Notes on a collection of birds from Mindoro Island, Philippines

The 1954 Yale Peabody Museum-Silliman University Mindoro Zoological Expedition, headed by D. S. Rabor, stayed in the field from March 21 until June 7, 1954….https://elischolar.library.yale.edu/peabody_museum_natural_history_bulletin/1012/thumbnail.jp

New birds from Palawan and Culion Islands, Philippines

The Palawan Expedition of 1962 was sponsored jointly by the Yale Peabody Museum, the Entomology Section of the U. S. Army Medical Research and Development Command of the Office of the Surgeon General

Spatially embedded random networks

Many real-world networks analyzed in modern network theory have a natural spatial element; e.g., the Internet, social networks, neural networks, etc. Yet, aside from a comparatively small number of somewhat specialized and domain-specific studies, the spatial element is mostly ignored and, in particular, its relation to network structure disregarded. In this paper we introduce a model framework to analyze the mediation of network structure by spatial embedding; specifically, we model connectivity as dependent on the distance between network nodes. Our spatially embedded random networks construction is not primarily intended as an accurate model of any specific class of real-world networks, but rather to gain intuition for the effects of spatial embedding on network structure; nevertheless we are able to demonstrate, in a quite general setting, some constraints of spatial embedding on connectivity such as the effects of spatial symmetry, conditions for scale free degree distributions and the existence of small-world spatial networks. We also derive some standard structural statistics for spatially embedded networks and illustrate the application of our model framework with concrete examples

Differential regulation of different human papilloma virus variants by the POU family transcription factor Brn-3a

The Brn-3a POU family transcription factor is over-expressed in human cervical carcinoma biopsies and is able to activate expression of the human papilloma virus type 16 (HPV-16) upstream regulatory region (URR), which drives the expression of the E6 and E7 oncoproteins. Inhibition of Brn-3a expression in human cervical cancer cells inhibits HPV gene expression and reduces cellular growth and anchorage independence in vitro as well as the ability to form tumours in vivo. Here we show that Brn-3a differentially regulates different HPV-16 variants that have previously been shown to be associated with different risks of progression to cervical carcinoma. In human cervical material Brn-3a levels correlate directly with HPV E6 levels in individuals infected with a high risk variant of HPV-16 whereas this is not the case for a low risk variant. Moreover, the URRs of high and intermediate risk variants are activated by Brn-3a in transfection assays whereas the URR of a low risk variant is not. The change of one or two bases in a low risk variant URR to their equivalent in a higher risk URR can render the URR responsive to Brn-3a and vice versa. These results help explain why the specific interplay between viral and cellular factors necessary for the progression to cervical carcinoma, only occurs in a minority of those infected with HPV-16

Non-equilibrium dynamics of stochastic point processes with refractoriness

Stochastic point processes with refractoriness appear frequently in the quantitative analysis of physical and biological systems, such as the generation of action potentials by nerve cells, the release and reuptake of vesicles at a synapse, and the counting of particles by detector devices. Here we present an extension of renewal theory to describe ensembles of point processes with time varying input. This is made possible by a representation in terms of occupation numbers of two states: Active and refractory. The dynamics of these occupation numbers follows a distributed delay differential equation. In particular, our theory enables us to uncover the effect of refractoriness on the time-dependent rate of an ensemble of encoding point processes in response to modulation of the input. We present exact solutions that demonstrate generic features, such as stochastic transients and oscillations in the step response as well as resonances, phase jumps and frequency doubling in the transfer of periodic signals. We show that a large class of renewal processes can indeed be regarded as special cases of the model we analyze. Hence our approach represents a widely applicable framework to define and analyze non-stationary renewal processes.Comment: 8 pages, 4 figure

