Blocking Coloured Point Sets

This paper studies problems related to visibility among points in the plane. A point $x$ \emph{blocks} two points $v$ and $w$ if $x$ is in the interior of the line segment $\bar{vw}$. A set of points $P$ is \emph{$k$-blocked} if each point in $P$ is assigned one of $k$ colours, such that distinct points $v,w\in P$ are assigned the same colour if and only if some other point in $P$ blocks $v$ and $w$. The focus of this paper is the conjecture that each $k$-blocked set has bounded size (as a function of $k$). Results in the literature imply that every 2-blocked set has at most 3 points, and every 3-blocked set has at most 6 points. We prove that every 4-blocked set has at most 12 points, and that this bound is tight. In fact, we characterise all sets $\{n_1,n_2,n_3,n_4\}$ such that some 4-blocked set has exactly $n_i$ points in the $i$-th colour class. Amongst other results, for infinitely many values of $k$, we construct $k$-blocked sets with $k^{1.79...}$ points

The mitotic-spindle-associated protein astrin is essential for progression through mitosis

Astrin is a mitotic-spindle-associated protein expressed in most human cell lines and tissues. However, its functions in spindle organization and mitosis have not yet been determined. Sequence analysis revealed that astrin has an N-terminal globular domain and an extended coiled-coil domain. Recombinant astrin was purified and characterized by CD spectroscopy and electron microscopy. Astrin showed parallel dimers with head- stalk structures reminiscent of motor proteins, although no sequence similarities to known motor proteins were found. In physiological buffers, astrin dimers oligomerized via their globular head domains and formed aster-like structures. Silencing of astrin in HeLa cells by RNA interference resulted in growth arrest, with formation of multipolar and highly disordered spindles. Chromosomes did not congress to the spindle equator and remained dispersed. Cells depleted of astrin were normal during interphase but were unable to progress through mitosis and finally ended in apoptotic cell death. Possible functions of astrin in mitotic spindle organization are discussed

On the Maximum Crossing Number

Research about crossings is typically about minimization. In this paper, we consider \emph{maximizing} the number of crossings over all possible ways to draw a given graph in the plane. Alpert et al. [Electron. J. Combin., 2009] conjectured that any graph has a \emph{convex} straight-line drawing, e.g., a drawing with vertices in convex position, that maximizes the number of edge crossings. We disprove this conjecture by constructing a planar graph on twelve vertices that allows a non-convex drawing with more crossings than any convex one. Bald et al. [Proc. COCOON, 2016] showed that it is NP-hard to compute the maximum number of crossings of a geometric graph and that the weighted geometric case is NP-hard to approximate. We strengthen these results by showing hardness of approximation even for the unweighted geometric case and prove that the unweighted topological case is NP-hard.Comment: 16 pages, 5 figure

Triangle-Free Penny Graphs: Degeneracy, Choosability, and Edge Count

We show that triangle-free penny graphs have degeneracy at most two, list coloring number (choosability) at most three, diameter $D=\Omega(\sqrt n)$, and at most $\min\bigl(2n-\Omega(\sqrt n),2n-D-2\bigr)$ edges.Comment: 10 pages, 2 figures. To appear at the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

Nucleoplasmic LAP2 alpha-lamin A complexes are required to maintain a proliferative state in human fibroblasts

In human diploid fibroblasts (HDFs), expression of lamina-associated polypeptide 2 (LAP2) upon entry and exit from G0 is tightly correlated with phosphorylation and subnuclear localization of retinoblastoma protein (Rb). Phosphoisoforms of Rb and LAP2 are down-regulated in G0. Although RbS780 phosphoform and LAP2 are up-regulated upon reentry into G1 and colocalize in the nucleoplasm, RbS795 migrates between nucleoplasmic and speckle compartments. In HDFs, which are null for lamins A/C, LAP2 is mislocalized within nuclear aggregates, and this is correlated with cell cycle arrest and accumulation of Rb within speckles. Nuclear retention of nucleoplasmic Rb during G1 phase but not of speckle-associated Rb depends on lamin A/C. siRNA knock down of LAP2 or lamin A/C in HDFs leads to accumulation of Rb in speckles and G1 arrest, probably because of activation of a cell cycle checkpoint. Our results suggest that LAP2 and lamin A/C are involved in controlling Rb localization and phosphorylation, and a lack or mislocalization of either protein leads to cell cycle arrest in HDFs

Comprehensive analysis of NuMA variation in breast cancer

<p>Abstract</p> <p>Background</p> <p>A recent genome wide case-control association study identified <it>NuMA </it>region on 11q13 as a candidate locus for breast cancer susceptibility. Specifically, the variant Ala794Gly was suggested to be associated with increased risk of breast cancer.</p> <p>Methods</p> <p>In order to evaluate the <it>NuMa </it>gene for breast cancer susceptibility, we have here screened the entire coding region and exon-intron boundaries of <it>NuMa </it>in 92 familial breast cancer patients and constructed haplotypes of the identified variants. Five missense variants were further screened in 341 breast cancer cases with a positive family history and 368 controls. We examined the frequency of Ala794Gly in an extensive series of familial (n = 910) and unselected (n = 884) breast cancer cases and controls (n = 906), with a high power to detect the suggested breast cancer risk. We also tested if the variant is associated with histopathologic features of breast tumors.</p> <p>Results</p> <p>Screening of <it>NuMA </it>resulted in identification of 11 exonic variants and 12 variants in introns or untranslated regions. Five missense variants that were further screened in breast cancer cases with a positive family history and controls, were each carried on a unique haplotype. None of the variants, or the haplotypes represented by them, was associated with breast cancer risk although due to low power in this analysis, very low risk alleles may go unrecognized. The <it>NuMA </it>Ala794Gly showed no difference in frequency in the unselected breast cancer case series or familial case series compared to control cases. Furthermore, Ala794Gly did not show any significant association with histopathologic characteristics of the tumors, though Ala794Gly was slightly more frequent among unselected cases with lymph node involvement.</p> <p>Conclusion</p> <p>Our results do not support the role of <it>NuMA </it>variants as breast cancer susceptibility alleles.</p

Contact numbers for congruent sphere packings in Euclidean 3-space

Continuing the investigations of Harborth (1974) and the author (2002) we study the following two rather basic problems on sphere packings. Recall that the contact graph of an arbitrary finite packing of unit balls (i.e., of an arbitrary finite family of non-overlapping unit balls) in Euclidean 3-space is the (simple) graph whose vertices correspond to the packing elements and whose two vertices are connected by an edge if the corresponding two packing elements touch each other. One of the most basic questions on contact graphs is to find the maximum number of edges that a contact graph of a packing of n unit balls can have in Euclidean 3-space. Our method for finding lower and upper estimates for the largest contact numbers is a combination of analytic and combinatorial ideas and it is also based on some recent results on sphere packings. Finally, we are interested also in the following more special version of the above problem. Namely, let us imagine that we are given a lattice unit sphere packing with the center points forming the lattice L in Euclidean 3-space (and with certain pairs of unit balls touching each other) and then let us generate packings of n unit balls such that each and every center of the n unit balls is chosen from L. Just as in the general case we are interested in finding good estimates for the largest contact number of the packings of n unit balls obtained in this way.Comment: 18 page

String Matching and 1d Lattice Gases

We calculate the probability distributions for the number of occurrences $n$ of a given $l$ letter word in a random string of $k$ letters. Analytical expressions for the distribution are known for the asymptotic regimes (i) $k \gg r^l \gg 1$ (Gaussian) and $k,l \to \infty$ such that $k/r^l$ is finite (Compound Poisson). However, it is known that these distributions do now work well in the intermediate regime $k \gtrsim r^l \gtrsim 1$. We show that the problem of calculating the string matching probability can be cast into a determining the configurational partition function of a 1d lattice gas with interacting particles so that the matching probability becomes the grand-partition sum of the lattice gas, with the number of particles corresponding to the number of matches. We perform a virial expansion of the effective equation of state and obtain the probability distribution. Our result reproduces the behavior of the distribution in all regimes. We are also able to show analytically how the limiting distributions arise. Our analysis builds on the fact that the effective interactions between the particles consist of a relatively strong core of size $l$, the word length, followed by a weak, exponentially decaying tail. We find that the asymptotic regimes correspond to the case where the tail of the interactions can be neglected, while in the intermediate regime they need to be kept in the analysis. Our results are readily generalized to the case where the random strings are generated by more complicated stochastic processes such as a non-uniform letter probability distribution or Markov chains. We show that in these cases the tails of the effective interactions can be made even more dominant rendering thus the asymptotic approximations less accurate in such a regime.Comment: 44 pages and 8 figures. Major revision of previous version. The lattice gas analogy has been worked out in full, including virial expansion and equation of state. This constitutes the main part of the paper now. Connections with existing work is made and references should be up to date now. To be submitted for publicatio