Information filtering via Iterative Refinement

With the explosive growth of accessible information, expecially on the Internet, evaluation-based filtering has become a crucial task. Various systems have been devised aiming to sort through large volumes of information and select what is likely to be more relevant. In this letter we analyse a new ranking method, where the reputation of information providers is determined self-consistently.Comment: 10 pages, 3 figures. Accepted for publication on Europhysics Letter

Epiblast-specific loss of HCF-1 leads to failure in anterior-posterior axis specification.

Mammalian Host-Cell Factor 1 (HCF-1), a transcriptional co-regulator, plays important roles during the cell-division cycle in cell culture, embryogenesis as well as adult tissue. In mice, HCF-1 is encoded by the X-chromosome-linked Hcfc1 gene. Induced Hcfc1(cKO/+) heterozygosity with a conditional knockout (cKO) allele in the epiblast of female embryos leads to a mixture of HCF-1-positive and -deficient cells owing to random X-chromosome inactivation. These embryos survive owing to the replacement of all HCF-1-deficient cells by HCF-1-positive cells during E5.5 to E8.5 of development. In contrast, complete epiblast-specific loss of HCF-1 in male embryos, Hcfc1(epiKO/Y), leads to embryonic lethality. Here, we characterize this lethality. We show that male epiblast-specific loss of Hcfc1 leads to a developmental arrest at E6.5 with a rapid progressive cell-cycle exit and an associated failure of anterior visceral endoderm migration and primitive streak formation. Subsequently, gastrulation does not take place. We note that the pattern of Hcfc1(epiKO/Y) lethality displays many similarities to loss of β-catenin function. These results reveal essential new roles for HCF-1 in early embryonic cell proliferation and development

Two-Stage Rotational Disordering of a Molecular Crystal Surface: C60

We propose a two-stage mechanism for the rotational surface disordering phase transition of a molecular crystal, as realized in C$_{60}$ fullerite. Our study, based on Monte Carlo simulations, uncovers the existence of a new intermediate regime, between a low temperature ordered $(2 \times 2)$ state, and a high temperature $(1 \times 1)$ disordered phase. In the intermediate regime there is partial disorder, strongest for a subset of particularly frustrated surface molecules. These concepts and calculations provide a coherent understanding of experimental observations, with possible extension to other molecular crystal surfaces.Comment: 4 pages, 2 figure

Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat

Background Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction. Results We extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR using divergent chloroplast genomes from land plants and green algae recovers the phylogeny congruent with prior studies, while analysis that do not consider IR structure fail to obtain the accepted topology. Our extensive simulation study also confirms that GRAPPA has better accuracy then the existing methods. Conclusions Tests on a biological and simulated dataset show GRAPPA-IR can accurately recover the genome phylogeny as well as ancestral gene orders. Close analysis of the ancestral genome structure suggests that genome rearrangement in chloroplasts is probably limited by inverted repeats with a conserved core region. In addition, the boundaries of inverted repeats are hot spots for gene duplications or deletions. The new GRAPPA-IR is available from http://phylo.cse.sc.ed

Simultaneous Orthogonal Planarity

We introduce and study the $\textit{OrthoSEFE}-k$ problem: Given $k$ planar graphs each with maximum degree 4 and the same vertex set, do they admit an OrthoSEFE, that is, is there an assignment of the vertices to grid points and of the edges to paths on the grid such that the same edges in distinct graphs are assigned the same path and such that the assignment induces a planar orthogonal drawing of each of the $k$ graphs? We show that the problem is NP-complete for $k \geq 3$ even if the shared graph is a Hamiltonian cycle and has sunflower intersection and for $k \geq 2$ even if the shared graph consists of a cycle and of isolated vertices. Whereas the problem is polynomial-time solvable for $k=2$ when the union graph has maximum degree five and the shared graph is biconnected. Further, when the shared graph is biconnected and has sunflower intersection, we show that every positive instance has an OrthoSEFE with at most three bends per edge.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Evidence for distinct polymer chain orientations in KC60 and RbC60

The KC60 and RbC60 polymer phases exhibit contrasting electronic properties while powder diffraction studies have revealed no definite structural difference. We have performed single crystal X-ray diffraction and diffuse scattering studies of these compounds. It is found that KC60 and RbC60 possess different chain orientations about their axes, which are described by distinct space groups Pmnn and I2/m, respectively. Such a structural difference will be of great importance to a complete understanding of the physical properties.Comment: To be published in Phys. Rev. Let

Heuristics for the inversion median problem

Background: The study of genome rearrangements has become a mainstay of phylogenetics and comparative genomics. Fundamental in such a study is the median problem: given three gene arrangements, find a fourth that minimizes the sum of the evolutionary distances between itself and the given three. Many exact algorithms and heuristics have been developped for the inversion median problem, of which the best known is MGR. Results: We present a unifying framework for median heuristics, which enables us to clarify existing strategies and to place them in a partial ordering. Analysis of this framework leads to a new insight: the best strategies continue to refer to the input data rather than just to updated estimates. Using this insight, we develop a new heuristic for inversion medians that uses input data to the end of its computation and leverages our previous work with DCJ medians. Finally, we present the results of extensive experimentation showing that our new heuristic outperforms all others in accuracy and, especially, in running time: the heuristic typically returns solutions within 1 % of optimal and runs in seconds to minutes even on genomes with 25’000 genes—in contrast, MGR can take days on instances of 200 genes and cannot be used beyond 1’000 genes. Conclusions: Finding good rearrangement medians, in particular inversion medians, had long been regarded as the computational bottleneck in whole-genome studies. Our new heuristic for inversion medians, ASM, which dominates all others in our framework, puts that issue to rest by providing near-optimal solutions within seconds to minutes on even the largest genomes

Довідкові регіональні видання з геральдики

Одним з джерел інформації про наявність історичних гербів міст України та новотворів 60-х–80-х рр. ХХ ст. виступає «Алфавитный каталог городов, поселков, сел, губерний и областей России, СНГ, бывших союзных республик СССР, имеющих старые и современные гербы». Автор рецензії проаналізував принципи укладання подібних джерел інформації, зробив свої зауваження та висловив побажання щодо їх вдосконалення.«Alphabetical catalogue of towns, settlements, villages, provinces and regions of Russia, Commonwealth of Independent States, former Soviet Republics of the USSR, which have old and present-day coat of arms» is one of the sources that gives information about historical coat of arms and newly formed emblems of Ukraine during 60th – 80th of XX century. The author of the review analysed the structure of similar sources and made her remarks and suggestion regarding to its improvement