A Naive Bayes Source Classifier for X-ray Sources

The Chandra Carina Complex Project (CCCP) provides a sensitive X-ray survey of a nearby starburst region over >1 square degree in extent. Thousands of faint X-ray sources are found, many concentrated into rich young stellar clusters. However, significant contamination from unrelated Galactic and extragalactic sources is present in the X-ray catalog. We describe the use of a naive Bayes classifier to assign membership probabilities to individual sources, based on source location, X-ray properties, and visual/infrared properties. For the particular membership decision rule adopted, 75% of CCCP sources are classified as members, 11% are classified as contaminants, and 14% remain unclassified. The resulting sample of stars likely to be Carina members is used in several other studies, which appear in a Special Issue of the ApJS devoted to the CCCP.Comment: Accepted for the ApJS Special Issue on the Chandra Carina Complex Project (CCCP), scheduled for publication in May 2011. All 16 CCCP Special Issue papers are available at http://cochise.astro.psu.edu/Carina_public/special_issue.html through 2011 at least. 19 pages, 7 figure

Limits of Abductivism About Logic

I argue against abductivism about logic, which is the view that rational theory choice in logic happens by abduction. Abduction cannot serve as a neutral arbiter in many foundational disputes in logic because, in order to use abduction, one must first identify the relevant data. Which data one deems relevant depends on what I call one's conception of logic. One's conception of logic is, however, not independent of one's views regarding many of the foundational disputes that one may hope to solve by abduction

Frequency Dependent Rheology of Vesicular Rhyolite

Frequency dependent rheology of magmas may result from the presence of inclusions (bubbles, crystals) in the melt and/or from viscoelastic behavior of the melt itself. With the addition of deformable inclusions to a melt possessing viscoelastic properties one might expect changes in the relaxation spectrum of the shear stresses of the material (e.g., broadening of the relaxation spectrum) resulting from the viscously deformable geometry of the second phase. We have begun to investigate the effect of bubbles on the frequency dependent rheology of rhyolite melt. The present study deals with the rheology of bubble-free and vesicular rhyolite melts containing spherical voids of 10 and 30 vol %. We used a sinusoidal torsion deformation device. Vesicular rhyolite melts were generated by the melting (at 1 bar) of an Armenian obsidian (Dry Fountain, Erevan, Armenia) and Little Glass Mountain obsidian (California). The real and imaginary parts of shear viscosity and shear modulus have been determined in a frequency range of 0.005–10 Hz and temperature range of 600°–900°C. The relaxed shear viscosities of samples obtained at low frequencies and high temperatures compare well with data previously obtained by parallel plate viscometry. The relaxed shear viscosity of vesicular rhyolites decreases progressively with increasing bubble content. The relaxation spectrum for rhyolite melt without bubbles has an asymmetric form and fits an extended exponent relaxation. The presence of deformable bubbles results in an imaginary component of the shear modulus that becomes more symmetrical and extends into the low-frequency/high-temperature range. The internal friction Q −1 is unaffected in the high-frequency/low-temperature range by the presence of bubbles and depends on the bubble content in the high-temperature/low-frequency range. The present work, in combination with the previous study of Stein and Spera (1992), illustrates that magma viscosity can either increase or decrease with bubble content, depending upon the rate of style of strain during magmatic flow

Extracting galactic binary signals from the first round of Mock LISA Data Challenges

We report on the performance of an end-to-end Bayesian analysis pipeline for detecting and characterizing galactic binary signals in simulated LISA data. Our principal analysis tool is the Blocked-Annealed Metropolis Hasting (BAM) algorithm, which has been optimized to search for tens of thousands of overlapping signals across the LISA band. The BAM algorithm employs Bayesian model selection to determine the number of resolvable sources, and provides posterior distribution functions for all the model parameters. The BAM algorithm performed almost flawlessly on all the Round 1 Mock LISA Data Challenge data sets, including those with many highly overlapping sources. The only misses were later traced to a coding error that affected high frequency sources. In addition to the BAM algorithm we also successfully tested a Genetic Algorithm (GA), but only on data sets with isolated signals as the GA has yet to be optimized to handle large numbers of overlapping signals.Comment: 13 pages, 4 figures, submitted to Proceedings of GWDAW-11 (Berlin, Dec. '06

Optimum sample size to estimate mean parasite abundance in fi sh parasite surveys

