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The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.
Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood.
Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes.
Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.
DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.
Modern 3D geovisualization systems (3DGeoVSs) are complex and evolving systems that are required to be adaptable and leverage distributed resources, including massive geodata. This article focuses on 3DGeoVSs built based on the principles of service-oriented architectures, standards and image-based representations (SSI) to address practically relevant challenges and potentials. Such systems facilitate resource sharing and agile and efficient system construction and change in an interoperable manner, while exploiting images as efficient, decoupled and interoperable representations. The software architecture of a 3DGeoVS and its underlying visualization model have strong effects on the system's quality attributes and support various system life cycle activities. This article contributes a software reference architecture (SRA) for 3DGeoVSs based on SSI that can be used to design, describe and analyze concrete software architectures with the intended primary benefit of an increase in effectiveness and efficiency in such activities. The SRA integrates existing, proven technology and novel contributions in a unique manner. As the foundation for the SRA, we propose the generalized visualization pipeline model that generalizes and overcomes expressiveness limitations of the prevalent visualization pipeline model. To facilitate exploiting image-based representations (IReps), the SRA integrates approaches for the representation, provisioning and styling of and interaction with IReps. Five applications of the SRA provide proofs of concept for the general applicability and utility of the SRA. A qualitative evaluation indicates the overall suitability of the SRA, its applications and the general approach of building 3DGeoVSs based on SSI.
This paper reports a problematic case of unequivocally evidencing participant orientation to the projective force of some turn-initial demonstrative wh-clefts (DCs) within the framework of Conversation Analysis (CA) and Interactional Linguistics (IL). Conducting rhythmic analyses appears helpful in this regard, in that they disclose rhythmic regularities which suggest a speaker's orientation towards a projected turn continuation. In this particular case, rhythmic analyses can therefore be shown to meaningfully complement sequential analyses and analyses of turn-design, so as to gather additional evidence for participant orientations. In conclusion, I will point to possibly more extensive relations between rhythmicity and projection and proffer a tentative outlook for the usability of rhythmic analyses as an analytic tool in CA and IL.
Background
The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures.
Results
To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya.
Conclusions
The results suggests that, as in mice, moa tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa’s remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa.
Biosensors for the detection of benzaldehyde and g-aminobutyric acid (GABA) are reported using aldehyde oxidoreductase PaoABC from Escherichia coli immobilized in a polymer containing bound low potential osmium redox complexes. The electrically connected enzyme already electrooxidizes benzaldehyde at potentials below −0.15 V (vs. Ag|AgCl, 1 M KCl). The pH-dependence of benzaldehyde oxidation can be strongly influenced by the ionic strength. The effect is similar with the soluble osmium redox complex and therefore indicates a clear electrostatic effect on the bioelectrocatalytic efficiency of PaoABC in the osmium containing redox polymer. At lower ionic strength, the pH-optimum is high and can be switched to low pH-values at high ionic strength. This offers biosensing at high and low pH-values. A “reagentless” biosensor has been formed with enzyme wired onto a screen-printed electrode in a flow cell device. The response time to addition of benzaldehyde is 30 s, and the measuring range is between 10–150 µM and the detection limit of 5 µM (signal to noise ratio 3:1) of benzaldehyde. The relative standard deviation in a series (n = 13) for 200 µM benzaldehyde is 1.9%. For the biosensor, a response to succinic semialdehyde was also identified. Based on this response and the ability to work at high pH a biosensor for GABA is proposed by coimmobilizing GABA-aminotransferase (GABA-T) and PaoABC in the osmium containing redox polymer.
Biosensors for the detection of benzaldehyde and g-aminobutyric acid (GABA) are reported using aldehyde oxidoreductase PaoABC from Escherichia coli immobilized in a polymer containing bound low potential osmium redox complexes. The electrically connected enzyme already electrooxidizes benzaldehyde at potentials below −0.15 V (vs. Ag|AgCl, 1 M KCl). The pH-dependence of benzaldehyde oxidation can be strongly influenced by the ionic strength. The effect is similar with the soluble osmium redox complex and therefore indicates a clear electrostatic effect on the bioelectrocatalytic efficiency of PaoABC in the osmium containing redox polymer. At lower ionic strength, the pH-optimum is high and can be switched to low pH-values at high ionic strength. This offers biosensing at high and low pH-values. A “reagentless” biosensor has been formed with enzyme wired onto a screen-printed electrode in a flow cell device. The response time to addition of benzaldehyde is 30 s, and the measuring range is between 10–150 µM and the detection limit of 5 µM (signal to noise ratio 3:1) of benzaldehyde. The relative standard deviation in a series (n = 13) for 200 µM benzaldehyde is 1.9%. For the biosensor, a response to succinic semialdehyde was also identified. Based on this response and the ability to work at high pH a biosensor for GABA is proposed by coimmobilizing GABA-aminotransferase (GABA-T) and PaoABC in the osmium containing redox polymer.
