplored.
2. We compiled data on 90 species and 812 species x study combinations from 18 studies across Europe that determined species' distribution patterns in ancient (i.e. continuously forested since the first available land use maps) and post-agricultural forests. The recovery rate (RR) of species in each landscape was quantified as the log-response ratio of the percentage occurrence in post-agricultural over ancient forest and related to the species-specific life-history traits and local (soil characteristics and light availability) and regional factors (landscape properties as habitat availability, time available for colonization, and climate).
3. For the herb species, we demonstrate a strong (interactive) effect of species' life-history traits and forest habitat availability on the RR of post-agricultural forest. In graminoids, however, none of the investigated variables were significantly related to the RR.
4. The better colonizing species that mainly belonged to the short-lived herbs group showed the largest interregional variability. Their recovery significantly increased with the amount of forest habitat within the landscape, whereas, surprisingly, the time available for colonization, climate, soil characteristics and light availability had no effect.
5. Synthesis. By analysing 18 independent studies across Europe, we clearly showed for the first time on a continental scale that the recovery of short-lived forest herbs increased with the forest habitat availability in the landscape. Small perennial forest herbs, however, were generally unsuccessful in colonizing post-agricultural forest even in relatively densely forested landscapes. Hence, our results stress the need to avoid ancient forest clearance to preserve the typical woodland flora.
Slow-colonizing forest understorey plants are probably not able to rapidly adjust their distribution range following large-scale climate change. Therefore, the acclimation potential to climate change within their actual occupied habitats will likely be key for their short-and long-term persistence. We combined transplant experiments along a latitudinal gradient with open-top chambers to assess the effects of temperature on phenology, growth and reproductive performance of multiple populations of slow-colonizing understorey plants, using the spring flowering geophytic forb Anemone nemorosa and the early summer flowering grass Milium effusum as study species. In both species, emergence time and start of flowering clearly advanced with increasing temperatures. Vegetative growth (plant height, aboveground biomass) and reproductive success (seed mass, seed germination and germinable seed output) of A. nemorosa benefited from higher temperatures. Climate warming may thus increase future competitive ability and colonization rates of this species. Apart from the effects on phenology, growth and reproductive performance of M. effusum generally decreased when transplanted southwards (e. g., plant size and number of individuals decreased towards the south) and was probably more limited by light availability in the south. Specific leaf area of both species increased when transplanted southwards, but decreased with open-top chamber installation in A. nemorosa. In general, individuals of both species transplanted at the home site performed best, suggesting local adaptation. We conclude that contrasting understorey plants may display divergent plasticity in response to changing temperatures which may alter future understorey community dynamics.
We measured LHS traits in 41 Anemone nemorosa and 44 Milium effusum populations along a 1900-2300 km latitudinal gradient from N France to N Sweden. We then applied multilevel models to identify the effects of regional (temperature, latitude) and local (soil fertility and acidity, overstorey canopy cover) environmental factors on LHS traits.
Both species displayed a significant 4% increase in plant height with every degree northward shift (almost a two-fold plant height difference between the southernmost and northernmost populations). Neither seed mass nor SLA showed a significant latitudinal cline. Temperature had a large effect on the three LHS traits of Anemone. Latitude, canopy cover and soil nutrients were related to the SLA and plant height of Milium. None of the investigated variables appeared to be related to the seed mass of Milium.
The variation in LHS traits indicates that the ecological strategy determined by the position of each population in this three-factor triangle is not constant along the latitudinal gradient. The significant increase in plant height suggests greater competitive abilities for both species in the northernmost populations. We also found that the studied environmental factors affected the LHS traits of the two species on various scales: spring-flowering Anemone was affected more by temperature, whereas early-summer flowering Milium was affected more by local and other latitude-related factors. Finally, previously reported cross-species correlations between LHS traits and latitude were generally unsupported by our within-species approach.