[EN] To reach ethically and scientifically valid mean abundance values in parasitological and epidemiological studies this paper considers analytic and simulation approaches for sample size determination. The sample size estimation was carried out by applying mathematical formula with predetermined precision level and parameter of the negative binomial distribution estimated from the empirical data. A simulation approach to optimum sample size determination aimed at the estimation of true value of the mean abundance and its confidence interval (CI) was based on the Bag of Little Bootstraps (BLB). The abundance of two species of monogenean parasites Ligophorus cephali and L. mediterraneus from Mugil cephalus across the Azov-Black Seas localities were subjected to the analysis. The dispersion pattern of both helminth species could be characterized as a highly aggregated distribution with the variance being substantially larger than the mean abundance. The holistic approach applied here offers a wide range of appropriate methods in searching for the optimum sample size and the understanding about the expected precision level of the mean. Given the superior performance of the BLB relative to formulae with its few assumptions, the bootstrap procedure is the preferred method. Two important assessments were performed in the present study: i) based on CIs width a reasonable precision level for the mean abundance in parasitological surveys of Ligophorus spp. could be chosen between 0.8 and 0.5 with 1.6 and 1x mean of the CIs width, and ii) the sample size equal 80 or more host individuals allows accurate and precise estimation of mean abundance. Meanwhile for the host sample size in range between 25 and 40 individuals, the median estimates showed minimal bias but the sampling distribution skewed to the low values; a sample size of 10 host individuals yielded to unreliable estimates.SS and VS were supported by MEDEA project fellowships, Erasmus Mundus Action 2. CC-S was funded by project #MTM2014-52975-C2-1-R:" Inference in Structured Additive Regression (STAR) Models with Extensions to Multivariate Responses. Applications in Biomedicine", cofinanced by the Ministry of Economy and Competitiveness (SPAIN) and by the European Regional Development Fund (FEDER). This study is partially supported by Ministry of Education and Science of Ukraine, project #1/17.Shvydka, S.; Sarabeev, V.; Estruch, VD.; Cadarso-Suarez, C. (2018). Optimum sample size to estimate mean parasite abundance in fi sh parasite surveys. Helminthologia. 55(1):52-59. https://doi.org/10.1515/helm-2017-0054S5259551Rohde, K., Hayward, C., & Heap, M. (1995). Aspects of the ecology of metazoan ectoparasites of marine fishes. International Journal for Parasitology, 25(8), 945-970. doi:10.1016/0020-7519(95)00015-tAnderson, R. M., & Gordon, D. M. (1982). Processes influencing the distribution of parasite numbers within host populations with special emphasis on parasite-induced host mortalities. Parasitology, 85(2), 373-398. doi:10.1017/s0031182000055347Poiani, A. (1992). Ectoparasitism as a possible cost of social life: a comparative analysis using Australian passerines (Passeriformes). Oecologia, 92(3), 429-441. doi:10.1007/bf00317470Kleiner, A., Talwalkar, A., Sarkar, P., & Jordan, M. I. (2014). A scalable bootstrap for massive data. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 76(4), 795-816. doi:10.1111/rssb.12050Jovani, R., & Tella, J. L. (2006). Parasite prevalence and sample size: misconceptions and solutions. Trends in Parasitology, 22(5), 214-218. doi:10.1016/j.pt.2006.02.011BAGGE, A. M., SASAL, P., VALTONEN, E. T., & KARVONEN, A. (2005). Infracommunity level aggregation in the monogenean communities of crucian carp (Carassius carassius). Parasitology, 131(3), 367-372. doi:10.1017/s0031182005007626Belghyti, D., Berrada-rkhami, O., Boy, V., Aguesse, P., & Gabrion, C. (1994). Population biology of two helminth parasites of flatfishes from the Atlantic coast of Morocco. Journal of Fish Biology, 44(6), 1005-1021. doi:10.1111/j.1095-8649.1994.tb01272.xTAYLOR, L. R. (1961). Aggregation, Variance and the Mean. Nature, 189(4766), 732-735. doi:10.1038/189732a