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A $q$-analogue of a $t$-design is a set $S$ of subspaces (of dimension $k$) of a finite vector space $V$ over a field of order $q$ such that each $t$ subspace is contained in a constant $\lambda$ number of elements of $S$. The smallest nontrivial feasible parameters occur when $V$ has dimension $7$, $t=2$, $q=2$, and $k=3$; which is the $q$-analogue of a $2$-$(7,3,1)$ design, the Fano plane. The existence of the binary $q$-analogue of the Fano plane has yet to be resolved, and it was shown by Kiermaier et al. (2016) that such a configuration must have an automorphism group of order at most $2$. We show that the binary $q$-analogue of the Fano plane has a trivial automorphism group., Comment: A crucial mistake in the computations was pointed out to us

The cage problem asks for the smallest number $c(k,g)$ of vertices in a $k$-regular graph of girth $g$ and graphs meeting this bound are known as cages. While cages are known to exist for all integers $k \ge 2$ and $g \ge 3$, the exact value of $c(k, g)$ is known only for some small values of $k, g$ and three infinite families where $g \in \{6, 8, 12\}$ and $k - 1$ is a prime power. These infinite families come from the incidence graphs of generalized polygons. Some of the best known upper bounds on $c(k,g)$ for $g \in \{6, 8, 12\}$ have been obtained by constructing small regular induced subgraphs of these cages. In this paper, we first use the Expander Mixing Lemma to give a general lower bound on the size of an induced $k$-regular subgraph of a regular bipartite graph in terms of the second largest eigenvalue of the host graph. We use this bound to show that the known construction of $(k,6)$-graphs using Baer subplanes of the Desarguesian projective plane is the best possible. For generalized quadrangles and hexagons, our bounds are new. In particular, we improve the known lower bound on the size of a $q$-regular induced subgraphs of the classical generalized quadrangle $\mathsf{Q}(4,q)$ and show that the known constructions are asymptotically sharp. For prime powers $q$, we also improve the known upper bounds on $c(q,8)$ and $c(q,12)$ by giving new geometric constructions of $q$-regular induced subgraphs in the symplectic generalized quadrangle $\mathsf{W}(3,q)$ and the split Cayley hexagon $\mathsf{H}(q)$, respectively. Our constructions show that \[c(q,8) \le 2(q^3 - q\sqrt{q} - q)\] for $q$ an even power of a prime, and \[c(q, 12) \le 2(q^5 - 3q^3)\] for all prime powers $q$. For $q \in \{3,4,5\}$ we also give a computer classification of all $q$-regular induced subgraphs of the classical generalized quadrangles of order $q$., Comment: Published version, proof of Lemma 5.3 simplified, for computer code see previous version

Solid-density plasmas driven by intense x-ray free-electron laser (XFEL) radiation are seeded by sources of non-thermal photoelectrons and Auger electrons that ionize and heat the target via collisions. Simulation codes that are commonly used to model such plasmas, such as collisional-radiative (CR) codes, typically assume a Maxwellian distribution and thus instantaneous thermalization of the source electrons. In this study, we present a detailed description and initial applications of a collisional particle-in-cell code, PICLS, that has been extended with a self-consistent radiation transport model and Monte-Carlo models for photoionization and KLL Auger ionization, enabling the fully kinetic simulation of XFEL-driven plasmas. The code is used to simulate two experiments previously performed at the Linac Coherent Light Source investigating XFEL-driven solid-density Al plasmas. It is shown that PICLS-simulated pulse transmissions using the Ecker-Kr\"oll continuum-lowering model agree much better with measurements than do simulations using the Stewart-Pyatt model. Good quantitative agreement is also found between the time-dependent PICLS results and those of analogous simulations by the CR code SCFLY, which was used in the analysis of the experiments to accurately reproduce the observed K{\alpha} emissions and pulse transmissions. Finally, it is shown that the effects of the non-thermal electrons are negligible for the conditions of the particular experiments under investigation., Comment: 12 pages, 11 figures

This note exhibits graphs whose chromatic polynomials have the Beraha number $B_{10} = (5 + \sqrt{5})/2$ as a root. It was previously known that no other non-integer Beraha number is a chromatic root, and so these examples complete the determination of precisely which Beraha numbers can be chromatic roots.

We classify finite primitive permutation groups having a suborbit of length 5. As a corollary, we obtain a classification of finite vertex-primitive graphs of valency 5. In the process, we also classify finite almost simple groups that have a maximal subgroup isomorphic to $\mathrm{Alt}(5)$ or $\mathrm{Sym}(5)$.

Markov community models have been applied to sessile organisms because such models facilitate estimation of transition probabilities by tracking species occupancy at many fixed observation points over multiple periods of time. Estimation of transition probabilities of sessile communities seems easy in principle but may still be difficult in practice because resampling error (i.e., a failure to resample exactly the same location at fixed points) may cause significant estimation bias. Previous studies have developed novel analytical methods to correct for this estimation bias. However, they did not consider the local structure of community composition induced by the aggregated distribution of organisms that is typically observed in sessile assemblages and is very likely to affect observations. In this study, we developed a multistate dynamic site occupancy model to estimate transition probabilities that accounts for resampling errors associated with local community structure. The model applies a nonparametric multivariate kernel smoothing methodology to the latent occupancy component to estimate the local state composition near each observation point, which is assumed to determine the probability distribution of data conditional on the occurrence of resampling error. By using computer simulations, we confirmed that an observation process that depends on local community structure may bias inferences about transition probabilities. By applying the proposed model to a real dataset of intertidal sessile communities, we also showed that estimates of transition probabilities and of the properties of community dynamics may differ considerably when spatial dependence is taken into account. Our approach can even accommodate an anisotropic spatial correlation of species composition, and may serve as a basis for inferring complex nonlinear ecological dynamics., Comment: 14 pages, 3 figures

The Frontier Fields are a director's discretionary time campaign with HST and the Spitzer Space Telescope to see deeper into the universe than ever before. The Frontier Fields combine the power of HST and Spitzer with the natural gravitational telescopes of massive high-magnification clusters of galaxies to produce the deepest observations of clusters and their lensed galaxies ever obtained. Six clusters - Abell 2744, MACSJ0416.1-2403, MACSJ0717.5+3745, MACSJ1149.5+2223, Abell S1063, and Abell 370 - were selected based on their lensing strength, sky darkness, Galactic extinction, parallel field suitability, accessibility to ground-based facilities, HST, Spitzer and JWST observability, and pre-existing ancillary data. These clusters have been targeted by the HST ACS/WFC and WFC3/IR with coordinated parallels of adjacent blank fields for over 840 HST orbits. The Spitzer Space Telescope has dedicated > 1000 hours of director's discretionary time to obtain IRAC 3.6 and 4.5 micron imaging to ~26.5, 26.0 ABmag 5-sigma point-source depths in the six cluster and six parallel Frontier Fields. The Frontier Field parallel fields are the second-deepest observations thus far by HST with ~29th ABmag 5-sigma point source depths in seven optical - near-infrared bandpasses. Galaxies behind the Frontier Field cluster lenses experience typical magnification factors of a few, with small regions near the critical curves magnified by factors 10-100. Therefore, the Frontier Field cluster HST images achieve intrinsic depths of ~30-33 magnitudes over very small volumes. Early studies of the Frontier Fields have probed galaxies fainter than any seen before during the epoch of reionization 6 < z < 10, mapped out the cluster dark matter to unprecedented resolution, and followed lensed transient events., Comment: submitted to ApJ; 18 pages; see http://www.stsci.edu/hst/campaigns/frontier-fields/ and http://ssc.spitzer.caltech.edu/warmmission/scheduling/approvedprograms/ddt/frontier/ for data and more information

Gunasekaran et al (Pramana J. Phys. 75 683-690 (2010)) report to have grown the nonlinear optical crystals urea thiourea mercuric chloride (UTHC) and urea thiourea mercuric sulphate (UTHS). We argue that UTHC and UTHS are dubious crystals and are not what the authors propose., Comment: 2 pages

Let $\Omega$ be a set of cardinality $n$, $G$ a permutation group on $\Omega$, and $f:\Omega\to\Omega$ a map which is not a permutation. We say that $G$ \emph{synchronizes} $f$ if the transformation semigroup $\langle G,f\rangle$ contains a constant map, and that $G$ is a \emph{synchronizing group} if $G$ synchronizes \emph{every} non-permutation. A synchronizing group is necessarily primitive, but there are primitive groups that are not synchronizing. Every non-synchronizing primitive group fails to synchronize at least one uniform transformation (that is, transformation whose kernel has parts of equal size), and it has previously been conjectured that a primitive group synchronizes every non-uniform transformation. The first goal of this paper is to prove that this conjecture is false, by exhibiting primitive groups that fail to synchronize specific non-uniform transformations of ranks $5$ and $6$. In addition we produce graphs whose automorphism groups have approximately $\sqrt{n}$ \emph{non-synchronizing ranks}, thus refuting another conjecture on the number of non-synchronizing ranks of a primitive group. The second goal of this paper is to extend the spectrum of ranks for which it is known that primitive groups synchronize every non-uniform transformation of that rank. It has previously been shown that a primitive group of degree $n$ synchronizes every non-uniform transformation of rank $n-1$ and $n-2$, and here this is extended to $n-3$ and $n-4$. Determining the exact spectrum of ranks for which there exist non-uniform transformations not synchronized by some primitive group is just one of several natural, but possibly difficult, problems on automata, primitive groups, graphs and computational algebra arising from this work; these are outlined in the final section., Comment: One broken link fixed; some changes on the ordering of the sections

We develop an inference framework for spatial capture-recapture data when two methods are used in which individuality cannot generally be reconciled between the two methods. A special case occurs in camera trapping when left-side (method 1) and right-side (method 2) photos are obtained but not simultaneously. We specify a spatially explicit capture-recapture model for the latent "perfect" data set which is conditioned on known identity of individuals between methods. We regard the identity variable which associates individuals of the two data sets as an unknown in the model and we propose a Bayesian analysis strategy for the model in which the identity variable is updated using a Metropolis component algorithm. The work extends previous efforts to deal with incomplete data by recognizing that there is information about individuality in the spatial juxtaposition of captures. Thus, individual records obtained by both sampling methods that are in close proximity are more likely to be the same individual than individuals that are not in close proximity. The model proposed here formalizes this trade-off between spatial proximity and probabilistic determination of individuality using spatially explicit capture-recapture models., Comment: Revision 4/19/2015

2834 inequivalent spreads under the group $\mathrm{P}\Gamma\mathrm{L}(4,8)$. Therefore there are the same number of translation planes of order 64 with kernel containing $\mathrm{GF}(8)$, and we describe various properties of these planes. Each portion of the search was performed at least twice with independently-written software, and the results checked for internal consistency by computation of the numbers of spreads rooted at a line not in the spread, thus enhancing confidence in the correctness of the search.

We provide explicit combinatorial formulas for Ottaviani's degree 15 invariant which detects cubics in 5 variables that are sums of 7 cubes. Our approach is based on the chromatic properties of certain graphs and relies on computer searches and calculations., Comment: 10 pages, 4 figures, 1 ancillary file

We characterise the quartic (i.e. 4-regular) multigraphs with the property that every edge lies in a triangle. The main result is that such graphs are either squares of cycles, line multigraphs of cubic multigraphs, or are obtained from these by a number of simple subgraph-replacement operations. A corollary of this is that a simple quartic graph with every edge in a triangle is either the square of a cycle, the line graph of a cubic graph or a graph obtained from the line multigraph of a cubic multigraph by replacing triangles with copies of K_{1,1,3}.

We prove that the (real or complex) chromatic roots of a series-parallel graph with maxmaxflow Lambda lie in the disc |q-1| < (Lambda-1)/log 2. More generally, the same bound holds for the (real or complex) roots of the multivariate Tutte polynomial when the edge weights lie in the "real antiferromagnetic regime" -1 \le v_e \le 0. This result is within a factor 1/log 2 \approx 1.442695 of being sharp

This is a review of the book "Mixed Effects Models and Extensions in Ecology with R" by Zuur, Ieno, Walker, Saveliev and Smith (2009, Springer). I was asked to review this book for The American Statistician in 2010. After I wrote the review, the invitation was revoked. This is the review.

We prove that the maximum size of a simple binary matroid of rank $r \geq 5$ with no AG(3,2)-minor is $\binom{r+1}{2}$ and characterise those matroids achieving this bound. When $r \geq 6$, the graphic matroid $M(K_{r+1})$ is the unique matroid meeting the bound, but there are a handful of smaller examples. In addition, we determine the size function for non-regular simple binary matroids with no AG(3,2)-minor and characterise the matroids of maximum size for each rank.

The Merino-Welsh conjecture asserts that the number of spanning trees of a graph is no greater than the maximum of the numbers of totally cyclic orientations and acyclic orientations of that graph. We prove this conjecture for the class of series-parallel graphs., Comment: 12 pages, includes Mathematica code in Appendix

Capture-recapture studies are widely used to obtain information about abundance (population size or density) of animal populations. A common design is that in which multiple distinct populations are sampled, and the research objective is modeling variation in population size $N_{s}; s=1,2,...,S$ among the populations such as estimating a treatment effect or some other source of variation related to landscape structure. The problem is naturally resolved using hierarchical models. We provide a Bayesian formulation of such models using data augmentation which preserves the individual encounter histories in the model and, as such, is amenable to modeling individual effects. We formulate the model by conditioning on the total population size among all populations. In this case, the abundance model can be formulated as a multinomial model that allocates individuals among sites. MCMC is easily carried out by the introduction of a categorical individual effect, $g_{i}$, which partitions the total population size. The prior distribution for the latent variable $g$ is derived from the model assumed for the population sizes $N_{s}$., Comment: 2 figures

Understanding space usage and resource selection is a primary focus of many studies of animal populations. Usually, such studies are based on location data obtained from telemetry, and resource selection functions (RSF) are used for inference. Another important focus of wildlife research is estimation and modeling population size and density. Recently developed spatial capture-recapture (SCR) models accomplish this objective using individual encounter history data with auxiliary spatial information on location of capture. SCR models include encounter probability functions that are intuitively related to RSFs, but to date, no one has extended SCR models to allow for explicit inference about space usage and resource selection. We develop a statistical framework for jointly modeling space usage, resource selection, and population density by integrating SCR data, such as from camera traps, mist-nets, or conventional catch-traps, with resource selection data from telemetered individuals. We provide a framework for estimation based on marginal likelihood, wherein we estimate simultaneously the parameters of the SCR and RSF models. Our method leads to increases in precision for estimating population density and parameters of ordinary SCR models. Importantly, we also find that SCR models alone can estimate parameters of resource selection functions and, as such, SCR methods can be used as the sole source for studying space-usage; however, precision will be higher when telemetry data are available. Finally, we find that SCR models using standard symmetric and stationary encounter probability models produce biased estimates of density when animal space usage is related to a landscape covariate. Therefore, it is important that space usage be taken into consideration, if possible, in studies focused on estimating density using capture-recapture methods.

Let AG(3,2)xU(1,1) denote the binary matroid obtained from the direct sum of AG(3,2) and a coloop by completing the 3-point lines between every element in AG(3,2) and the coloop. We prove that every internally 4-connected binary matroid that does not have a minor isomorphic to M(K5\e) is isomorphic to a minor of (AG(3,2)xU(1,1))*., Comment: 16 pages, 4 figures

Recently developed spatial capture-recapture (SCR) models represent a major advance over traditional capture-recapture (CR) models because they yield explicit estimates of animal density instead of population size within an unknown area. Furthermore, unlike nonspatial CR methods, SCR models account for heterogeneity in capture probability arising from the juxtaposition of animal activity centers and sample locations. Although the utility of SCR methods is gaining recognition, the requirement that all individuals can be uniquely identified excludes their use in many contexts. In this paper, we develop models for situations in which individual recognition is not possible, thereby allowing SCR concepts to be applied in studies of unmarked or partially marked populations. The data required for our model are spatially referenced counts made on one or more sample occasions at a collection of closely spaced sample units such that individuals can be encountered at multiple locations. Our approach includes a spatial point process for the animal activity centers and uses the spatial correlation in counts as information about the number and location of the activity centers. Camera-traps, hair snares, track plates, sound recordings, and even point counts can yield spatially correlated count data, and thus our model is widely applicable. A simulation study demonstrated that while the posterior mean exhibits frequentist bias on the order of 5-10% in small samples, the posterior mode is an accurate point estimator as long as adequate spatial correlation is present. Marking a subset of the population substantially increases posterior precision and is recommended whenever possible. We applied our model to avian point count data collected on an unmarked population of the northern parula (Parula americana) and obtained a density estimate (posterior mode) of 0.38 (95% CI: 0.19-1.64) birds/ha. Our paper challenges sampling and analytical conventions in ecology by demonstrating that neither spatial independence nor individual recognition is needed to estimate population density - rather, spatial dependence can be informative about individual distribution and density., Comment: Published in at http://dx.doi.org/10.1214/12-AOAS610 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org)

We show that if G is a group of automorphisms of a thick finite generalised quadrangle Q acting primitively on both the points and lines of Q, then G is almost simple. Moreover, if G is also flag-transitive then G is of Lie type., Comment: 20 pages

In this paper, we describe a complete computer classification of the hemisystems in the two known flock generalized quadrangles of order $(5^2,5)$ and give numerous further examples of hemisystems in all the known flock generalized quadrangles of order $(s^2,s)$ for $s \le 11$. By analysing the computational data, we identify two possible new infinite families of hemisystems in the classical generalized quadrangle $H(3,q^2)$., Comment: slight revisions made following referee's reports, and included raw data

A directed graph is set-homogeneous if, whenever U and V are isomorphic finite subdigraphs, there is an automorphism g of the digraph with U^g=V. Here, extending work of Lachlan on finite homogeneous digraphs, we classify finite set-homogeneous digraphs, where we allow some pairs of vertices to have arcs in both directions. Under the assumption that such pairs of vertices are not allowed, we obtain initial results on countably infinite set-homogeneous digraphs, classifying those which are not 2-homogeneous., Comment: 43 pages

We prove that every flock generalised quadrangle contains a hemisystem, and we provide a construction method which unifies our results with the examples of Cossidente and Penttila in the classical case.