Second order ancillary: A differential view from continuity

Second order approximate ancillaries have evolved as the primary ingredient for recent likelihood development in statistical inference. This uses quantile functions rather than the equivalent distribution functions, and the intrinsic ancillary contour is given explicitly as the plug-in estimate of the vector quantile function. The derivation uses a Taylor expansion of the full quantile function, and the linear term gives a tangent to the observed ancillary contour. For the scalar parameter case, there is a vector field that integrates to give the ancillary contours, but for the vector case, there are multiple vector fields and the Frobenius conditions for mutual consistency may not hold. We demonstrate, however, that the conditions hold in a restricted way and that this verifies the second order ancillary contours in moderate deviations. The methodology can generate an appropriate exact ancillary when such exists or an approximate ancillary for the numerical or Monte Carlo calculation of $p$-values and confidence quantiles. Examples are given, including nonlinear regression and several enigmatic examples from the literature.Comment: Published in at http://dx.doi.org/10.3150/10-BEJ248 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm

Higher Accuracy for Bayesian and Frequentist Inference: Large Sample Theory for Small Sample Likelihood

Recent likelihood theory produces $p$-values that have remarkable accuracy and wide applicability. The calculations use familiar tools such as maximum likelihood values (MLEs), observed information and parameter rescaling. The usual evaluation of such $p$-values is by simulations, and such simulations do verify that the global distribution of the $p$-values is uniform(0, 1), to high accuracy in repeated sampling. The derivation of the $p$-values, however, asserts a stronger statement, that they have a uniform(0, 1) distribution conditionally, given identified precision information provided by the data. We take a simple regression example that involves exact precision information and use large sample techniques to extract highly accurate information as to the statistical position of the data point with respect to the parameter: specifically, we examine various $p$-values and Bayesian posterior survivor $s$-values for validity. With observed data we numerically evaluate the various $p$-values and $s$-values, and we also record the related general formulas. We then assess the numerical values for accuracy using Markov chain Monte Carlo (McMC) methods. We also propose some third-order likelihood-based procedures for obtaining means and variances of Bayesian posterior distributions, again followed by McMC assessment. Finally we propose some adaptive McMC methods to improve the simulation acceptance rates. All these methods are based on asymptotic analysis that derives from the effect of additional data. And the methods use simple calculations based on familiar maximizing values and related informations. The example illustrates the general formulas and the ease of calculations, while the McMC assessments demonstrate the numerical validity of the $p$-values as percentage position of a data point. The example, however, is very simple and transparent, and thus gives little indication that in a wide generality of models the formulas do accurately separate information for almost any parameter of interest, and then do give accurate $p$-value determinations from that information. As illustration an enigmatic problem in the literature is discussed and simulations are recorded; various examples in the literature are cited.Comment: Published in at http://dx.doi.org/10.1214/07-STS240 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Water system virus detection

The performance of a waste water reclamation system is monitored by introducing a non-pathogenic marker virus, bacteriophage F2, into the waste-water prior to treatment and, thereafter, testing the reclaimed water for the presence of the marker virus. A test sample is first concentrated by absorbing any marker virus onto a cellulose acetate filter in the presence of a trivalent cation at low pH and then flushing the filter with a limited quantity of a glycine buffer solution to desorb any marker virus present on the filter. Photo-optical detection of indirect passive immune agglutination by polystyrene beads indicates the performance of the water reclamation system in removing the marker virus. A closed system provides for concentrating any marker virus, initiating and monitoring the passive immune agglutination reaction, and then flushing the system to prepare for another sample

