Top PDF On the validity of evolutionary models with site-specific parameters.

On the validity of evolutionary models with site-specific parameters.

On the validity of evolutionary models with site-specific parameters.

sizing: site-specific parameters cannot be estimated reliably (at least using currently typical data sets with no more than hundreds of taxa) and models that contain such parameters are not (or should not be) developed with the aim of obtaining and interpreting point estimates of parameters. Thus, although caution is always advisable especially in the absence of theoretical guarantees, unreliable point estimates do not constitute ‘‘inappro- priate statistical properties’’ as charged by Rodrigue, nor do they justify the conclusion [13] that these models ‘‘should be approached with particular caution when the site-specific variables are high dimensional’’. Maximum likelihood point estimates have been reported as unreliable even in cases where asymptotic guarantees are available, for example in random effects branch site models [16,17], and in neither class of models can the validity of hypotheses be judged solely on the basis of parameter point estimates. Instead, the models are intended for use in a statistical hypothesis testing framework (not addressed in Rodrigue’s study), which takes the uncertainty in the parameter estimates into account. For instance, it is popular to use the likelihood ratio test to determine whether the hypothesis of neutrality can be rejected. In many cases one obtains an estimate of the traditional dN/dS value that is highly uncertain in the sense of having a broad confidence interval and no reliable point estimate, but for which one can nevertheless be confident that the value is larger than 1, implying positive selection. Thus unreliable point estimates cannot be interpreted as grounds to distrust hypothesis tests. We cannot blame the use of site-specific parameters when researchers choose, inappropriately, to ignore the quantifiable uncertainty in param- eter estimates.
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An integrated in silico approach to design specific inhibitors targeting human poly(a)-specific ribonuclease.

An integrated in silico approach to design specific inhibitors targeting human poly(a)-specific ribonuclease.

Poly(A)-specific ribonuclease (PARN) is an exoribonuclease/deadenylase that degrades 39-end poly(A) tails in almost all eukaryotic organisms. Much of the biochemical and structural information on PARN comes from the human enzyme. However, the existence of PARN all along the eukaryotic evolutionary ladder requires further and thorough investigation. Although the complete structure of the full-length human PARN, as well as several aspects of the catalytic mechanism still remain elusive, many previous studies indicate that PARN can be used as potent and promising anti-cancer target. In the present study, we attempt to complement the existing structural information on PARN with in-depth bioinformatics analyses, in order to get a hologram of the molecular evolution of PARNs active site. In an effort to draw an outline, which allows specific drug design targeting PARN, an unequivocally specific platform was designed for the development of selective modulators focusing on the unique structural and catalytic features of the enzyme. Extensive phylogenetic analysis based on all the publicly available genomes indicated a broad distribution for PARN across eukaryotic species and revealed structurally important amino acids which could be assigned as potentially strong contributors to the regulation of the catalytic mechanism of PARN. Based on the above, we propose a comprehensive in silico model for the PARN’s catalytic mechanism and moreover, we developed a 3D pharmacophore model, which was subsequently used for the introduction of DNP-poly(A) amphipathic substrate analog as a potential inhibitor of PARN. Indeed, biochemical analysis revealed that DNP- poly(A) inhibits PARN competitively. Our approach provides an efficient integrated platform for the rational design of pharmacophore models as well as novel modulators of PARN with therapeutic potential.
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Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices.

Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices.

The impact of site-class specific matrices on phylogenomic inference, divergence date estimation, and studies of functional divergence are important directions for further research, but are beyond the scope of this study. Within the context of those activities, it will be interesting to explore the effect of clustering according to alternative measures of physiochemical properties. Furthermore, we expect that site-class specific exchangeability matrices will differ among the more divergent lineages of metazoans (e.g., cnidarians, arthropods, lophotrochozoans), as has been observed among joint matrices (e.g., [20–22]). Beyond the more practical benefits to these research activities, clustering of sites and estimating exchangeabilities can be used to directly investigate questions of molecular evolution. For example, the approach could shed some light on the relative importance of the genetic code versus physiochemical constraints in explaining the differences observed between the more divergent lineages of metazoans. Because the adequacy of an evolutionary model is central to so many different research activities, we predict that our general approach to grouping sites for the purpose of estimating exchangeabilities could have value beyond mitogenomic datasets. Figure 6. Comparison of branch lengths estimated under group-specific matrices and an overall matrix. Reduced datasets were used to investigate the impact of model-choice on branch lengths. A. A phylogenetic tree for 21 fish taxa. B. A plot showing differences between branch lengths estimated under partition-specific matrices and the mtFishR0 matrix. C. A plot showing the differences between the corrected branch lengths under a mixture of the partition specific matrices and mtFishR0 for the whole data. Differences between branch lengths (Bl) are measured as (Bl_R i /
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Application of Site- and Time- Heterogeneous Evolutionary Models to Mitochondrial Phylogenomics

