Parametric and non-parametric gradient matching for network inference:a comparison

Abstract Background Reverse engineering of gene regulatory networks from time series gene-expression data is a challenging problem, not only because of the vast sets of candidate interactions but also due to the stochastic nature of gene expression. We limit our analysis to nonlinear differential equation based inference methods. In order to avoid the computational cost of large-scale simulations, a two-step Gaussian process interpolation based gradient matching approach has been proposed to solve differential equations approximately. Results We apply a gradient matching inference approach to a large number of candidate models, including parametric differential equations or their corresponding non-parametric representations, we evaluate the network inference performance under various settings for different inference objectives. We use model averaging, based on the Bayesian Information Criterion (BIC), to combine the different inferences. The performance of different inference approaches is evaluated using area under the precision-recall curves. Conclusions We found that parametric methods can provide comparable, and often improved inference compared to non-parametric methods; the latter, however, require no kinetic information and are computationally more efficient

Effective lattice theories for Polyakov loops

We derive effective actions for SU(2) Polyakov loops using inverse Monte Carlo techniques. In a first approach, we determine the effective couplings by requiring that the effective ensemble reproduces the single-site distribution of the Polyakov loops. The latter is flat below the critical temperature implying that the (untraced) Polyakov loop is distributed uniformly over its target space, the SU(2) group manifold. This allows for an analytic determination of the Binder cumulant and the distribution of the mean-field, which turns out to be approximately Gaussian. In a second approach, we employ novel lattice Schwinger-Dyson equations which reflect the SU(2) x SU(2) invariance of the functional Haar measure. Expanding the effective action in terms of SU(2) group characters makes the numerics sufficiently stable so that we are able to extract a total number of 14 couplings. The resulting action is short-ranged and reproduces the Yang-Mills correlators very well.Comment: 27 pages, 8 figures, v2: method refined, chapter and references adde

Practical Low Data-Complexity Subspace-Trail Cryptanalysis of Round-Reduced PRINCE

Subspace trail cryptanalysis is a very recent new cryptanalysis technique, and includes differential, truncated differential, impossible differential, and integral attacks as special cases. In this paper, we consider PRINCE, a widely analyzed block cipher proposed in 2012. After the identification of a 2.5 rounds subspace trail of PRINCE, we present several (truncated differential) attacks up to 6 rounds of PRINCE. This includes a very practical attack with the lowest data complexity of only 8 plaintexts for 4 rounds, which co-won the final round of the PRINCE challenge in the 4-round chosen-plaintext category. The attacks have been verified using a C implementation. Of independent interest, we consider a variant of PRINCE in which ShiftRows and MixLayer operations are exchanged in position. In particular, our result shows that the position of ShiftRows and MixLayer operations influences the security of PRINCE. The same analysis applies to follow-up designs inspired by PRINCE

Nearby Doorways, Parity Doublets and Parity Mixing in Compound Nuclear States

We discuss the implications of a doorway state model for parity mixing in compound nuclear states. We argue that in order to explain the tendency of parity violating asymmetries measured in $^{233}$Th to have a common sign, doorways that contribute to parity mixing must be found in the same energy neighbourhood of the measured resonance. The mechanism of parity mixing in this case of nearby doorways is closely related to the intermediate structure observed in nuclear reactions in which compound states are excited. We note that in the region of interest ($^{233}$Th) nuclei exhibit octupole deformations which leads to the existence of nearby parity doublets. These parity doublets are then used as doorways in a model for parity mixing. The contribution of such mechanism is estimated in a simple model.Comment: 11 pages, REVTE

A Genome-Scale Metabolic Model for <i>Methylococcus capsulatus </i>(Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

Background: Genome-scale metabolic models allow researchers to calculate yields, to predict consumption and production rates, and to study the effect of genetic modifications in silico, without running resource-intensive experiments. While these models have become an invaluable tool for optimizing industrial production hosts like Escherichia coli and S. cerevisiae, few such models exist for one-carbon (C1) metabolizers.Results: Here, we present a genome-scale metabolic model for Methylococcus capsulatus (Bath), a well-studied obligate methanotroph, which has been used as a production strain of single cell protein (SCP). The model was manually curated, and spans a total of 879 metabolites connected via 913 reactions. The inclusion of 730 genes and comprehensive annotations, make this model not only a useful tool for modeling metabolic physiology, but also a centralized knowledge base for M. capsulatus (Bath). With it, we determined that oxidation of methane by the particulate methane monooxygenase could be driven both through direct coupling or uphill electron transfer, both operating at reduced efficiency, as either scenario matches well with experimental data and observations from literature.Conclusion: The metabolic model will serve the ongoing fundamental research of C1 metabolism, and pave the way for rational strain design strategies toward improved SCP production processes in M. capsulatus