Asymptotic first exit times of the chafee-infante equation with small heavy-tailed levy noise
(2011)
This article studies the behavior of stochastic reaction-diffusion equations driven by additive regularly varying pure jump Levy noise in the limit of small noise intensity. It is shown that the law of the suitably renormalized first exit times from the domain of attraction of a stable state converges to an exponential law of parameter 1 in a strong sense of Laplace transforms, including exponential moments. As a consequence, the expected exit times increase polynomially in the inverse intensity, in contrast to Gaussian perturbations, where this growth is known to be of exponential rate.
With the rise of electronic integration between organizations, the need for a precise specification of interaction behavior increases. Information systems, replacing interaction previously carried out by humans via phone, faxes and emails, require a precise specification for handling all possible situations. Such interaction behavior is described in process choreographies. While many proposals for choreography languages have already been made, most of them fall into the category of interconnection models, where the observable behavior of the different partners is described and then related via message flow. As this article will show, this modeling approach fails to support fundamental design principles of choreographies and typically leads to modeling errors. This motivates an alternative modeling style, namely interaction modeling, for overcoming these limitations. While the main concepts are independent of a concrete modeling language, iBPMN is introduced as novel interaction modeling language. Formal execution semantics are provided and a comprehensive toolset implementing the approach is presented.
In the Himalaya of Chamba, NW India, a major orographic barrier in front of the Greater Himalayan Range extracts a high proportion of the monsoonal rainfall along its southern slopes and effectively shields the orogen interior from moisture-bearing winds. Along a similar to 100-km-long orogen perpendicular transect, 28 new apatite fission track (AFT) and 30 new zircon (U-Th)/He (ZHe) cooling ages reveal marked variations in age distributions and long-term exhumation rates between the humid frontal range and the semi-arid orogen interior. On the southern topographic front, very young, elevation-invariant AFT ages of <4 Ma have been obtained that are concentrated in a similar to 30-km-wide zone; 1-D-thermal modeling suggests a Plio-Pleistocene mean erosion rate of 0.8-1.9 mm yr(-1). In contrast, AFT and ZHe ages within the orogen interior are older (4-9 and 7-18 Ma, respectively), are positively correlated with sample elevation, and yield lower mean erosion rates (0.3-0.9 mm yr(-1)). Protracted low exhumation rates within the orogen interior over the last similar to 15 Myr prevailed contemporaneously with overall humid conditions and an effective erosional regime within the southern Himalaya. This suggests that the frontal Dhauladar Range was sufficiently high during this time to form an orographic barrier, focusing climatically enhanced erosional processes and tectonic deformation there. Thrusting along the two frontal range-bounding thrust, the Main Central Thrust and the Main Boundary Thrusts, was initiated at least similar to 15 Ma ago and has remained localized since then. The lack of evidence for localized uplift farther north indicates either a rather flat decollement with no ramp or the absence of active duplex systems beneath the interior of Chamba. Exhumational variability within Chamba is best explained as the result of continuous thrusting along a major basal decollement, with a flat beneath the slowly exhuming internal compartments and a steep frontal ramp at the rapidly exhuming frontal range. The pattern in Chamba contrasts with what is observed elsewhere along the Himalaya, where exhumation is focused in a zone similar to 150 km north of the orogenic front. In the NW Himalaya, preserved High Himalayan Crystalline nappes and Lesser Himalayan windows alternate on a relatively small scale of <100 km; these alternations are closely correlated with the pattern of exhumation. Although the spatial distribution of high-exhumation zones varies considerably between individual Himalayan sectors, all of these zones are closely correlated with locally higher rock-uplift rates, sharp topographic discontinuities, and focused orographic precipitation, suggesting strong feedbacks between tectonically driven rock uplift, orographically enhanced precipitation, and erosional processes.