Application of Site- and Time- Heterogeneous Evolutionary Models to Mitochondrial Phylogenomics

Smith (1984) was the first to study the phylogeny of Echinoderms using anatomical and developmental characters from both larvae and adults, since previous studies showed that larval characters alone and the fossil characters of the echinoderms could contribute for misleading evolutionary relationships between echinoderm classes. Under a parsimony analysis, the obtained topology (Table 1) supported the relationships between four of five classes of echinoderms, with the position of holothuroids being less clear (low support). This group (holothuroids) shares a number of derived characters with ophiuroids and echinoids and several others only with echinoids, while there are a number of other derived characters that are common to asteroids, ophiuroids and echinoids (Smith, 1984). A few years later, Strathmann (1988) reanalyzed larvae morphological characters but found no supported topology; whereas Pearse and Pearse (1994) presented a phylogenetic analysis based on anatomical characters of adult individuals supporting crinoids as sister group of the clades formed by the echinoids-holothuroids and of the ophiuroids-asteroid pairs. All these studies suggested that crinoids are the representatives of extant echinoderms that diverged earlier from the rest, but conflicting results still exist for the relationships between the remaining classes, which can result from a misinterpretation of morphological characters (Smith, 1984) (Table 1). For example, different studies presented different topologies using the same morphological characters dataset because authors had different opinions regarding character homology and polarity (Littlewood, 1995).
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Effect of water glass modification with nanoparticles of zinc oxide on selected physical and chemical properties of binder and mechanical properties of sand mixture

Effect of water glass modification with nanoparticles of zinc oxide on selected physical and chemical properties of binder and mechanical properties of sand mixture

In this study, an attempt was made to carry out the modification of water glass with zinc nanoxide. The aim of the research was to determine what effect the modifier added to binder may have on the wettability of quartz sand grains and on the mechanical properties of the resulting moulding sand mixture.

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EFFECT OF SEVERAL STRUCTURES OF CONTEMPORARY GROUPS ON ESTIMATES OF (CO)VARIANCE AND GENETIC PARAMETERS FOR WEANING WEIGHT IN NELLORE CATTLE

EFFECT OF SEVERAL STRUCTURES OF CONTEMPORARY GROUPS ON ESTIMATES OF (CO)VARIANCE AND GENETIC PARAMETERS FOR WEANING WEIGHT IN NELLORE CATTLE

According to the BIC and CAIC criteria, models that had sex of calf effect separated from CG, provided a better fit to the data. These models allowed the construction of contemporary groups with larger number of individuals and permitted better genetic connections among CG and higher accuracies of prediction of genetic evaluations. These results are in agreement with those found by REYES et al. (2006) for growth between birth and weaning in a multibreed Nellore x Hereford cattle population.
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Anselmo Ramalho Pitombeira Neto1 , Francisco Moraes de Oliveira Neto2, Carlos Felipe Grangeiro Loureiro3

Anselmo Ramalho Pitombeira Neto1 , Francisco Moraes de Oliveira Neto2, Carlos Felipe Grangeiro Loureiro3

For analytical convenience, many researchers have assumed that OD lows follow independent Poisson distributions, with the implication that traf ic volumes will also follow Poisson distributions with mean values equal to their variances. Nevertheless, Hazelton (2003) has argued that link volumes may be overdispersed, i.e., the variances may be greater than the mean values. This empirical inding poses the following research question: Do we incur severe errors if we assume Poisson distributions in the presence of overdispersion? In case link volumes depart considerably from the Poisson assumption, we should consider the use of more lexible probability distributions for OD lows which can accommodate the possibility of overdispersion or underdispersion.
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Spanish pharmacies valuation: what determines their price-to-sales ratio?