A systematic review of reported reassortant viral lineages of influenza A

BACKGROUND: Most previous evolutionary studies of influenza A have focussed on genetic drift, or reassortment of specific gene segments, hosts or subtypes. We conducted a systematic literature review to identify reported claimed reassortant influenza A lineages with genomic data available in GenBank, to obtain 646 unique first-report isolates out of a possible 20,781 open-access genomes. RESULTS: After adjusting for correlations, only: swine as host, China, Europe, Japan and years between 1997 and 2002; remained as significant risk factors for the reporting of reassortant viral lineages. For swine H1, more reassortants were observed in the North American H1 clade compared with the Eurasian avian-like H1N1 clade. Conversely, for avian H5 isolates, a higher number of reported reassortants were observed in the European H5N2/H3N2 clade compared with the H5N2 North American clade. CONCLUSIONS: Despite unavoidable biases (publication, database choice and upload propensity) these results synthesize a large majority of the current literature on novel reported influenza A reassortants and are a potentially useful prerequisite to inform further algorithmic studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-015-1298-9) contains supplementary material, which is available to authorized users

Aerosol scattering of ultraviolet sunlight in the tropical maritime atmosphere

The effects of atmospheric aerosol scattering on the vertical profile of solar ultraviolet radiation are investigated. Measurements of diffuse and total ultraviolet radiation were made using a rocketborne optical sonde in the marine atmosphere of Antigua. During observations, the sun was at zenith. Vertical profiles of directly transmitted solar radiation were calculated by subtraction of the diffuse component from the total radiance. Using these values of direct downward solar UV-flux, the optical thickness of the atmosphere was derived as a function of altitude. Absorption by ozone was also considered. In the troposphere the values of observed optical thickness were in general equal to or lower than those expected theoretically from Rayleigh scattering alone. The measured radiation profiles were compared with those computed for a multiple scattering model atmosphere. Some computations regarding the interaction of UV-sunlight with maritime aerosols are presented

The pathway of hepatitis C virus mRNA recruitment to the human ribosome.

Eukaryotic protein synthesis begins with mRNA positioning in the ribosomal decoding channel in a process typically controlled by translation-initiation factors. Some viruses use an internal ribosome entry site (IRES) in their mRNA to harness ribosomes independently of initiation factors. We show here that a ribosome conformational change that is induced upon hepatitis C viral IRES binding is necessary but not sufficient for correct mRNA positioning. Using directed hydroxyl radical probing to monitor the assembly of IRES-containing translation-initiation complexes, we have defined a crucial step in which mRNA is stabilized upon initiator tRNA binding. Unexpectedly, however, this stabilization occurs independently of the AUG codon, underscoring the importance of initiation factor-mediated interactions that influence the configuration of the decoding channel. These results reveal how an IRES RNA supplants some, but not all, of the functions normally carried out by protein factors during initiation of protein synthesis

Infrared spectra of van de Waals complexes of importance in planetary atmospheres

It has been suggested that (CO2)2 and Ar-CO2 are important constituents of the planetary atmospheres of Venus and Mars. Recent results on the laboratory spectroscopy of CO2 containing van der Waals complexes which may be of use in the modeling of the spectra of planetary atmospheres are presented. Sub-Doppler infrared spectra were obtained for (CO2)2, (CO2)3, and rare-gas-CO2 complexes in the vicinity of the CO2 Fermi diad at 2.7 micrometers using a color-center-laser optothermal spectrometer. From the spectroscopic constants the geometries of the complexes have been determined and van der Waals vibrational frequencies have been estimated. The equilibrium configurations are C2h, C3h, and C2v, for (CO2)2, (CO2)3, and the rare-gas-CO2 complexes, respectively. Most of the homogeneous linewidths for the revibrational transitions range from 0.5 to 22 MHz, indicating that predissociation is as much as four orders of magnitude faster than radiative processes for vibrational relaxation in these complexes

Evolving collective behavior in an artificial ecology

Collective behavior refers to coordinated group motion, common to many animals. The dynamics of a group can be seen as a distributed model, each “animal” applying the same rule set. This study investigates the use of evolved sensory controllers to produce schooling behavior. A set of artificial creatures “live” in an artificial world with hazards and food. Each creature has a simple artificial neural network brain that controls movement in different situations. A chromosome encodes the network structure and weights, which may be combined using artificial evolution with another chromosome, if a creature should choose to mate. Prey and predators coevolve without an explicit fitness function for schooling to produce sophisticated, nondeterministic, behavior. The work highlights the role of species’ physiology in understanding behavior and the role of the environment in encouraging the development of sensory systems