Phylogenomic analyses data of the avian phylogenomics project.

BACKGROUND: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. FINDINGS: Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. CONCLUSIONS: The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

On stratifiable locally convex spaces

In the present paper we prove several results on the stratifiability of locally convex spaces. In particular, we show that a free locally convex sum of an arbitrary set of stratifiable LCS is a stratifiable LCS, and that all locally convex F'-spaces whose bounded subsets are metrizable are stratifiable. Moreover, we prove that a strict inductive limit of metrizable LCS is stratifiable and establish the stratifiability of many important general and specific spaces used in functional analysis. We also construct some examples that clarify the relationship between the stratifiability and other properties.

Recent advances in understanding CO oxidation on gold nanoparticles using density functional theory

Since the discovery of a series of Au-based catalysts by Haruta et al. considerable progress has been made in understanding the active role of Au in CO oxidation catalysis. This review provides a summary of recent theoretical work performed in this field; in particular it addresses DFT studies of CO oxidation catalysis over free and supported gold nanoparticles. Several properties of the Au particles have been found to contribute to their unique catalytic activity. Of these properties, the low-coordination state of the Au atoms is arguably the most pertinent, although other properties of the Au cluster atoms, such as electronic charge, cannot be ignored. The current consensuses regarding the mechanism for CO oxidation over Au-based catalysts is also discussed. Finally, water-enhanced catalysis of CO oxidation on Au clusters is summarized.

Experimental Design to Optimize High-Volume Ash Grout in the Presence of Welan Gum and Superplasticizer

Applications such as soil, rock and oil-well grouting all require enormous amounts of cement and are good examples of areas where a high volume of fly ash could partially replace cement to produce low-cost, environmentally safe and durable concrete. There is an increasing need to identify the rheological properties of cement grout using a simple test to determine the fluidity, and other properties of underwater grouts such as washout resistance and compressive strength. This paper presents statistical models developed using a fractorial design which was carried out to model the influence of key parameters on properties affecting the performance of underwater grout. Such responses of fluidity included mini-slump and flow time measured by Marsh cone, washout resistance, unit weight and compressive strength. The models are valid for mixes with 0.40 to 0.60 water-to-cementitious materials ratio, 0.02 to 0.08% of anti-washout admixture, by mass of binder, and 0.6 to 1.8% of superplasticizer, by mass of cementitious materials. The grout was made with 50% of pulverized-fuel ash replacement, by mass ofcementitious materials. Also presented are the derived models that enable the identification of underlying primary factors and their interactions that influence the modelled responses of underwater cement grout. Such parameters can be useful to reduce the test protocol needed for proportioning of underwater cement grout. This paper highlighted the influence of W/CM and dosage of antiwashout admixture and superplasticizer on fluidity, washout resistance and compressive strength and attempted also to demonstrate the usefulness of the models to improve understanding of trade-offs between parameters.

Factorial Design of Modelling Mix Proportion Parameters of Underwater Composite Cement Grouts

There is an increasing need to identify the rheological properties of cement grout using a simple test to determine the fluidity, and other properties of underwater applications such as washout resistance and compressive strength. This paper reviews statistical models developed using a factorial design that was carried out to model the influence of key parameters on properties affecting the performance of underwater cement grout. Such responses of fluidity included minislump and flow time measured by Marsh cone, washout resistance, unit weight, and compressive strength. The models are valid for mixes with 0.35–0.55 water-to-binder ratio (W/B), 0.053–0.141% of antiwashout admixture (AWA), by mass of water, and 0.4–1.8% (dry extract) of superplasticizer (SP), by mass of binder. Two types of underwater grout were tested: the first one made with cement and the second one made with 20% of pulverised fuel ash (PFA) replacement, by mass of binder. Also presented are the derived models that enable the identification of underlying primary factors and their interactions that influence the modelled responses of underwater cement grout. Such parameters can be useful to reduce the test protocol needed for proportioning of underwater cement grout. This paper attempts also to demonstrate the usefulness of the models to better understand trade-offs between parameters and compare the responses obtained from the various test methods that are highlighted.

FROM LINE-DRAWINGS TO IMPRESSIONS OF 3D OBJECTS - DEVELOPING A MODEL TO ACCOUNT FOR THE SHAPES THAT PEOPLE SEE

The interpretations people attach to line drawings reflect shape-related processes in human vision. Their divergences from expectations embodied in related machine vision traditions are summarized, and used to suggest how human vision decomposes the task of interpretation. A model called IO implements this idea. It first identifies geometrically regular, local fragments. Initial decisions fix edge orientations, and this information constrains decisions about other properties. Relations between fragments are explored, beginning with weak consistency checks and moving to fuller ones. IO's output captures multiple distinctive characteristics of human performance, and it suggests steady progress towards understanding shape-related visual processes is possible.

The role of secretory leucoprotease inhibitor in the resolution of inflammatory responses

Chronic lung disease is one of the most common causes of death and disability worldwide. This group of diseases is characterized by a protease burden, an infective process and a dominant pro-inflammatory profile. While SLPI (secretory leucoprotease inhibitor) was initially identified as a serine protease inhibitor, it has since been shown that SLPI possesses other properties distinct from those associated with its antiprotease capabilities that play an important role in protecting the host from infection and injury. In the course of this review, we will highlight the findings from a range of studies that illustrate the multiple functions of SLPI and its role in the resolution of the immune response.

Good news-bad news:the Yin and Yang of immune privilege in the eye

The eye and the brain are prototypical tissues manifesting immune privilege (IP) in which immune responses to foreign antigens, particularly alloantigens are suppressed, and even completely inhibited. Explanations for this phenomenon are numerous and mostly reflect our evolving understanding of the molecular and cellular processes underpinning immunological responses generally. IP is now viewed as a property of many tissues and the level of expression of IP varies not only with the tissue but with the nature of the foreign antigen and changes in the limited conditions under which privilege can operate as a mechanism of immunological tolerance. As a result, IP functions normally as a homeostatic mechanism preserving normal function in tissues, particularly those with highly specialized function and limited capacity for renewal such as the eye and brain. However, IP is relatively easily bypassed in the face of a sufficiently strong immunological response, and the privileged tissues may be at greater risk of collateral damage because its natural defenses are more easily breached than in a fully immunocompetent tissue which rapidly rejects foreign antigen and restores integrity. This two-edged sword cuts its swathe through the eye: under most circumstances, IP mechanisms such as blood-ocular barriers, intraocular immune modulators, induction of T regulatory cells, lack of lymphatics, and other properties maintain tissue integrity; however, when these are breached, various degrees of tissue damage occur from severe tissue destruction in retinal viral infections and other forms of uveoretinal inflammation, to less severe inflammatory responses in conditions such as macular degeneration. Conversely, ocular IP and tumor-related IP can combine to permit extensive tumor growth and increased risk of metastasis thus threatening the survival of the host.

Toward Characterization Of The Type IIP Supernova Progenitor Population: A Statistical Sample Of Light Curves From Pan-STARRS1

In recent years, wide-field sky surveys providing deep multi-band imaging have presented a new path for indirectly characterizing the progenitor populations of core-collapse supernovae (SN): systematic light curve studies. We assemble a set of 76 grizy-band Type IIP SN light curves from Pan-STARRS1, obtained over a constant survey program of 4 years and classified using both spectroscopy and machine learning-based photometric techniques. We develop and apply a new Bayesian model for the full multi-band evolution of each light curve in the sample. We find no evidence of a sub-population of fast-declining explosions (historically referred to as "Type IIL" SNe). However, we identify a highly significant relation between the plateau phase decay rate and peak luminosity among our SNe IIP. These results argue in favor of a single parameter, likely determined by initial stellar mass, predominantly controlling the explosions of red supergiants. This relation could also be applied for supernova cosmology, offering a standardizable candle good to an intrinsic scatter of 0.2 mag. We compare each light curve to physical models from hydrodynamic simulations to estimate progenitor initial masses and other properties of the Pan-STARRS1 Type IIP SN sample. We show that correction of systematic discrepancies between modeled and observed SN IIP light curve properties and an expanded grid of progenitor properties, are needed to enable robust progenitor inferences from multi-band light curve samples of this kind. This work will serve as a pathfinder for photometric studies of core-collapse SNe to be conducted through future wide field transient searches.

Young Stellar Object VARiability (YSOVAR): Long Timescale Variations in the Mid-infrared

The YSOVAR (Young Stellar Object VARiability) Spitzer Space Telescope observing program obtained the first extensive mid-infrared (3.6 and 4.5 μm) time series photometry of the Orion Nebula Cluster plus smaller footprints in 11 other star-forming cores (AFGL 490, NGC 1333, Mon R2, GGD 12-15, NGC 2264, L1688, Serpens Main, Serpens South, IRAS 20050+2720, IC 1396A, and Ceph C). There are ~29,000 unique objects with light curves in either or both IRAC channels in the YSOVAR data set. We present the data collection and reduction for the Spitzer and ancillary data, and define the "standard sample" on which we calculate statistics, consisting of fast cadence data, with epochs roughly twice per day for ~40 days. We also define a "standard sample of members" consisting of all the IR-selected members and X-ray-selected members. We characterize the standard sample in terms of other properties, such as spectral energy distribution shape. We use three mechanisms to identify variables in the fast cadence data—the Stetson index, a χ2 fit to a flat light curve, and significant periodicity. We also identified variables on the longest timescales possible of six to seven years by comparing measurements taken early in the Spitzer mission with the mean from our YSOVAR campaign. The fraction of members in each cluster that are variable on these longest timescales is a function of the ratio of Class I/total members in each cluster, such that clusters with a higher fraction of Class I objects also have a higher fraction of long-term variables. For objects with a YSOVAR-determined period and a [3.6]-[8] color, we find that a star with a longer period is more likely than those with shorter periods to have an IR excess. We do not find any evidence for variability that causes [3.6]-[4.5] excesses to appear or vanish within our data set; out of members and field objects combined, at most 0.02% may have transient IR excesses.

Lanthanide-organic frameworks for optical and catalytic applications

Este projecto de doutoramento tem como objetivo isolar e caracterizar sistematicamente novos polímeros de coordenação, no estado sólido. A presença de grupos rígidos possuindo, em particular, átomos de oxigénio e de azoto, deverá induzir interessantes propriedades fotoluminescentes (rendimentos quânticos e tempos de vida elevados, assim como vias de transferência de energia eficientes), que poderão permitir a utilização dos compostos poliméricos na produção de dispositivos funcionais. As diferentes abordagens sintéticas foram ajustadas para cada material e basearam-se, preferencialmente, nas sínteses hidrotérmicas e nas assistidas por radiação de microondas. A estrutura dos materiais foi elucidada a partir de métodos de difracção de raios X (de cristal único ou de pós) em conjunto com outras técnicas, tais como RMN de estado sólido, microscopia eletrónica, análises térmicas, espectroscopia vibracional e estudos de composição elementar. Os compostos microcristalinos foram sistematicamente estudados a fim de investigar outras propriedades além das de fotoluminescência. Alguns dos materiais revelaram multifuncionalidade apresentando simultaneamente tempos de vida na ordem dos milisegundos, elevados rendimentos quânticos e elevado desempenho como catalisadores heterogéneos. As propriedades magnéticas de um composto baseado em érbio foram igualmente estudadas, assim como as de adsorpção e permuta de solvente de uma estrutura porosa baseada em cério.

Second Welland Canal - Book 3, Survey Map 18 - Through Humberstone

Survey map of the Second Welland Canal created by the Welland Canal Company showing the area through Humberstone Township. Identified structures associated with the Canal are the north and south back ditches, Towing Path and spoil banks. Surveyor measurements and notes can be seen in red and black ink and pencil. Local area landmarks include Tram Way to Peat Beds. Roads running parallel to Canal are the Road to Port Colborn and the northern Road Allowance. Roads running parallel to Canal are Road Allowance between the 2nd and 3rd Concession, Road Allowance between the 3rd and 4th Concession. Properties and property owners are noted as follows: J. Thompson, J. Sullivan, J. Leady, John Neff and Peter Neff. Other properties include: Lot No. 27, 3rd Concession, Lot No. 26, 3rd Concession and Lot No. 25, 3rd Concession."Humberstone" - Scale 4 Chs. per Inch

Magnetic and processability studies of nitrile rubber vulcanisates containing barium ferrite and carbon black

Fine particles of barium ferrite (BaFe12O19) belonging to the M-type hexagonal ferrites were prepared by the conventional ceramic techniques. They were incorporated into a nitrile rubber matrix according to a specific recipe for various loadings to produce rubber ferrite composites (RFC). The percolation threshold is not reached for a maximum loading of 130 phr (parts per hundred rubber). Here in this paper, the magnetic properties and processability of the nitrile rubber based RFCs containing barium ferrite (BaF) and HAF carbon black is reported. The magnetic properties of the ceramic ferrite and these rubber ferrite composites were evaluated and it was found that the coercivity values of RFCs were less than that of the ceramic BaF, but remained constant with the loading of both the ferrite filler and carbon black. However, other properties like saturation magnetization and magnetic remanence increased with the loading of ferrite filler.

A Detailed Look at Scale and Translation Invariance in a Hierarchical Neural Model of Visual Object Recognition

The HMAX model has recently been proposed by Riesenhuber & Poggio as a hierarchical model of position- and size-invariant object recognition in visual cortex. It has also turned out to model successfully a number of other properties of the ventral visual stream (the visual pathway thought to be crucial for object recognition in cortex), and particularly of (view-tuned) neurons in macaque inferotemporal cortex, the brain area at the top of the ventral stream. The original modeling study only used ``paperclip'' stimuli, as in the corresponding physiology experiment, and did not explore systematically how model units' invariance properties depended on model parameters. In this study, we aimed at a deeper understanding of the inner workings of HMAX and its performance for various parameter settings and ``natural'' stimulus classes. We examined HMAX responses for different stimulus sizes and positions systematically and found a dependence of model units' responses on stimulus position for which a quantitative description is offered. Interestingly, we find that scale invariance properties of hierarchical neural models are not independent of stimulus class, as opposed to translation invariance, even though both are affine transformations within the image plane.

Option pricing in market models driven by telegraph processes with jumps

Esta tesis está dividida en dos partes: en la primera parte se presentan y estudian los procesos telegráficos, los procesos de Poisson con compensador telegráfico y los procesos telegráficos con saltos. El estudio presentado en esta primera parte incluye el cálculo de las distribuciones de cada proceso, las medias y varianzas, así como las funciones generadoras de momentos entre otras propiedades. Utilizando estas propiedades en la segunda parte se estudian los modelos de valoración de opciones basados en procesos telegráficos con saltos. En esta parte se da una descripción de cómo calcular las medidas neutrales al riesgo, se encuentra la condición de no arbitraje en este tipo de modelos y por último se calcula el precio de las opciones Europeas de compra y venta.