Functional hybrid materials on the basis of inorganic hosts and ionic liquids (ILs) as guests hold promise for a virtually unlimited number of applications. In particular, the interaction and the combination of properties of a defined inorganic matrix and a specific IL could lead to synergistic effects in property selection and tuning. Such hybrid materials, generally termed ionogels, are thus an emerging topic in hybrid materials research. The current article addresses some of the recent developments and focuses on the question why silica is currently the dominating matrix used for (inorganic) ionogel fabrication. In comparison to silica, matrix materials such as layered simple hydroxides, layered double hydroxides, clay-type substances, magnetic or catalytically active solids, and many other compounds could be much more interesting because they themselves may carry useful functionalities, which could also be exploited for multifunctional hybrid materials synthesis. The current article combines experimental results with some arguments as to how new, advanced functional hybrid materials can be generated and which obstacles will need to be overcome to successfully achieve the synthesis of a desired target material.
Context. The Galactic gamma-ray diffuse emission is currently observed in the GeV-TeV energy range with unprecedented accuracy by the Fermi satellite. Understanding this component is crucial because it provides a background to many different signals, such as extragalactic sources or annihilating dark matter. It is timely to reinvestigate how it is calculated and to assess the various uncertainties that are likely to affect the accuracy of the predictions.
Aims. The Galactic gamma-ray diffuse emission is mostly produced above a few GeV by the interactions of cosmic ray primaries impinging on the interstellar material. The theoretical error on that component is derived by exploring various potential sources of uncertainty. Particular attention is paid to cosmic ray propagation. Nuclear cross sections, the proton and helium fluxes at the Earth's position, the Galactic radial profile of supernova remnants, and the hydrogen distribution can also severely affect the signal.
Methods. The propagation of cosmic ray species throughout the Galaxy is described in the framework of a semi-analytic two-zone diffusion/convection model. The gamma-ray flux is reliably and quickly determined. This allows conversion of the constraints set by the boron-to-carbon data into a theoretical uncertainty on the diffuse emission. New deconvolutions of the HI and CO sky maps are also used to get the hydrogen distribution within the Galaxy.
Results. The thickness of the cosmic ray diffusive halo is found to have a significant effect on the Galactic gamma-ray diffuse emission, while the interplay between diffusion and convection has little influence on the signal. The uncertainties related to nuclear cross sections and to the primary cosmic ray fluxes at the Earth are significant. The radial distribution of supernova remnants along the Galactic plane turns out to be a key ingredient. As expected, the predictions are extremely sensitive to the spatial distribution of hydrogen within the Milky Way.
Conclusions. Most of the sources of uncertainty are likely to be reduced in the near future. The stress should be put (i) on better determination of the thickness of the cosmic ray diffusive halo; and (ii) on refined observations of the radial profile of supernova remnants.
AM symbiosis has a positive influence on plant P-nutrition and growth, but little is known about the molecular mechanism of the symbiosis adaptation to different phosphate conditions. The recently described induction of several pri-miR399 transcripts in mycorrhizal shoots and subsequent accumulation of mature miR399 in mycorrhizal roots indicates that local PHO2 expression must be controlled during symbiosis, presumably in order to sustain AM symbiosis development, in spite of locally increased Pi-concentration. A reverse genetic approach used in this study demonstrated that PHO2 and thus the PHR1-miR399-PHO2 signaling pathway, is involved in certain stages of progressive root colonization. In addition, a transcriptomic approach using a split-root system provided a comprehensive insight into the systemic transcriptional changes in mycorrhizal roots and shoots of M. truncatula in response to high phosphate conditions. With regard to the transcriptional responses of the root system, the results indicate that, although the colonization is drastically reduced, AM symbiosis is still functional at high Pi concentrations and might still be beneficial to the plant. Additionally, the data suggest that a specific root-borne mycorrhizal signal systemically induces protein synthesis, amino acid metabolism and photosynthesis at low Pi conditions, which is abolished at high Pi conditions. MiRNAs, such as miR399, are involved in long-distance signaling and are therefore potential systemic signals involved in AM symbiosis. A deep-sequencing approach identified 243 novel miRNAs in the root tissue of M. truncatula. Read-count analysis, qRT-PCR measurements and in situ hybridizations clearly indicated a regulation of miR5229a/b, miR5204, miR160f*, miR160c, miR169 and miR169d*/l*/m*/e.2* during arbuscular mycorrhizal symbiosis. Moreover, miR5204* represses a GRAS TF, which is specifically transcribed in mycorrhizal roots. Since miR5204* is induced by high Pi it might represent a further Pi status-mediating signal beside miR399. This study provides additional evidence that MtNsp2, a key regulator of symbiosis-signaling, is regulated and presumably spatially restricted by miR171h cleavage. In summary, a repression of mycorrhizal root colonization at high phosphate status is most likely due to a repression of the phosphate starvation responses and the loss of beneficial responses in mycorrhizal shoots. These findings provide a new basis for investigating the regulatory network leading to cellular reprogramming during interaction between plants, arbuscular mycorrhizal fungi and different phosphate conditions.
