Modelling complex geological circular data with the projected normal distribution and mixtures of von Mises distributions

Circular data are commonly encountered in the earth sciences and statistical descriptions and inferences about such data are necessary in structural geology. In this paper we compare two statistical distributions appropriate for complex circular data sets: the mixture of von Mises and the projected normal distribution. We show how the number of components in a mixture of von Mises distribution may be chosen, and how one may choose between the projected normal distribution and the mixture of von Mises for a particular data set. We illustrate these methods with a few structural geological data, showing how the fitted models can complement geological interpretation and permit statistical inference. One of our data sets suggests a special case of the projected normal distribution which we discuss briefly

Dictionary matching in a stream

We consider the problem of dictionary matching in a stream. Given a set of strings, known as a dictionary, and a stream of characters arriving one at a time, the task is to report each time some string in our dictionary occurs in the stream. We present a randomised algorithm which takes O(log log(k + m)) time per arriving character and uses O(k log m) words of space, where k is the number of strings in the dictionary and m is the length of the longest string in the dictionary

Combinatorial Markov chains on linear extensions

We consider generalizations of Schuetzenberger's promotion operator on the set L of linear extensions of a finite poset of size n. This gives rise to a strongly connected graph on L. By assigning weights to the edges of the graph in two different ways, we study two Markov chains, both of which are irreducible. The stationary state of one gives rise to the uniform distribution, whereas the weights of the stationary state of the other has a nice product formula. This generalizes results by Hendricks on the Tsetlin library, which corresponds to the case when the poset is the anti-chain and hence L=S_n is the full symmetric group. We also provide explicit eigenvalues of the transition matrix in general when the poset is a rooted forest. This is shown by proving that the associated monoid is R-trivial and then using Steinberg's extension of Brown's theory for Markov chains on left regular bands to R-trivial monoids.Comment: 35 pages, more examples of promotion, rephrased the main theorems in terms of discrete time Markov chain

Replication, Pathogenesis and Transmission of Pandemic (H1N1) 2009 Virus in Non-Immune Pigs

The declaration of the human influenza A pandemic (H1N1) 2009 (H1N1/09) raised important questions, including origin and host range [1,2]. Two of the three pandemics in the last century resulted in the spread of virus to pigs (H1N1, 1918; H3N2, 1968) with subsequent independent establishment and evolution within swine worldwide [3]. A key public and veterinary health consideration in the context of the evolving pandemic is whether the H1N1/09 virus could become established in pig populations [4]. We performed an infection and transmission study in pigs with A/California/07/09. In combination, clinical, pathological, modified influenza A matrix gene real time RT-PCR and viral genomic analyses have shown that infection results in the induction of clinical signs, viral pathogenesis restricted to the respiratory tract, infection dynamics consistent with endemic strains of influenza A in pigs, virus transmissibility between pigs and virus-host adaptation events. Our results demonstrate that extant H1N1/09 is fully capable of becoming established in global pig populations. We also show the roles of viral receptor specificity in both transmission and tissue tropism. Remarkably, following direct inoculation of pigs with virus quasispecies differing by amino acid substitutions in the haemagglutinin receptor-binding site, only virus with aspartic acid at position 225 (225D) was detected in nasal secretions of contact infected pigs. In contrast, in lower respiratory tract samples from directly inoculated pigs, with clearly demonstrable pulmonary pathology, there was apparent selection of a virus variant with glycine (225G). These findings provide potential clues to the existence and biological significance of viral receptor-binding variants with 225D and 225G during the 1918 pandemic [5]

Surface Terms as Counterterms in the AdS/CFT Correspondence

We examine the recently proposed technique of adding boundary counterterms to the gravitational action for spacetimes which are locally asymptotic to anti-de Sitter. In particular, we explicitly identify higher order counterterms, which allow us to consider spacetimes of dimensions d<=7. As the counterterms eliminate the need of ``background subtraction'' in calculating the action, we apply this technique to study examples where the appropriate background was ambiguous or unknown: topological black holes, Taub-NUT-AdS and Taub-Bolt-AdS. We also identify certain cases where the covariant counterterms fail to render the action finite, and we comment on the dual field theory interpretation of this result. In some examples, the case of vanishing cosmological constant may be recovered in a limit, which allows us to check results and resolve ambiguities in certain asymptotically flat spacetime computations in the literature.Comment: Revtex, 18 pages. References updated and few typo's fixed. Final versio