Spanish pharmacies valuation: what determines their price-to-sales ratio?

An important issue is the choice of the explanatory variables set included in the hedonic equation and how to stratify by groups as some of the characteristics that are relevant for a certain type of goods could be not useful for some others. The hedonic regression method recognizes that for heterogeneous economic goods, normally real estate, values are determined by their influencing factors, therefore, by measuring their correlation and significance it is possible to establish the intrinsic value of each attribute to get a pricing model. In further studies regulation effects also have been taken into account, normally for land and housing markets. In the Spanish pharmacies context, this bundle may contain attributes of both the region and the business and as the buying process is similar to buying a housing property rather than a business, the hypothesis is that factors selected will be relevant enough to set a model to explain gaps among regional ratios.
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Chromium and copper influence on the nodular cast iron with carbides microstructure

Chromium and copper influence on the nodular cast iron with carbides microstructure

In this cast iron eutectic transformation takes place in the temperature of 7 C less, than in cast iron with 0,50% Cu, but it is still higher than in cast iron with chromium. Molybdenum pres- ence caused ledeburitic carbides forming (HKL thermal effect, Fig. 10 a). Copper increase caused small amount of martensite forming, but did not change significantly carbides amount. It is important, that ferrite amount is decreased and pearlite disap- peared in cast iron metal matrix microstructure.

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The studies of scale surface produced on outer diffusion layers

The studies of scale surface produced on outer diffusion layers

[9] S. Kobayashi, T. Yakou, Control of intermetallic compound layers at interface steel and aluminum by diffusion-treatment, Materials Science and Engineering, vol. A338 (2002) 44÷53. [10] K. Murakami, N. Nishida, K. Osamura , Y. Tomota, T. Suzuki, Aluminization of high purity iron and stainless steel by powder liquid coating, Acta Materialia vol. 52 (2004) 2173÷2184. [11] T. L. Hu, H. L. Huang, D. Gan, T. Y. Lee, The microstructure of aluminized type 310 stainless steel, Surface & Coatings Technology vol. 201 (2006) 3502-3509.

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Winning the Oil Lottery: The Impact of Natural Resource Extraction on Growth Tiago Cavalcanti Daniel Da Mata Frederik Toscani

Winning the Oil Lottery: The Impact of Natural Resource Extraction on Growth Tiago Cavalcanti Daniel Da Mata Frederik Toscani

The evolution of knowledge of how to identify potentially oil-bearing formations com- prises both advances in the theory of petroleum-bearing formations and ever-improving technology. In the early days of oil exploration, conspicuous targets were searched for oil, either without applying geology theory (e.g., surface pools in the form of natural oil seeps) or by using knowledge of geology (e.g., anticlines and salt domes). Investigation of the sur- face (topography) of a region could point to conspicuous areas of oil-bearing formations. In the 1920s and 1930s, aerial photography expanded the possibilities for mapping areas suitable for drilling. In the mid 1900s, seismic technology improved subsurface mapping for the location of potential petroleum-bearing formations. By and large, seismic activity produces sound waves that can be used to characterize subsurface formations, that is, sound waves are generated and recorded by receivers, and that information could be used to infer rock formations. The idea is to map the subsurface rock layers by using sound waves as different rock layers have different acoustical properties. The recorded sounds are processed and assembled for interpretation. Existing seismic and well information highlights the potential for exploration of large hydrocarbon resources. Computerization of seismic data provided a great leap forward for the extraction industry: A large body of data can be processed at high speed and precision. Another revolution in the oil industry
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Identification of boundary heat flux on the continuous casting surface