Gamow-Teller Strength in the Region of 100^{100}Sn

New calculations are presented for Gamow-Teller beta decay of nuclei near $^{100}$Sn. Essentially all of the $^{100}$Sn Gamow-Teller decay strength is predicted to go to a single state at an excitation energy of 1.8 MeV in $^{100}$In. The first calculations are presented for the decays of neighboring odd-even and odd-odd nuclei which show, in contrast to $^{100}$Sn, surprisingly complex and broad Gamow-Teller strength distributions. The results are compared to existing experimental data and the resulting hindrance factors are discussed.Comment: 12 pages (latex) and 2 figures available on reques

Affinities and Beyond! Developing Ways of Seeing in Online Spaces

This article presents an insider view of an online community of adults involved in sharing digital photography through a host website, Flickr. It describes how reciprocal teaching and learning partnerships in a dynamic multimodal environment are achieved through the creation of a ‘Third Space’ or ‘Affinity Space’, where ‘Funds of Knowledge’ are shared and processed in such a way that new meanings and discourses are generated. It is argued that this process is evidence of valuable learning and of the deepening of global understandings within the local space of Flickr. The new understandings are at least partly identifiable on the Flickr space, through the co-constructed ‘folksonomy’ or ‘online taxonomy’ of ways of looking at the world. Further, the article provides evidence for broadening existing definitions of literacy, at a time when the visual mode increasingly works interactively with verbal cues and explanations

Staggering effects in nuclear and molecular spectra

It is shown that the recently observed Delta J = 2 staggering effect (i.e. the relative displacement of the levels with angular momenta J, J+4, J+8, ..., relatively to the levels with angular momenta J+2, J+6, J+10, ...) seen in superdeformed nuclear bands is also occurring in certain electronically excited rotational bands of diatomic molecules (YD, CrD, CrH, CoH), in which it is attributed to interband interactions (bandcrossings). In addition, the Delta J = 1 staggering effect (i.e. the relative displacement of the levels with even angular momentum J with respect to the levels of the same band with odd J) is studied in molecular bands free from Delta J = 2 staggering (i.e. free from interband interactions/bandcrossings). Bands of YD offer evidence for the absence of any Delta J = 1 staggering effect due to the disparity of nuclear masses, while bands of sextet electronic states of CrD demonstrate that Delta J = 1 staggering is a sensitive probe of deviations from rotational behaviour, due in this particular case to the spin-rotation and spin-spin interactions.Comment: LaTeX, 16 pages plus 30 figures given in separate .ps files. To appear in the proceedings of the 4th European Workshop on Quantum Systems in Chemistry and Physics (Marly-le-Roi, France, 1999), ed. J. Maruani et al. (Kluwer, Dordrecht

Photometric Monitoring of Open Clusters I. The Survey

Open clusters, which have age, abundance, and extinction information from studies of main-sequence turn off stars, are the ideal location in which to determine the mass-luminosity-radius relation for low-mass stars. We have undertaken a photometric monitoring survey of open clusters in the Galaxy designed to detect low-mass eclipsing binary systems through variations in their relative light curves. Our aim is to provide an improved calibration of the mass-luminosity-radius relation for low-mass stars and brown dwarfs, to test stellar structure and evolution models, and to help quantify the contribution of low-mass stars to the global mass census in the Galaxy. In this paper we present our survey, describing the data and outlining the analysis techniques. We study six nearby open clusters, with a range of ages from $\sim 0.2$ to 4 Gyr and metallicities from approximately solar to -0.2dex. We monitor a field-of-view of > 1 square degree per target cluster, well beyond the characteristic cluster radius, over timescales of hours, days, and months with a sampling rate optimised for the detection of eclipsing binaries with periods of hours to days. Our survey depth is designed to detect eclipse events in a binary with a primary star of \lesssim 0.3~M_{\sun}. Our data have a photometric precision of $\sim 3$ mmag at $I\approx 16$.Comment: 50 pages, 18 figures, accepted for publication in A

Cluster Interpretation of Properties of Alternating Parity Bands in Heavy Nuclei

The properties of the states of the alternating parity bands in actinides, Ba, Ce and Nd isotopes are analyzed within a cluster model. The model is based on the assumption that cluster type shapes are produced by the collective motion of the nuclear system in the mass asymmetry coordinate. The calculated spin dependences of the parity splitting and of the electric multipole transition moments are in agreement with the experimental data.Comment: 29 pages, 10 figure