We present an electrochemical MIP sensor for tamoxifen (TAM)-a nonsteroidal anti-estrogen-which is based on the electropolymerisation of an O-phenylenediamine. resorcinol mixture directly on the electrode surface in the presence of the template molecule. Up to now only. bulk. MIPs for TAM have been described in literature, which are applied for separation in chromatography columns. Electro-polymerisation of the monomers in the presence of TAM generated a film which completely suppressed the reduction of ferricyanide. Removal of the template gave a markedly increased ferricyanide signal, which was again suppressed after rebinding as expected for filling of the cavities by target binding. The decrease of the ferricyanide peak of the MIP electrode depended linearly on the TAM concentration between 1 and 100 nM. The TAM-imprinted electrode showed a 2.3 times higher recognition of the template molecule itself as compared to its metabolite 4-hydroxytamoxifen and no cross-reactivity with the anticancer drug doxorubucin was found. Measurements at + 1.1 V caused a fouling of the electrode surface, whilst pretreatment of TAM with peroxide in presence of HRP generated an oxidation product which was reducible at 0 mV, thus circumventing the polymer formation and electrochemical interferences.
The structures and synthesis of polyzwitterions ("polybetaines") are reviewed, emphasizing the literature of the past decade. Particular attention is given to the general challenges faced, and to successful strategies to obtain polymers with a true balance of permanent cationic and anionic groups, thus resulting in an overall zero charge. Also, the progress due to applying new methodologies from general polymer synthesis, such as controlled polymerization methods or the use of "click" chemical reactions is presented. Furthermore, the emerging topic of responsive ("smart") polyzwitterions is addressed. The considerations and critical discussions are illustrated by typical examples.
Dimensional psychiatry
(2014)
A dimensional approach in psychiatry aims to identify core mechanisms of mental disorders across nosological boundaries.
We compared anticipation of reward between major psychiatric disorders, and investigated whether reward anticipation is impaired in several mental disorders and whether there is a common psychopathological correlate (negative mood) of such an impairment.
We used functional magnetic resonance imaging (fMRI) and a monetary incentive delay (MID) task to study the functional correlates of reward anticipation across major psychiatric disorders in 184 subjects, with the diagnoses of alcohol dependence (n = 26), schizophrenia (n = 44), major depressive disorder (MDD, n = 24), bipolar disorder (acute manic episode, n = 13), attention deficit/hyperactivity disorder (ADHD, n = 23), and healthy controls (n = 54). Subjects' individual Beck Depression Inventory-and State-Trait Anxiety Inventory-scores were correlated with clusters showing significant activation during reward anticipation.
During reward anticipation, we observed significant group differences in ventral striatal (VS) activation: patients with schizophrenia, alcohol dependence, and major depression showed significantly less ventral striatal activation compared to healthy controls. Depressive symptoms correlated with dysfunction in reward anticipation regardless of diagnostic entity. There was no significant correlation between anxiety symptoms and VS functional activation.
Our findings demonstrate a neurobiological dysfunction related to reward prediction that transcended disorder categories and was related to measures of depressed mood. The findings underline the potential of a dimensional approach in psychiatry and strengthen the hypothesis that neurobiological research in psychiatric disorders can be targeted at core mechanisms that are likely to be implicated in a range of clinical entities.
Background
Nucleic acid amplification is the most sensitive and specific method to detect Plasmodium falciparum. However the polymerase chain reaction remains laboratory-based and has to be conducted by trained personnel. Furthermore, the power dependency for the thermocycling process and the costly equipment necessary for the read-out are difficult to cover in resource-limited settings. This study aims to develop and evaluate a combination of isothermal nucleic acid amplification and simple lateral flow dipstick detection of the malaria parasite for point-of-care testing.
Methods
A specific fragment of the 18S rRNA gene of P. falciparum was amplified in 10 min at a constant 38°C using the isothermal recombinase polymerase amplification (RPA) method. With a unique probe system added to the reaction solution, the amplification product can be visualized on a simple lateral flow strip without further labelling. The combination of these methods was tested for sensitivity and specificity with various Plasmodium and other protozoa/bacterial strains, as well as with human DNA. Additional investigations were conducted to analyse the temperature optimum, reaction speed and robustness of this assay.
Results
The lateral flow RPA (LF-RPA) assay exhibited a high sensitivity and specificity. Experiments confirmed a detection limit as low as 100 fg of genomic P. falciparum DNA, corresponding to a sensitivity of approximately four parasites per reaction. All investigated P. falciparum strains (n = 77) were positively tested while all of the total 11 non-Plasmodium samples, showed a negative test result. The enzymatic reaction can be conducted under a broad range of conditions from 30-45°C with high inhibitory concentration of known PCR inhibitors. A time to result of 15 min from start of the reaction to read-out was determined.
Conclusions
Combining the isothermal RPA and the lateral flow detection is an approach to improve molecular diagnostic for P. falciparum in resource-limited settings. The system requires none or only little instrumentation for the nucleic acid amplification reaction and the read-out is possible with the naked eye. Showing the same sensitivity and specificity as comparable diagnostic methods but simultaneously increasing reaction speed and dramatically reducing assay requirements, the method has potential to become a true point-of-care test for the malaria parasite.
