Positional information, positional error, and read-out precision in morphogenesis: a mathematical framework

The concept of positional information is central to our understanding of how cells in a multicellular structure determine their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine which features of expression patterns increase or decrease positional information. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with single cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail

Rapid changes in ice core gas records Part 2: Understanding the rapid rise in atmospheric CO2 at the onset of the Bølling/Allerød

During the last glacial/interglacial transition the Earth's climate underwent rapid changes around 14.6 kyr ago. Temperature proxies from ice cores revealed the onset of the Bølling/Allerød (B/A) warm period in the north and the start of the Antarctic Cold Reversal in the south. Furthermore, the B/A is accompanied by a rapid sea level rise of about 20 m during meltwater pulse (MWP) 1A, whose exact timing is matter of current debate. In situ measured CO₂ in the EPICA Dome C (EDC) ice core also revealed a remarkable jump of 10±1 ppmv in 230 yr at the same time. Allowing for the age distribution of CO₂ in firn we here show, that atmospheric CO₂ rose by 20–35 ppmv in less than 200 yr, which is a factor of 2–3.5 larger than the CO₂ signal recorded in situ in EDC. Based on the estimated airborne fraction of 0.17 of CO₂ we infer that 125 Pg of carbon need to be released to the atmosphere to produce such a peak. Most of the carbon might have been activated as consequence of continental shelf flooding during MWP-1A. This impact of rapid sea level rise on atmospheric CO₂ distinguishes the B/A from other Dansgaard/Oeschger events of the last 60 kyr, potentially defining the point of no return during the last deglaciation

Structural Descriptions in Human-Assisted Robot Visual Learning

The paper presents an approach to using structural descriptions, obtained through a human-robot tutoring dialogue, as labels for the visual object models a robot learns. The paper shows how structural descriptions enable relating models for different aspects of one and the same object, and how being able to relate descriptions for visual models and discourse referents enables incremental updating of model descriptions through dialogue (either robot- or human-initiated). The approach has been implemented in an integrated architecture for human-assisted robot visual learning

Dynamic Kerr effect responses in the Terahertz-range

Dynamic Kerr effect measurements provide a simple realization of a nonlinear experiment. We propose a field-off experiment where an electric field of one or several sinusoidal cycles is applied to a sample in thermal equilibrium. Afterwards, the evolution of the polarizability is measured. If such an experiment is performed in the Terahertz-range it might provide valuable information about the low-frequency dynamics in disordered systems. We treat these dynamics in terms of a Brownian oscillator model and calculate the Kerr effect response. It is shown that frequency-selective behaviour can be expected. In the interesting case of underdamped vibrational motion we find that the frequency-dependence of the phonon-damping can be determined from the experiment. Also the behaviour of overdamped relaxational modes is discussed. For typical glassy materials we estimate the magnitude of all relevant quantities, which we believe to be helpful in experimental realizations.Comment: 26 pages incl. 5 figure

Real Exchange Rates, Preferences, and Incomplete Markets: Evidence, 1961-2001

Many international macroeconomic models link the real exchange rate to a ratio of marginal utilities. We examine this link empirically, allowing the marginal utility of consumption to depend on government expenditure, real money balances, or external habit. We also consider two environments with incomplete asset markets; one with exogenously missing markets but an endogenous discount rate that anchors the distribution of wealth and one with endogenous market segmentation. Although none of these satisfies theoretical and over-identifying restrictions for every country, utility with external habit persistence provides the best match with real exchange rates for OECD countries between 1961 and 2001.real exchange rate, consumption, marginal utility

High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase in Complex with Magnesium Ions

Lassa virus (LASV) causes deadly hemorrhagic fever disease for which there are no vaccines and limited treatments. LASV-encoded L polymerase is required for viral RNA replication and transcription. The functional domains of L–a large protein of 2218 amino acid residues–are largely undefined, except for the centrally located RNA-dependent RNA polymerase (RdRP) motif. Recent structural and functional analyses of the N-terminal region of the L protein from lymphocytic choriomeningitis virus (LCMV), which is in the same Arenaviridae family as LASV, have identified an endonuclease domain that presumably cleaves the cap structures of host mRNAs in order to initiate viral transcription. Here we present a high-resolution crystal structure of the N-terminal 173-aa region of the LASV L protein (LASV L173) in complex with magnesium ions at 1.72 Å. The structure is highly homologous to other known viral endonucleases of arena- (LCMV NL1), orthomyxo- (influenza virus PA), and bunyaviruses (La Crosse virus NL1). Although the catalytic residues (D89, E102 and K122) are highly conserved among the known viral endonucleases, LASV L endonuclease structure shows some notable differences. Our data collected from in vitro endonuclease assays and a reporter-based LASV minigenome transcriptional assay in mammalian cells confirm structural prediction of LASV L173 as an active endonuclease. The high-resolution structure of the LASV L endonuclease domain in complex with magnesium ions should aid the development of antivirals against lethal Lassa hemorrhagic fever

Gunrock: A High-Performance Graph Processing Library on the GPU

For large-scale graph analytics on the GPU, the irregularity of data access and control flow, and the complexity of programming GPUs have been two significant challenges for developing a programmable high-performance graph library. "Gunrock", our graph-processing system designed specifically for the GPU, uses a high-level, bulk-synchronous, data-centric abstraction focused on operations on a vertex or edge frontier. Gunrock achieves a balance between performance and expressiveness by coupling high performance GPU computing primitives and optimization strategies with a high-level programming model that allows programmers to quickly develop new graph primitives with small code size and minimal GPU programming knowledge. We evaluate Gunrock on five key graph primitives and show that Gunrock has on average at least an order of magnitude speedup over Boost and PowerGraph, comparable performance to the fastest GPU hardwired primitives, and better performance than any other GPU high-level graph library.Comment: 14 pages, accepted by PPoPP'16 (removed the text repetition in the previous version v5

Parametric down-conversion in photonic crystal waveguides

Photonic crystals create dramatic new possibilities for nonlinear optics. Line defects are shown to support modes suitable for the production of pairs of photons by the material's second order nonlinearity even if the phase-matching conditions cannot be satisfied in the bulk. These structures offer the flexibility to achieve specific dispersion characteristics and potentially very high brightness. In this work, two phase matching schemes are identified and analyzed regarding their dispersive properties.Comment: Due to a miscommunication the unrevised version of this paper was published instead of this one. v2 has quite some modifications and corrections. 7 pages, 4 figure

Targeting determinants of dosage compensation in Drosophila

The dosage compensation complex (DCC) in Drosophila melanogaster is responsible for up-regulating transcription from the single male X chromosome to equal the transcription from the two X chromosomes in females. Visualization of the DCC, a large ribonucleoprotein complex, on male larval polytene chromosomes reveals that the complex binds selectively to many interbands on the X chromosome. The targeting of the DCC is thought to be in part determined by DNA sequences that are enriched on the X. So far, lack of knowledge about DCC binding sites has prevented the identification of sequence determinants. Only three binding sites have been identified to date, but analysis of their DNA sequence did not allow the prediction of further binding sites. We have used chromatin immunoprecipitation to identify a number of new DCC binding fragments and characterized them in vivo by visualizing DCC binding to autosomal insertions of these fragments, and we have demonstrated that they possess a wide range of potential to recruit the DCC. By varying the in vivo concentration of the DCC, we provide evidence that this range of recruitment potential is due to differences in affinity of the complex to these sites. We were also able to establish that DCC binding to ectopic high-affinity sites can allow nearby low-affinity sites to recruit the complex. Using the sequences of the newly identified and previously characterized binding fragments, we have uncovered a number of short sequence motifs, which in combination may contribute to DCC recruitment. Our findings suggest that the DCC is recruited to the X via a number of binding sites of decreasing affinities, and that the presence of high-and moderate-affinity sites on the X may ensure that lower-affinity sites are occupied in a context-dependent manner. Our bioinformatics analysis suggests that DCC binding sites may be composed of variable combinations of degenerate motifs