Identification of boundary heat flux on the continuous casting surface

In the paper the numerical solution of the inverse problem consisting in the identification of the heat flux on the continuous casting surface is presented. The additional information results from the measured surface or interior temperature histories. In particular the sequential function specification method using future time steps is applied. On the stage of numerical computations the 1st scheme of the boundary element method for parabolic equations is used. Because the problem is strongly non-linear the additional procedure 'linearizing' the task discussed is introduced. This procedure is called the artificial heat source method. In the final part of the paper the examples of computations are shown.
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A Commentary on de Sousa′s towards an Integrative Theory of Consciousness

A Commentary on de Sousa′s towards an Integrative Theory of Consciousness

The ending of the section is a bit frustrating, because De Sousa presents his sketch for a scientiic methodology for consciousness research, instead of further developing the interesting philosophical issues he had raised. The proposed methodology is again based on the assumption of conscious modules, to be studied in their physical-biological and psychological aspects. Although consistent with DAM, no argument is presented in favour of the existence of psychological modules; the reader is left with an impression that the impossibility to overcome neural modularity is imposed on psychological phenomena. However, considering that brain networks are made not only of neurons, but also glial cells (forming a syncytium where information is processed by ionic waves), it is possible to conceive a physical-biological continuum that-according to the monist assumption-would correspond to integrated conscious episodes; in this case, we could have DAM without the modularity assumption.
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Structural stability of the high-aluminium zinc alloys modified with Ti addition

Structural stability of the high-aluminium zinc alloys modified with Ti addition

During these examinations samples of the Zn-25wt%Al after supersaturation at 370 o C/48 hours were quenched in water of room temperature, and then directly used in the XRD examinations. It was determined that the alloy Zn-25wt%Al with the addition of Ti undergoes phase changes in a shorter time after quenching than in the case of the same alloy without the addition of Ti [9], [11] – Fig. 1. This can suggest that Ti intensifies initial stage of the phase transformations, i.e. decomposition of the primary α' solid solution. On the other hand, the examined ZnAl25 with Ti addition did not display dimensional changes during natural ageing after supersaturation and quenching [10], [12]. This suggests that Ti addition stabilizes the α phase. As it was mentioned above, the Cu addition, which beneficially influences strength and wear properties of the Zn-Al alloys, forms metastable ε-CuZn 4 phase. The ε-CuZn 4 phase transforms to
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The application of optical measurements for the determination of accuracy of gear wheels casts manufactured in the RT/RP process

The application of optical measurements for the determination of accuracy of gear wheels casts manufactured in the RT/RP process

The first stage of manufacturing the casting mould was the creation of a gear wheel 3D-CAD model. Next, the gear model was supplemented with a gating system. The mould shape and its parting plane were defined. The last operation was the removal of the gear wheel model and the gating system from the mould solid. This way, a

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Genomic reaction norms for tick resistance in Hereford and Braford beef cattle

Genomic reaction norms for tick resistance in Hereford and Braford beef cattle

The 4,363 animals having records were born between 2008 and 2011 and originated from 197 sires and 3,966 dams with 10 generations of pedigree depth. Pedigree information recovered from historical breeding records comprised 11,967 animals and was highly incomplete due to use of multiple-sire matings. This resulted in 65% of the animals with tick count records having unknown paternity. For genotyped parent-progeny pairs and trios (sire, dam and progeny) pedigree errors were checked by the percentage of Mendelian conflicts (Wiggans et al., 2009) using seekparentf90 software (http://nce.ads.uga.edu), with maximum tolerance of 1% to allow for genotyping errors. If a parent-progeny pair conflict was found or if one or neither parent had been genotyped, the animal’s genotypes were compared with those of every other animal to determine if there was a parent-progeny relationship with an animal in the dataset. Unique putative parents of the appropriate sex with less than 1% Mendelian conflicts and suitable birthdates were designated as true parents, when identified.
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The Impact of E-Commerce Securi ty, and National Environment  on Consumer adoption of Intern et Banking in Malaysia and  Singapore

The Impact of E-Commerce Securi ty, and National Environment on Consumer adoption of Intern et Banking in Malaysia and Singapore

Relative advantage is defined as the extent to which a person views an innovation as offering an advantage over previous ways of performing the same task (Roger, 1983; Agarwal & Prasad, 1997). Because Internet banking services allow customers to access their banking account from any location 24 hours a day and 7 days a week, it provides an enormous advantage and convenience to users (Tan & