Inferential mistakes in population proxies: A response to Torfing's "Neolithic population and summed probability distribution of 14Cdates"

In his paper "Neolithic population and summed probability distribution of 14C-dates" Torfing opposes the widely held principle originally proposed by Rick (1987) that variation through time in the amount of archaeological material discovered in a region will reflect variation in the size of that local human population. His argument illustrates a persistent divide in archaeology between analytical and descriptive approaches when using proxies for past population size. We critically evaluate the numerous inferential mistakes he makes, showing that his conclusion is unjustified

Topological entropy and blocking cost for geodesics in riemannian manifolds

For a pair of points $x,y$ in a compact, riemannian manifold $M$ let $n_t(x,y)$ (resp. $s_t(x,y)$) be the number of geodesic segments with length $\leq t$ joining these points (resp. the minimal number of point obstacles needed to block them). We study relationships between the growth rates of $n_t(x,y)$ and $s_t(x,y)$ as $t\to\infty$. We derive lower bounds on $s_t(x,y)$ in terms of the topological entropy $h(M)$ and its fundamental group. This strengthens the results of Burns-Gutkin \cite{BG06} and Lafont-Schmidt \cite{LS}. For instance, by \cite{BG06,LS}, $h(M)>0$ implies that $s$ is unbounded; we show that $s$ grows exponentially, with the rate at least $h(M)/2$.Comment: 13 page

Exploratory Analysis of Highly Heterogeneous Document Collections

We present an effective multifaceted system for exploratory analysis of highly heterogeneous document collections. Our system is based on intelligently tagging individual documents in a purely automated fashion and exploiting these tags in a powerful faceted browsing framework. Tagging strategies employed include both unsupervised and supervised approaches based on machine learning and natural language processing. As one of our key tagging strategies, we introduce the KERA algorithm (Keyword Extraction for Reports and Articles). KERA extracts topic-representative terms from individual documents in a purely unsupervised fashion and is revealed to be significantly more effective than state-of-the-art methods. Finally, we evaluate our system in its ability to help users locate documents pertaining to military critical technologies buried deep in a large heterogeneous sea of information.Comment: 9 pages; KDD 2013: 19th ACM SIGKDD Conference on Knowledge Discovery and Data Minin

Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex

Campylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation

Sofic-Dyck shifts

We define the class of sofic-Dyck shifts which extends the class of Markov-Dyck shifts introduced by Inoue, Krieger and Matsumoto. Sofic-Dyck shifts are shifts of sequences whose finite factors form unambiguous context-free languages. We show that they correspond exactly to the class of shifts of sequences whose sets of factors are visibly pushdown languages. We give an expression of the zeta function of a sofic-Dyck shift

Measurement of correlations between low-frequency vibrational modes and particle rearrangements in quasi-two-dimensional colloidal glasses

We investigate correlations between low-frequency vibrational modes and rearrangements in two-dimensional colloidal glasses composed of thermosensitive microgel particles which readily permit variation of sample packing fraction. At each packing fraction, the particle displacement covariance matrix is measured and used to extract the vibrational spectrum of the "shadow" colloidal glass (i.e., the particle network with the same geometry and interactions as the sample colloid but absent damping). Rearrangements are induced by successive, small reductions in packing fraction. The experimental results suggest that low-frequency quasi-localized phonon modes in colloidal glasses, i.e., modes that present low energy barriers for system rearrangements, are spatially correlated with rearrangements in this thermal system

Why is the condensed phase of DNA preferred at higher temperature? DNA compaction in the presence of a multivalent cation

Upon the addition of multivalent cations, a giant DNA chain exhibits a large discrete transition from an elongated coil into a folded compact state. We performed single-chain observation of long DNAs in the presence of a tetravalent cation (spermine), at various temperatures and monovalent salt concentrations. We confirmed that the compact state is preferred at higher temperatures and at lower monovalent salt concentrations. This result is interpreted in terms of an increase in the net translational entropy of small ions due to ionic exchange between higher and lower valence ions.Comment: 4pages,3figure