The Effective Field Theory of Inflation

We study the effective field theory of inflation, i.e. the most general theory describing the fluctuations around a quasi de Sitter background, in the case of single field models. The scalar mode can be eaten by the metric by going to unitary gauge. In this gauge, the most general theory is built with the lowest dimension operators invariant under spatial diffeomorphisms, like g^{00} and K_{mu nu}, the extrinsic curvature of constant time surfaces. This approach allows us to characterize all the possible high energy corrections to simple slow-roll inflation, whose sizes are constrained by experiments. Also, it describes in a common language all single field models, including those with a small speed of sound and Ghost Inflation, and it makes explicit the implications of having a quasi de Sitter background. The non-linear realization of time diffeomorphisms forces correlation among different observables, like a reduced speed of sound and an enhanced level of non-Gaussianity.Comment: 26 pages. v2: minor corrections, JHEP published versio

Charged AdS Black Holes and Catastrophic Holography

We compute the properties of a class of charged black holes in anti-de Sitter space-time, in diverse dimensions. These black holes are solutions of consistent Einstein-Maxwell truncations of gauged supergravities, which are shown to arise from the inclusion of rotation in the transverse space. We uncover rich thermodynamic phase structures for these systems, which display classic critical phenomena, including structures isomorphic to the van der Waals-Maxwell liquid-gas system. In that case, the phases are controlled by the universal `cusp' and `swallowtail' shapes familiar from catastrophe theory. All of the thermodynamics is consistent with field theory interpretations via holography, where the dual field theories can sometimes be found on the world volumes of coincident rotating branes.Comment: 19 pages, revtex, psfig, 6 multicomponent figures, typos, references and a few remarks have been repaired, and adde

General Brane Geometries from Scalar Potentials: Gauged Supergravities and Accelerating Universes

We find broad classes of solutions to the field equations for d-dimensional gravity coupled to an antisymmetric tensor of arbitrary rank and a scalar field with non-vanishing potential. Our construction generates these configurations from the solution of a single nonlinear ordinary differential equation, whose form depends on the scalar potential. For an exponential potential we find solutions corresponding to brane geometries, generalizing the black p-branes and S-branes known for the case of vanishing potential. These geometries are singular at the origin with up to two (regular) horizons. Their asymptotic behaviour depends on the parameters of the model. When the singularity has negative tension or the cosmological constant is positive we find time-dependent configurations describing accelerating universes. Special cases give explicit brane geometries for (compact and non-compact) gauged supergravities in various dimensions, as well as for massive 10D supergravity, and we discuss their interrelation. Some examples lift to give new solutions to 10D supergravity. Limiting cases with a domain wall structure preserve part of the supersymmetries of the vacuum. We also consider more general potentials, including sums of exponentials. Exact solutions are found for these with up to three horizons, having potentially interesting cosmological interpretation. We give several additional examples which illustrate the power of our techniques.Comment: 54 pages, 6 figures. Uses JHEP3. Published versio

Novel genetic loci associated with hippocampal volume

The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg =-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness

Emergence and maintenance of actionable genetic drivers at medulloblastoma relapse

Background Less than 5% of medulloblastoma (MB) patients survive following failure of contemporary radiation-based therapies. Understanding the molecular drivers of medulloblastoma relapse (rMB) will be essential to improve outcomes. Initial genome-wide investigations have suggested significant genetic divergence of the relapsed disease. Methods We undertook large-scale integrated characterization of the molecular features of rMB—molecular subgroup, novel subtypes, copy number variation (CNV), and driver gene mutation. 119 rMBs were assessed in comparison with their paired diagnostic samples (n = 107), alongside an independent reference cohort sampled at diagnosis (n = 282). rMB events were investigated for association with outcome post-relapse in clinically annotated patients (n = 54). Results Significant genetic evolution occurred over disease-course; 40% of putative rMB drivers emerged at relapse and differed significantly between molecular subgroups. Non-infant MBSHH displayed significantly more chromosomal CNVs at relapse (TP53 mutation-associated). Relapsed MBGroup4 demonstrated the greatest genetic divergence, enriched for targetable (eg, CDK amplifications) and novel (eg, USH2A mutations) events. Importantly, many hallmark features of MB were stable over time; novel subtypes (>90% of tumors) and established genetic drivers (eg, SHH/WNT/P53 mutations; 60% of rMB events) were maintained from diagnosis. Critically, acquired and maintained rMB events converged on targetable pathways which were significantly enriched at relapse (eg, DNA damage signaling) and specific events (eg, 3p loss) predicted survival post-relapse. Conclusions rMB is characterised by the emergence of novel events and pathways, in concert with selective maintenance of established genetic drivers. Together, these define the actionable genetic landscape of rMB and provide a basis for improved clinical management and development of stratified therapeutics, across disease-course