Flood damage has increased significantly and is expected to rise further in many parts of the world. For assessing potential changes in flood risk, this paper presents an integrated model chain quantifying flood hazards and losses while considering climate and land use changes. In the case study region, risk estimates for the present and the near future illustrate that changes in flood risk by 2030 are relatively low compared to historic periods. While the impact of climate change on the flood hazard and risk by 2030 is slight or negligible, strong urbanisation associated with economic growth contributes to a remarkable increase in flood risk. Therefore, it is recommended to frequently consider land use scenarios and economic developments when assessing future flood risks. Further, an adapted and sustainable risk management is necessary to encounter rising flood losses, in which non-structural measures are becoming more and more important. The case study demonstrates that adaptation by non-structural measures such as stricter land use regulations or enhancement of private precaution is capable of reducing flood risk by around 30 %. Ignoring flood risks, in contrast, always leads to further increasing losses-with our assumptions by 17 %. These findings underline that private precaution and land use regulation could be taken into account as low cost adaptation strategies to global climate change in many flood prone areas. Since such measures reduce flood risk regardless of climate or land use changes, they can also be recommended as no-regret measures.
The Runge-Kutta type regularization method was recently proposed as a potent tool for the iterative solution of nonlinear ill-posed problems. In this paper we analyze the applicability of this regularization method for solving inverse problems arising in atmospheric remote sensing, particularly for the retrieval of spheroidal particle distribution. Our numerical simulations reveal that the Runge-Kutta type regularization method is able to retrieve two-dimensional particle distributions using optical backscatter and extinction coefficient profiles, as well as depolarization information.
Stress drop is a key factor in earthquake mechanics and engineering seismology. However, stress drop calculations based on fault slip can be significantly biased, particularly due to subjectively determined smoothing conditions in the traditional least-square slip inversion. In this study, we introduce a mechanically constrained Bayesian approach to simultaneously invert for fault slip and stress drop based on geodetic measurements. A Gaussian distribution for stress drop is implemented in the inversion as a prior. We have done several synthetic tests to evaluate the stability and reliability of the inversion approach, considering different fault discretization, fault geometries, utilized datasets, and variability of the slip direction, respectively. We finally apply the approach to the 2010 M8.8 Maule earthquake and invert for the coseismic slip and stress drop simultaneously. Two fault geometries from the literature are tested. Our results indicate that the derived slip models based on both fault geometries are similar, showing major slip north of the hypocenter and relatively weak slip in the south, as indicated in the slip models of other studies. The derived mean stress drop is 5-6 MPa, which is close to the stress drop of similar to 7 MPa that was independently determined according to force balance in this region Luttrell et al. (J Geophys Res, 2011). These findings indicate that stress drop values can be consistently extracted from geodetic data.
In a recent paper, the Lefschetz number for endomorphisms (modulo trace class operators) of sequences of trace class curvature was introduced. We show that this is a well defined, canonical extension of the classical Lefschetz number and establish the homotopy invariance of this number. Moreover, we apply the results to show that the Lefschetz fixed point formula holds for geometric quasiendomorphisms of elliptic quasicomplexes.
This reference paper describes the sampling and contents of the IZA Evaluation Dataset Survey and outlines its vast potential for research in labor economics. The data have been part of a unique IZA project to connect administrative data from the German Federal Employment Agency with innovative survey data to study the out-mobility of individuals to work. This study makes the survey available to the research community as a Scientific Use File by explaining the development, structure, and access to the data. Furthermore, it also summarizes previous findings with the survey data.
Fluid intelligence (fluid IQ), defined as the capacity for rapid problem solving and behavioral adaptation, is known to be modulated by learning and experience. Both stressful life events (SLES) and neural correlates of learning [specifically, a key mediator of adaptive learning in the brain, namely the ventral striatal representation of prediction errors (PE)] have been shown to be associated with individual differences in fluid IQ. Here, we examine the interaction between adaptive learning signals (using a well-characterized probabilistic reversal learning task in combination with fMRI) and SLES on fluid IQ measures. We find that the correlation between ventral striatal BOLD PE and fluid IQ, which we have previously reported, is quantitatively modulated by the amount of reported SLES. Thus, after experiencing adversity, basic neuronal learning signatures appear to align more closely with a general measure of flexible learning (fluid IQ), a finding complementing studies on the effects of acute stress on learning. The results suggest that an understanding of the neurobiological correlates of trait variables like fluid IQ needs to take socioemotional influences such as chronic stress into account.
The Arabidopsis Kinome
(2014)
Background
Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication.
Results
The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases.
Conclusions
The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.
Background
In the past, plyometric training (PT) has been predominantly performed on stable surfaces. The purpose of this pilot study was to examine effects of a 7-week lower body PT on stable vs. unstable surfaces. This type of exercise condition may be denoted as metastable equilibrium.
Methods
Thirty-three physically active male sport science students (age: 24.1 ± 3.8 years) were randomly assigned to a PT group (n = 13) exercising on stable (STAB) and a PT group (n = 20) on unstable surfaces (INST). Both groups trained countermovement jumps, drop jumps, and practiced a hurdle jump course. In addition, high bar squats were performed. Physical fitness tests on stable surfaces (hexagonal obstacle test, countermovement jump, hurdle drop jump, left-right hop, dynamic and static balance tests, and leg extension strength) were used to examine the training effects.
Results
Significant main effects of time (ANOVA) were found for the countermovement jump, hurdle drop jump, hexagonal test, dynamic balance, and leg extension strength. A significant interaction of time and training mode was detected for the countermovement jump in favor of the INST group. No significant improvements were evident for either group in the left-right hop and in the static balance test.
Conclusions
These results show that lower body PT on unstable surfaces is a safe and efficient way to improve physical performance on stable surfaces.
This paper reports a problematic case of unequivocally evidencing participant orientation to the projective force of some turn-initial demonstrative wh-clefts (DCs) within the framework of Conversation Analysis (CA) and Interactional Linguistics (IL). Conducting rhythmic analyses appears helpful in this regard, in that they disclose rhythmic regularities which suggest a speaker's orientation towards a projected turn continuation. In this particular case, rhythmic analyses can therefore be shown to meaningfully complement sequential analyses and analyses of turn-design, so as to gather additional evidence for participant orientations. In conclusion, I will point to possibly more extensive relations between rhythmicity and projection and proffer a tentative outlook for the usability of rhythmic analyses as an analytic tool in CA and IL.
The B fields in OB stars (BOB) survey is an ESO large programme collecting spectropolarimetric observations for a large number of early-type stars in order to study the occurrence rate, properties, and ultimately the origin of magnetic fields in massive stars. As of July 2014, a total of 98 objects were observed over 20 nights with FORS2 and HARPSpol. Our preliminary results indicate that the fraction of magnetic OB stars with an organised, detectable field is low. This conclusion, now independently reached by two different surveys, has profound implications for any theoretical model attempting to explain the field formation in these objects. We discuss in this contribution some important issues addressed by our observations (e.g., the lower bound of the field strength) and the discovery of some remarkable objects.
Nested application conditions generalise the well-known negative application conditions and are important for several application domains. In this paper, we present Local Church-Rosser, Parallelism, Concurrency and Amalgamation Theorems for rules with nested application conditions in the framework of M-adhesive categories, where M-adhesive categories are slightly more general than weak adhesive high-level replacement categories. Most of the proofs are based on the corresponding statements for rules without application conditions and two shift lemmas stating that nested application conditions can be shifted over morphisms and rules.
A key problem in automatic annotation of historical corpora is inconsistent spelling. Because the spelling of some word forms can differ between texts, a language model trained on already annotated treebanks may fail to recognize known word forms due to differences in spelling. In the present work, we explore the feasibility of an unsupervised method for spelling-adjustment for the purpose of improved part of speech (POS) tagging. To this end, we present a method for spelling normalization based on weighted edit distances, which exploits within-text spelling variation. We then evaluate the improvement in taging accuracy resulting from between-texts spelling normalization in two tagging experiments on several Early New High German (ENHG) texts.
Recently, interest in collecting and mining large sets of educational data on student background and performance to conduct research on learning and instruction has developed as an area generally referred to as learning analytics. Higher education leaders are recognising the value of learning analytics for improving not only learning and teaching but also the entire educational arena. However, theoretical concepts and empirical evidence need to be generated within the fast evolving field of learning analytics. In this paper, we introduce a holistic learning analytics framework. Based on this framework, student, learning, and curriculum profiles have been developed which include relevant static and dynamic parameters for facilitating the learning analytics framework. Based on the theoretical model, an empirical study was conducted to empirically validate the parameters included in the student profile. The paper concludes with practical implications and issues for future research.
Portal Wissen = Time
(2014)
“What then is time?”, Augustine of Hippo sighs melancholically in Book XI of “Confessions” and continues, “If no one asks me, I know; if I want to explain it to a questioner, I don’t know.” Even today, 1584 years after Augustine, time still appears mysterious. Treatises about the essence of time fill whole libraries – and this magazine.
However, questions of essence are alien to modern sciences. Time is – at least in physics – unproblematic: “Time is defined so that motion looks simple”, briefly and prosaically phrased, waves goodbye to Augustine’s riddle and to the Newtonian concept of absolute time, whose mathematical flow can only be approximately recorded with earthly instruments anyway.
In our everyday language and even in science we still speak of the flow of time but time has not been a natural condition for quite a while now. It is rather a conventional order parameter for change and movement. Processes are arranged by using a class of processes as a counting system in order to compare other processes and to organize them with the help of the temporary categories “before”, “during”, and “after”.
During Galileo’s time one’s own pulse was seen as the time standard for the flight of cannon balls. More sophisticated examination methods later made this seem too impractical. The distance-time diagrams of free-flying cannon balls turned out to be rather imprecise, difficult to replicate, and in no way “simple”. Nowadays, we use cesium atoms. A process is said to take one second when a caesium-133 atom completes 9,192,631,770 periods of the radiation corresponding to the transition between two hyperfine levels of the ground state. A meter is the length of the path travelled by light in a vacuum in exactly 1/299,792,458 of a second. Fortunately, these data are hard-coded in the Global Positioning System GPS so users do not have to reenter them each time they want to know where they are. In the future, however, they might have to download an app because the time standard has been replaced by sophisticated transitions to ytterbium.
The conventional character of the time concept should not tempt us to believe that everything is somehow relative and, as a result, arbitrary. The relation of one’s own pulse to an atomic clock is absolute and as real as the relation of an hourglass to the path of the sun. The exact sciences are relational sciences. They are not about the thing-initself as Newton and Kant dreamt, but rather about relations as Leibniz and, later, Mach pointed out.
It is not surprising that the physical time standard turned out to be rather impractical for other scientists. The psychology of time perception tells us – and you will all agree – that the perceived age is quite different from the physical age. The older we get the shorter the years seem. If we simply assume that perceived duration is inversely related to physical age and that a 20-year old also perceives a physical year as a psychological one, we come to the surprising discovery that at 90 years we are 90 years old. With an assumed life expectancy of 90 years, 67% (or 82%) of your felt lifetime is behind you at the age of 20 (or 40) physical years.
Before we start to wallow in melancholy in the face of the “relativity of time”, let me again quote Augustine. “But at any rate this much I dare affirm I know: that if nothing passed there would be no past time; if nothing were approaching, there would be no future time; if nothing were, there would be no present time.” Well, – or as Bob Dylan sings “The times they are a-changin”.
I wish you an exciting time reading this issue.
Prof. Martin Wilkens
Professor of Quantum Optics
Portal Wissen = Believe
(2014)
People want to know what is real. Children enjoy listening to a story but when my children were about four years old they started asking whether the story really happened or was just invented. Likewise, only on a higher level, our academic curiosity is fuelled by our interest in knowing what is real. When we analyze poetic texts or dreams we are trying to distinguish between the facts (e.g. neurological ones or linguistic structures) and merely assumed influences. Ideally we can present results that were logically understood by others and that we can repeat empirically. But in most cases this is not possible. We cannot read every book and cannot look through every microscope, not even within our own discipline. In the world we live in we depend on trusting the information of others, like how to get to the train station or what the weather is like in Ulaanbataar. This is why we are used to believing others, our friends or the news anchors. This is not a childish behavior but a necessity. Of course, it is risky because they could all be lying to us, like in a Truman Show situation. The only time we are able to know that we are in reality is when we transcend our selfconsciousness and when we accept two propositions: first, that we are not only objects but also subjects in the consciousness of others and second that our dialogic relations are again observed by a third party that is not part of this intersubjective world.
For religious people this is “belief” - belief as the assumption that all human relations only become real, serious and beyond any doubt if they know they are under the eyes of God. Only before Him something is in itself and not only “for me” or “among us”. That is why biblical language distinguishes between three forms of belief: the relationship with the world of things (“to believe that”), the relationship to the world of subjects (“to believe somebody”) and the assumption of a subjective supernatural reality (“to believe in” or “faith”). From an academic point of view belief is a holistic hypothesis. Belief is not the opposite of knowledge but it is the attempt to save reality from doubt by comprehending the fragile empirical world as an expression of a stable transcendent world.
When I talk to students they often ask not only about what I know but what I believe. As a professor for Religious Studies and a believing Catholic I am caught in the middle. On the one hand, it is my duty as a professor to doubt everything, i.e. to attribute each religious text to its historical context and sociological functions. On the other hand, I, as a Christian, consider certain religious documents, in my case the Bible, an interpretable but nevertheless irreversible, revealed text about the origin of reality. On weekdays the New Testament is a collection of ancient writings among many others, on Sundays it is the revelation. You can make a clear distinction between these two perspectives but it is difficult to decide whether doubt or belief is more real.
This issue of “Portal Wissen” explores this dual relationship of belief. What is the attitude of science towards belief – is it a religious one? Where does science bring things to light that we can hardly believe or that make us believe (again)? What happens if research clears up erroneous assumptions or myths? Is science able to investigate things that are convincing but inexplicable? How can it maintain its credibility and develop even so?
These questions appear again and again in the contributions of this “Portal Wissen”. They form a manifold, exciting and surprising picture of the research projects and academics at the University of Potsdam. Believe me, it will be an enjoyable read.
Prof. Johann Hafner
Professor of Religious Studies with Focus on Christianity Dean of the Faculty of Arts
We report on the development of an on-chip RPA (recombinase polymerase amplification) with simultaneous multiplex isothermal amplification and detection on a solid surface. The isothermal RPA was applied to amplify specific target sequences from the pathogens Neisseria gonorrhoeae, Salmonella enterica and methicillin-resistant Staphylococcus aureus (MRSA) using genomic DNA. Additionally, a positive plasmid control was established as an internal control. The four targets were amplified simultaneously in a quadruplex reaction. The amplicon is labeled during on-chip RPA by reverse oligonucleotide primers coupled to a fluorophore. Both amplification and spatially resolved signal generation take place on immobilized forward primers bount to expoxy-silanized glass surfaces in a pump-driven hybridization chamber. The combination of microarray technology and sensitive isothermal nucleic acid amplification at 38 °C allows for a multiparameter analysis on a rather small area. The on-chip RPA was characterized in terms of reaction time, sensitivity and inhibitory conditions. A successful enzymatic reaction is completed in <20 min and results in detection limits of 10 colony-forming units for methicillin-resistant Staphylococcus aureus and Salmonella enterica and 100 colony-forming units for Neisseria gonorrhoeae. The results show this method to be useful with respect to point-of-care testing and to enable simplified and miniaturized nucleic acid-based diagnostics.
The use of silver nanoparticles in medical and consumer products such as wound dressings, clothing and cosmetic has increased significantly in recent years. Still, the influence of these particles on our health and especially on our brain, has not been examined adequately up to now. We studied the influence of AgEO- (Ethylene Oxide) and AgCitrate-Nanoparticles (NPs) on the protective barriers of the brain, namely the blood-brain barrier (BBB) and the blood-cerebrospinal fluid (blood-CSF) barrier in vitro. The NPs toxicity was evaluated by examining changes in membrane integrity, cell morphology, barrier properties, oxidative stress and inflammatory reactions. AgNPs decreased cell viability, disturbed barrier integrity and tight junctions and triggered oxidative stress and DNA strand breaks. However, all mentioned effects were, at least partly, suppressed by a Citrate-coating and were most pronounced in the cells of the BBB as compared to the epithelial cells representing the blood-CSF barrier. AgEO- but not AgCitrate-NPs also triggered an inflammatory reaction in porcine brain capillary endothelial cells (PBCEC), which represent the BBB.
Our data indicate that AgNPs may cause adverse effects within the barriers of the brain, but their toxicity can be reduced by choosing an appropriate coating material.
Ultraschall Berlin
(2014)
The Babylonian Talmud (BT) attributes the idea of committing a transgression for the sake of God to R. Nahman b. Isaac (RNBI). RNBI's statement appears in two parallel sugyot in the BT (Nazir 23a; Horayot 10a). Each sugya has four textual witnesses. By comparing these textual witnesses, this paper will attempt to reconstruct the sugya's earlier (or, what some might term, original) dialectical form, from which the two familiar versions of the text in Nazir and Horayot evolved. This article reveals the specific ways in which, value-laden conceptualizations have a major impact on the Talmud's formulation, as we know it today.
Ultraschall Berlin
(2014)
We propose a novel cluster-based reduced-order modelling (CROM) strategy for unsteady flows. CROM combines the cluster analysis pioneered in Gunzburger's group (Burkardt, Gunzburger & Lee, Comput. Meth. Appl. Mech. Engng, vol. 196, 2006a, pp. 337-355) and transition matrix models introduced in fluid dynamics in Eckhardt's group (Schneider, Eckhardt & Vollmer, Phys. Rev. E, vol. 75, 2007, art. 066313). CROM constitutes a potential alternative to POD models and generalises the Ulam-Galerkin method classically used in dynamical systems to determine a finite-rank approximation of the Perron-Frobenius operator. The proposed strategy processes a time-resolved sequence of flow snapshots in two steps. First, the snapshot data are clustered into a small number of representative states, called centroids, in the state space. These centroids partition the state space in complementary non-overlapping regions (centroidal Voronoi cells). Departing from the standard algorithm, the probabilities of the clusters are determined, and the states are sorted by analysis of the transition matrix. Second, the transitions between the states are dynamically modelled using a Markov process. Physical mechanisms are then distilled by a refined analysis of the Markov process, e. g. using finite-time Lyapunov exponent (FTLE) and entropic methods. This CROM framework is applied to the Lorenz attractor (as illustrative example), to velocity fields of the spatially evolving incompressible mixing layer and the three-dimensional turbulent wake of a bluff body. For these examples, CROM is shown to identify non-trivial quasi-attractors and transition processes in an unsupervised manner. CROM has numerous potential applications for the systematic identification of physical mechanisms of complex dynamics, for comparison of flow evolution models, for the identification of precursors to desirable and undesirable events, and for flow control applications exploiting nonlinear actuation dynamics.
claspfolio 2
(2014)
Building on the award-winning, portfolio-based ASP solver claspfolio, we present claspfolio 2, a modular and open solver architecture that integrates several different portfolio-based algorithm selection approaches and techniques. The claspfolio 2 solver framework supports various feature generators, solver selection approaches, solver portfolios, as well as solver-schedule-based pre-solving techniques. The default configuration of claspfolio 2 relies on a light-weight version of the ASP solver clasp to generate static and dynamic instance features. The flexible open design of claspfolio 2 is a distinguishing factor even beyond ASP. As such, it provides a unique framework for comparing and combining existing portfolio-based algorithm selection approaches and techniques in a single, unified framework. Taking advantage of this, we conducted an extensive experimental study to assess the impact of different feature sets, selection approaches and base solver portfolios. In addition to gaining substantial insights into the utility of the various approaches and techniques, we identified a default configuration of claspfolio 2 that achieves substantial performance gains not only over clasp's default configuration and the earlier version of claspfolio, but also over manually tuned configurations of clasp.
Research in rodents has shown that dietary vitamin A reduces body fat by enhancing fat mobilisation and energy utilisation; however, their effects in growing dogs remain unclear. In the present study, we evaluated the development of body weight and body composition and compared observed energy intake with predicted energy intake in forty-nine puppies from two breeds (twenty-four Labrador Retriever (LAB) and twenty-five Miniature Schnauzer (MS)). A total of four different diets with increasing vitamin A content between 5.24 and 104.80 mu mol retinol (5000-100 000 IU vitamin A)/4184 kJ (1000 kcal) metabolisable energy were fed from the age of 8 weeks up to 52 (MS) and 78 weeks (LAB). The daily energy intake was recorded throughout the experimental period. The body condition score was evaluated weekly using a seven-category system, and food allowances were adjusted to maintain optimal body condition. Body composition was assessed at the age of 26 and 52 weeks for both breeds and at the age of 78 weeks for the LAB breed only using dual-energy X-ray absorptiometry. The growth curves of the dogs followed a breed-specific pattern. However, data on energy intake showed considerable variability between the two breeds as well as when compared with predicted energy intake. In conclusion, the data show that energy intakes of puppies particularly during early growth are highly variable; however, the growth pattern and body composition of the LAB and MS breeds are not affected by the intake of vitamin A at levels up to 104.80 mu mol retinol (100 000 IU vitamin A)/4184 kJ (1000 kcal).
The complementary advantages of high-rate Global Positioning System (GPS) and accelerometer observations for measuring seismic ground motion have been recognised in previous research. Here we propose an approach of tight integration of GPS and accelerometer measurements. The baseline shifts of the accelerometer are introduced as unknown parameters and estimated by a random walk process in the Precise Point Positioning (PPP) solution. To demonstrate the performance of the new strategy, we carried out several experiments using collocated GPS and accelerometer. The experimental results show that the baseline shifts of the accelerometer are automatically corrected, and high precision coseismic information of strong ground motion can be obtained in real-time. Additionally, the convergence and precision of the PPP is improved by the combined solution.
Object and action naming in Russian- and German- speaking monolingual and bilingual children*
(2014)
The present study investigates the influence of word category on naming performance in two populations: bilingual and monolingual children. The question is whether and, if so, to what extent monolingual and bilingual children differ with respect to noun and verb naming and whether a noun bias exists in the lexical abilities of bilingual children. Picture naming of objects and actions by Russian-German bilingual children (aged 4-7 years) was compared to age-matched monolingual children. The results clearly demonstrate a naming deficit of bilingual children in comparison to monolingual children that increases with age. Noun learning is more fragile in bilingual contexts than is verb learning. In bilingual language acquisition, nouns do not predominate over verbs as much as is seen in monolingual German and Russian children. The results are discussed with respect to semantic-conceptual aspects and language-specific features of nouns and verbs, and the impact of input on the acquisition of these word categories.
Bats are important components in tropical mammal assemblages. Unravelling the mechanisms allowing multiple syntopic bat species to coexist can provide insights into community ecology. However, dietary information on component species of these assemblages is often difficult to obtain. Here we measuredstable carbon and nitrogen isotopes in hair samples clipped from the backs of 94 specimens to indirectly examine whether trophic niche differentiation and microhabitat segregation explain the coexistence of 16 bat species at Ankarana, northern Madagascar. The assemblage ranged over 4.4% in delta N-15 and was structured into two trophic levels with phytophagous Pteropodidae as primary consumers (c. 3% enriched over plants) and different insectivorous bats as secondary consumers (c. 4% enriched over primary consumers). Bat species utilizing different microhabitats formed distinct isotopic clusters (metric analyses of delta C-13-delta N-15 bi-plots), but taxa foraging in the same microhabitat did not show more pronounced trophic differentiation than those occupying different microhabitats. As revealed by multivariate analyses, no discernible feeding competition was found in the local assemblage amongst congeneric species as compared with non-congeners. In contrast to ecological niche theory, but in accordance with studies on New and Old World bat assemblages, competitive interactions appear to be relaxed at Ankarana and not a prevailing structuring force.
Regular and irregular inflection in children's production has been examined in many previous studies. Yet, little is known about the processes involved in children's recognition of inflected words. To gain insight into how children process inflected words, the current study examines regular -t and irregular -n participles of German using the cross-modal priming technique testing 108 monolingual German-speaking children in two age groups (group I, mean age: 8;4, group II, mean age: 9;9) and a control group of.. adults. Although both age groups of children had the same full priming effect as adults for -t forms, only children of age group II showed an adult-like (partial) priming effect for -n participles. We argue that children (within the age range tested) employ the same mechanisms for regular inflection as adults but that the lexical retrieval processes required for irregular forms become more efficient when children get older.
This study investigates whether number dissimilarities on subject and object DPs facilitate the comprehension of subject-and object-extracted centre-embedded relative clauses in children with Grammatical Specific Language Impairment (G-SLI). We compared the performance of a group of English-speaking children with G-SLI (mean age: 12; 11) with that of two groups of younger typically developing (TD) children, matched on grammar and receptive vocabulary, respectively. All groups were more accurate on subject-extracted relative clauses than object-extracted ones and, crucially, they all showed greater accuracy for sentences with dissimilar number features (i.e., one singular, one plural) on the head noun and the embedded DP. These findings are interpreted in the light of current psycholinguistic models of sentence comprehension in TD children and provide further insight into the linguistic nature of G-SLI.
Two experiments tested how faithfully German children aged 4; 5 to 5; 6 reproduce ditransitive sentences that are unmarked or marked with respect to word order and focus (Exp1) or definiteness (Exp2). Adopting an optimality theory (OT) approach, it is assumed that in the German adult grammar word order is ranked lower than focus and definiteness. Faithfulness of children's reproductions decreased as markedness of inputs increased; unmarked structures were reproduced most faithfully and unfaithful outputs had most often an unmarked form. Consistent with the OT proposal, children were more tolerant against inputs marked for word order than for focus; in conflict with the proposal, children were less tolerant against inputs marked for word order than for definiteness. Our results suggest that the linearization of objects in German double object constructions is affected by focus and definiteness, but that prosodic principles may have an impact on the position of a focused constituent.
Masked priming research with late (non-native) bilinguals has reported facilitation effects following morphologically derived prime words (scanner - scan). However, unlike for native speakers, there are suggestions that purely orthographic prime-target overlap (scandal - scan) also produces priming in non-native visual word recognition. Our study directly compares orthographically related and derived prime-target pairs. While native readers showed morphological but not formal overlap priming, the two prime types yielded the same magnitudes of facilitation for non-natives. We argue that early word recognition processes in a non-native language are more influenced by surface-form properties than in one's native language.
In the aftermath of the severe flooding in Central Europe in August 2002, a number of changes in flood policies were launched in Germany and other European countries, aiming at improved risk management. The question arises as to whether these changes have already had an impact on the residents' ability to cope with floods, and whether flood-affected private households are now better prepared than they were in 2002. Therefore, computer-aided telephone interviews with private households in Germany that suffered from property damage due to flooding in 2005, 2006, 2010 or 2011 were performed and analysed with respect to flood awareness, precaution, preparedness and recovery. The data were compared to a similar investigation conducted after the flood in 2002.
After the flood in 2002, the level of private precautions taken increased considerably. One contributing factor is the fact that, in general, a larger proportion of people knew that they were at risk of flooding. The best level of precaution was found before the flood events in 2006 and 2011. The main reason for this might be that residents had more experience with flooding than residents affected in 2005 or 2010. Yet, overall, flood experience and knowledge did not necessarily result in building retrofitting or flood-proofing measures, which are considered as mitigating damages most effectively. Hence, investments still need to be stimulated in order to reduce future damage more efficiently.
Early warning and emergency responses were substantially influenced by flood characteristics. In contrast to flood-affected people in 2006 or 2011, people affected by flooding in 2005 or 2010 had to deal with shorter lead times and therefore had less time to take emergency measures. Yet, the lower level of emergency measures taken also resulted from the people's lack of flood experience and insufficient knowledge of how to protect themselves. Overall, it was noticeable that these residents suffered from higher losses. Therefore, it is important to further improve early warning systems and communication channels, particularly in hilly areas with rapid-onset flooding.
Extreme weather events are likely to occur more often under climate change and the resulting effects on ecosystems could lead to a further acceleration of climate change. But not all extreme weather events lead to extreme ecosystem response. Here, we focus on hazardous ecosystem behaviour and identify coinciding weather conditions. We use a simple probabilistic risk assessment based on time series of ecosystem behaviour and climate conditions. Given the risk assessment terminology, vulnerability and risk for the previously defined hazard are estimated on the basis of observed hazardous ecosystem behaviour.
We apply this approach to extreme responses of terrestrial ecosystems to drought, defining the hazard as a negative net biome productivity over a 12-month period. We show an application for two selected sites using data for 1981-2010 and then apply the method to the pan-European scale for the same period, based on numerical modelling results (LPJmL for ecosystem behaviour; ERA-Interim data for climate).
Our site-specific results demonstrate the applicability of the proposed method, using the SPEI to describe the climate condition. The site in Spain provides an example of vulnerability to drought because the expected value of the SPEI is 0.4 lower for hazardous than for non-hazardous ecosystem behaviour. In northern Germany, on the contrary, the site is not vulnerable to drought because the SPEI expectation values imply wetter conditions in the hazard case than in the non-hazard case.
At the pan-European scale, ecosystem vulnerability to drought is calculated in the Mediterranean and temperate region, whereas Scandinavian ecosystems are vulnerable under conditions without water shortages. These first model- based applications indicate the conceptual advantages of the proposed method by focusing on the identification of critical weather conditions for which we observe hazardous ecosystem behaviour in the analysed data set. Application of the method to empirical time series and to future climate would be important next steps to test the approach.
Ausgehend von der typischen IT‐Infrastruktur für E‐Learning an Hochschulen auf der einen Seite sowie vom bisherigen Stand der Forschung zu Personal Learning Environments (PLEs) auf der anderen Seite zeigt dieser Beitrag auf, wie bestehende Werkzeuge bzw. Dienste zusammengeführt und für die Anforderungen der modernen, rechnergestützten Präsenzlehre aufbereitet werden können. Für diesen interdisziplinären Entwicklungsprozess bieten sowohl klassische Softwareentwicklungsverfahren als auch bestehende PLE‐Modelle wenig Hilfestellung an. Der Beitrag beschreibt die in einem campusweiten Projekt an der Universität Potsdam verfolgten Ansätze und die damit erzielten Ergebnisse. Dafür werden zunächst typische Lehr‐/Lern‐bzw. Kommunikations‐Szenarien identifiziert, aus denen Anforderungen an eine unterstützende Plattform abgeleitet werden. Dies führt zu einer umfassenden Sammlung zu berücksichtigender Dienste und deren Funktionen, die gemäß den Spezifika ihrer Nutzung in ein Gesamtsystem zu integrieren sind. Auf dieser Basis werden grundsätzliche Integrationsansätze und technische Details dieses Mash‐Ups in einer Gesamtschau aller relevanten Dienste betrachtet und in eine integrierende Systemarchitektur überführt. Deren konkrete Realisierung mit Hilfe der Portal‐Technologie Liferay wird dargestellt, wobei die eingangs definierten Szenarien aufgegriffen und exemplarisch vorgestellt werden. Ergänzende Anpassungen im Sinne einer personalisierbaren bzw. adaptiven Lern‐(und Arbeits‐)Umgebung werden ebenfalls unterstützt und kurz aufgezeigt.