P>Computing the magnitude of an earthquake requires correcting for the propagation effects from the source to the receivers. This is often accomplished by performing numerical simulations using a suitable Earth model. In this work, the energy magnitude M(e) is considered and its determination is performed using theoretical spectral amplitude decay functions over teleseismic distances based on the global Earth model AK135Q. Since the high frequency part (above the corner frequency) of the source spectrum has to be considered in computing M(e), the influence of propagation and site effects may not be negligible and they could bias the single station M(e) estimations. Therefore, in this study we assess the inter- and intrastation distributions of errors by considering the M(e) residuals computed for a large data set of earthquakes recorded at teleseismic distances by seismic stations deployed worldwide. To separate the inter- and intrastation contribution of errors, we apply a maximum likelihood approach to the M(e) residuals. We show that the interstation errors (describing a sort of site effect for a station) are within +/- 0.2 magnitude units for most stations and their spatial distribution reflects the expected lateral variation affecting the velocity and attenuation of the Earth's structure in the uppermost layers, not accounted for by the 1-D AK135Q model. The variance of the intrastation error distribution (describing the record-to-record component of variability) is larger than the interstation one (0.240 against 0.159), and the spatial distribution of the errors is not random but shows specific patterns depending on the source-to-station paths. The set of coefficients empirically determined may be used in the future to account for the heterogeneities of the real Earth not considered in the theoretical calculations of the spectral amplitude decay functions used to correct the recorded data for propagation effects.
Experimental Unconditional Preparation and Detection of a Continuous Bound Entangled State of Light
(2011)
Among the possibly most intriguing aspects of quantum entanglement is that it comes in free and bound instances. The existence of bound entangled states certifies an intrinsic irreversibility of entanglement in nature and suggests a connection with thermodynamics. In this Letter, we present a first unconditional, continuous-variable preparation and detection of a bound entangled state of light. We use convex optimization to identify regimes rendering its bound character well certifiable, and continuously produce a distributed bound entangled state with an extraordinary and unprecedented significance of more than 10 standard deviations away from both separability and distillability. Our results show that the approach chosen allows for the efficient and precise preparation of multimode entangled states of light with various applications in quantum information, quantum state engineering, and high precision metrology.
Brain-electric correlates of reading have traditionally been studied with word-by-word presentation, a condition that eliminates important aspects of the normal reading process and precludes direct comparisons between neural activity and oculomotor behavior. In the present study, we investigated effects of word predictability on eye movements (EM) and fixation-related brain potentials (FRPs) during natural sentence reading. Electroencephalogram (EEG) and EM (via video-based eye tracking) were recorded simultaneously while subjects read heterogeneous German sentences, moving their eyes freely over the text. FRPs were time-locked to first-pass reading fixations and analyzed according to the cloze probability of the currently fixated word. We replicated robust effects of word predictability on EMs and the N400 component in FRPs. The data were then used to model the relation among fixation duration, gaze duration, and N400 amplitude, and to trace the time course of EEG effects relative to effects in EM behavior. In an extended Methodological Discussion section, we review 4 technical and data-analytical problems that need to be addressed when FRPs are recorded in free-viewing situations (such as reading, visual search, or scene perception) and propose solutions. Results suggest that EEG recordings during normal vision are feasible and useful to consolidate findings from EEG and eye-tracking studies.
This study addresses the effect of ionic strength and type of ions on the structure and water content of polyelectrolyte multilayers. Polyelectrolyte multilayers of poly(sodium-4-styrene sulfonate) (PSS) and poly(diallyl dimethyl ammonium chloride) (PDADMAC) prepared at different NaF, NaCl and NaBr concentrations have been investigated by neutron reflectometry against vacuum, H2O and D2O. Both thickness and water content of the multilayers increase with increasing ionic strength and increasing ion size. Two types of water were identified, "void water" which fills the voids of the multilayers and does not contribute to swelling but to a change in scattering length density and "swelling water" which directly contributes to swelling of the multilayers. The amount of void water decreases with increasing salt concentration and anion radius while the amount of swelling water increases with salt concentration and anion radius. This is interpreted as a denser structure in the dry state and larger ability to swell in water (sponge) for multilayers prepared from high ionic strengths and/or salt solution of large anions. No exchange of hydration water or replacement of H by D was detected even after eight hours incubation time in water of opposing isotopic composition.
The analysis of palaeoclimate time series is usually affected by severe methodological problems, resulting primarily from non-equidistant sampling and uncertain age models. As an alternative to existing methods of time series analysis, in this paper we argue that the statistical properties of recurrence networks - a recently developed approach - are promising candidates for characterising the system's nonlinear dynamics and quantifying structural changes in its reconstructed phase space as time evolves. In a first order approximation, the results of recurrence network analysis are invariant to changes in the age model and are not directly affected by non-equidistant sampling of the data. Specifically, we investigate the behaviour of recurrence network measures for both paradigmatic model systems with non-stationary parameters and four marine records of long-term palaeoclimate variations. We show that the obtained results are qualitatively robust under changes of the relevant parameters of our method, including detrending, size of the running window used for analysis, and embedding delay. We demonstrate that recurrence network analysis is able to detect relevant regime shifts in synthetic data as well as in problematic geoscientific time series. This suggests its application as a general exploratory tool of time series analysis complementing existing methods.
Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution
(2011)
Potential paleoclimatic driving mechanisms acting on human evolution present an open problem of cross-disciplinary scientific interest. The analysis of paleoclimate archives encoding the environmental variability in East Africa during the past 5 Ma has triggered an ongoing debate about possible candidate processes and evolutionary mechanisms. In this work, we apply a nonlinear statistical technique, recurrence network analysis, to three distinct marine records of terrigenous dust flux. Our method enables us to identify three epochs with transitions between qualitatively different types of environmental variability in North and East Africa during the (i) Middle Pliocene (3.35-3.15 Ma B. P.), (ii) Early Pleistocene (2.25-1.6 Ma B. P.), and (iii) Middle Pleistocene (1.1-0.7 Ma B. P.). A deeper examination of these transition periods reveals potential climatic drivers, including (i) large-scale changes in ocean currents due to a spatial shift of the Indonesian throughflow in combination with an intensification of Northern Hemisphere glaciation, (ii) a global reorganization of the atmospheric Walker circulation induced in the tropical Pacific and Indian Ocean, and (iii) shifts in the dominating temporal variability pattern of glacial activity during the Middle Pleistocene, respectively. A reexamination of the available fossil record demonstrates statistically significant coincidences between the detected transition periods and major steps in hominin evolution. This result suggests that the observed shifts between more regular and more erratic environmental variability may have acted as a trigger for rapid change in the development of humankind in Africa.
The northward movement and collision of the Arabian plate with Eurasia generates compressive stresses and resulting shortening in Iran. Within the Alborz Mountains, North Iran, a complex and not well understood system of strike-slip and thrust faults accomodates a fundamental part of the NNE-SSW oriented shortening. On 28th of May 2004 the Mw 6.3 Baladeh earthquake hit the north-central Alborz Mountains. It is one of the rare and large events in this region in modern time and thus a seldom chance to study earthquake mechanisms and the local ongoing deformation processes. It also demonstrated the high vulnerability of this densily populated region.
Recent discussions about violence against women have shifted their attention to specific forms of violence in relation to migration and Islam. In this article, I consider different modes of representing women's experiences in French immigrant communities. These representations relate to the French feminist movement Ni Putes Ni Soumises (neither whore nor submissive), a movement that in the early 2000s deplored both the sustained degradation of certain banlieue neighborhoods and also the charges and restrictions that this entails, particularly for young women. Drawing on different narratives and images of women's painful experience, I consider, in a first step, how the question of representing violence against (post) migrant women is framed in terms of the tension between universality and particularity within French republicanism. In the next part of my argument, I bring into focus the question of how to access women's suffering. For a perspective on pain not as an interiorized, private experience but as an accessible complex of practices, articulations, memories, visions and social reconfigurations, I consider Smain Laacher's sociological study (2008) about written testimonies of violent experience that had been addressed by (post) migrant women to French women organizations such as Ni Putes Ni Soumises. I finally suggest reading women's accounts on violence not in relation to a universal discourse of rights, but as a political contestation of the naturalized order of representing violence, suffering and agency inside French banlieue communities. Drawing on Jacques Ranciere's notion of dissensus, such a contestation can be staged through words by those who have no visibility in the representational order, words not to criticize the unaccomplished ideals of universal equality, but to create a universal community and a common language of experience in the mode of 'as-if'.
Protein expression in heterologous hosts for functional studies is a cumbersome effort. Here, we report a superior platform for parallel protein expression in vivo and in vitro. The platform combines highly efficient ligation-independent cloning (LIC) with instantaneous detection of expressed proteins through N- or C-terminal fusions to infrared fluorescent protein (IFP). For each open reading frame, only two PCR fragments are generated (with three PCR primers) and inserted by LIC into ten expression vectors suitable for protein expression in microbial hosts, including Escherichia coli, Kluyveromyces lactis, Pichia pastoris, the protozoon Leishmania tarentolae, and an in vitro transcription/translation system. Accumulation of IFP-fusion proteins is detected by infrared imaging of living cells or crude protein extracts directly after SDS-PAGE without additional processing. We successfully employed the LIC-IFP platform for in vivo and in vitro expression of ten plant and fungal proteins, including transcription factors and enzymes. Using the IFP reporter, we additionally established facile methods for the visualisation of protein-protein interactions and the detection of DNA-transcription factor interactions in microtiter and gel-free format. We conclude that IFP represents an excellent reporter for high-throughput protein expression and analysis, which can be easily extended to numerous other expression hosts using the setup reported here.
With its homo-pentameric structure and calcium-dependent specificity for phosphocholine (PCh), human c-reactive protein (CRP) is produced by the liver and secreted in elevated quantities in response to inflammation. CRP is widely accepted as a cardiac marker, e.g. in point-of-care diagnostics, however, its heterologous expression has proven difficult. Here, we demonstrate the expression of CRP in different Escherichia coli strains as well as by in vitro transcription/translation. Although expression in these systems was straightforward, most of the protein that accumulated was insoluble. We therefore expanded our study to include the expression of CRP in two eukaryotic hosts, namely the yeast Kluyveromyces lactis and the protozoon Leishmania tarentolae. Both expression systems are optimized for secretion of recombinant proteins and here allowed successful expression of soluble CRP. We also demonstrate the purification of recombinant CRP from Leishmania growth medium; the purification of protein expressed from K. lactis was not successful. Functional and intact CRP pentamer is known to interact with PCh in Ca(2+)-dependent manner. In this report we verify the binding specificity of recombinant CRP from L tarentolae (2 mu g/mL culture medium) for PCh.
Ionic liquid Crystals constitute highly versatile materials that have drawn much interest these past few years in the fields of academic research and industrial development. In this respect, the present article is intended as an update of K. Binnemans review published in 2005, but focusing exclusively on the imidazolium cation - the most widely studied. Herein, imidazolium-containing thermotropic liquid crystalline materials will be sorted by molecular structure (mono-, bis-, poly-imidazolium compounds, with symmetrical and non-symmetrical structures) and discussed. Their physico-chemical properties will be exposed in order to adduce the relevancy and potential of the imidazolium platform in various fields of research.
While it is widely acknowledged in the formal semantic literature that both the truth-functional focus particle only and it-clefts convey exhaustiveness, the nature and source of exhaustiveness effects with it-clefts remain contested. We describe a questionnaire study (n = 80) and an event-related brain potentials (ERP) study (n = 16) that investigated the violation of exhaustiveness in German only-foci versus it-clefts. The offline study showed that a violation of exhaustivity with only is less acceptable than the violation with it-clefts, suggesting a difference in the nature of exhaustivity interpretation in the two environments. The ERP-results confirm that this difference can be seen in online processing as well: a violation of exhaustiveness in only-foci elicited a centro-posterior positivity (600-800ms), whereas a violation in it-clefts induced a globally distributed N400 pattern (400-600ms). The positivity can be interpreted as a reanalysis process and more generally as a process of context updating. The N400 effect in it-clefts is interpreted as indexing a cancelation process that is functionally distinct from the only case. The ERP study is, to our knowledge, the first evidence from an online experimental paradigm which shows that the violation of exhaustiveness involves different underlying processes in the two structural environments.
The interaction of Cu(II) with three beta-diketone ligands of type R(1)C(O)CH(2)C(O)R(2) (where R(1) = 2-, 3-, or 4-pyridyl and R(2) = C(6)H(5), respectively), HL(1)-HL(3), along with the X-ray structures and the pK(a) values of each ligand, are reported. HL(1) yields a dimeric complex of type [Cu(L(1))(2)](2). In this structure, two deprotonated HL(1) ligands coordinate in a trans planar fashion around each Cu(II) center, one oxygen from each CuL(2) unit bridges to an axial site of the second complex unit such that both Cu(II) centers attain equivalent five-coordinate square pyramidal geometries. The two-substituted pyridyl groups in this complex do not coordinate, perhaps reflecting steric factors associated with the closeness of the pyridyl nitrogen to the attached (conjugated) beta-diketonato backbone of each ligand. The remaining two Cu(II) species, derived from HL(2) and HL(3), are both coordination polymers of type [Cu(L)(2)](n) in which the terminal pyridine group of each ligand is intermolecularly linked to an adjacent copper center to generate the respective infinite structures. HL(2) was also demonstrated to form a fibrous metallogel when reacted with CuCl(2) in an acetonitrile/water mixture under defined conditions.
Building biological models by inferring functional dependencies from experimental data is an important issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available approaches often yield a single model only, rely on specific assumptions, and/or use dedicated, heuristic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by appeal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several benefits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems.
Building biological models by inferring functional dependencies from experimental data is an important issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available approaches often yield a single model only, rely on specific assumptions, and/or use dedicated, heuristic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by appeal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several benefits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems.
Under natural conditions, plants are exposed to rapidly changing light intensities. To acclimate to such fluctuations, plants have evolved adaptive mechanisms that optimally exploit available light energy and simultaneously minimise damage of the photosynthetic apparatus through excess light. An important mechanism is the dissipation of excess excitation energy as heat which can be measured as nonphotochemical quenching of chlorophyll fluorescence (NPQ). In this paper, we present a highly simplified mathematical model that captures essential experimentally observed features of the short term adaptive quenching dynamics. We investigate the stationary and dynamic behaviour of the model and systematically analyse the dependence of characteristic system properties on key parameters such as rate constants and pool sizes. Comparing simulations with experimental data allows to derive conclusions about the validity of the simplifying assumptions and we further propose hypotheses regarding the role of the xanthophyll cycle in NPQ. We envisage that the presented theoretical description of the light reactions in conjunction with short term adaptive processes serves as a basis for the development of more detailed mechanistic models by which the molecular mechanisms of NPQ can be theoretically studied.
Indirect resource competition and interference are widely occurring mechanisms of interspecific interactions. We have studied the seasonal expression of these two interaction types within a two-species, boreal small mammal system. Seasons differ by resource availability, individual breeding state and intraspecific social system. Live-trapping methods were used to monitor space use and reproduction in 14 experimental populations of bank voles Myodes glareolus in large outdoor enclosures with and without a dominant competitor, the field vole Microtus agrestis. We further compared vole behaviour using staged dyadic encounters in neutral arenas in both seasons. Survival of the non-breeding overwintering bank voles was not affected by competition. In the spring, the numbers of male bank voles, but not of females, were reduced significantly in the competition populations. Bank vole home ranges expanded with vole density in the presence of competitors, indicating food limitation. A comparison of behaviour between seasons based on an analysis of similarity revealed an avoidance of costly aggression against opponents, independent of species. Interactions were more aggressive during the summer than during the winter, and heterospecific encounters were more aggressive than conspecific encounters. Based on these results, we suggest that interaction types and their respective mechanisms are not either-or categories and may change over the seasons. During the winter, energy constraints and thermoregulatory needs decrease direct aggression, but food constraints increase indirect resource competition. Direct interference appears in the summer, probably triggered by each individual's reproductive and hormonal state and the defence of offspring against conspecific and heterospecific intruders. Both interaction forms overlap in the spring, possibly contributing to spring declines in the numbers of subordinate species.
Indirect resource competition and interference are widely occurring mechanisms of interspecific interactions. We have studied the seasonal expression of these two interaction types within a two-species, boreal small mammal system. Seasons differ by resource availability, individual breeding state and intraspecific social system. Live-trapping methods were used to monitor space use and reproduction in 14 experimental populations of bank voles Myodes glareolus in large outdoor enclosures with and without a dominant competitor, the field vole Microtus agrestis. We further compared vole behaviour using staged dyadic encounters in neutral arenas in both seasons. Survival of the non-breeding overwintering bank voles was not affected by competition. In the spring, the numbers of male bank voles, but not of females, were reduced significantly in the competition populations. Bank vole home ranges expanded with vole density in the presence of competitors, indicating food limitation. A comparison of behaviour between seasons based on an analysis of similarity revealed an avoidance of costly aggression against opponents, independent of species. Interactions were more aggressive during the summer than during the winter, and heterospecific encounters were more aggressive than conspecific encounters. Based on these results, we suggest that interaction types and their respective mechanisms are not either–or categories and may change over the seasons. During the winter, energy constraints and thermoregulatory needs decrease direct aggression, but food constraints increase indirect resource competition. Direct interference appears in the summer, probably triggered by each individual’s reproductive and hormonal state and the defence of offspring against conspecific and heterospecific intruders. Both interaction forms overlap in the spring, possibly contributing to spring declines in the numbers of subordinate species.
A number of short-lived, iteroparous animal species have small broods in the early breeding season and larger broods in later breeding season. Brood size affects not only offspring size, but as recent results suggest, may also affect offspring's temperament, hormonal status, and aggression as adults. Most populations of short-lived, iteroparous mammals fluctuate predictably over the season, with low densities in winter, increasing densities in summer and a population peak in late summer followed by a population breakdown. If animals live only through parts of the season, possibly such differences in density and hence also in social environments among seasons require different personality types to increase individual fitness. We present data on behavior of European rabbits from a field enclosure study. These data clearly show that aggressiveness is higher in young from smaller litters than in young from larger litters, and smaller litters are usually born during the early breeding season. Moreover, our data suggest that behavioral types of the young rabbits are stable over time, at least during their subadult life. We suggest, that changes in mean litter size over the course of the breeding season may not only be a product of mothers' age or food availability, but may also have an adaptive function by preparing offspring characteristics for adulthood in a social environment undergoing predictable density changes within the season.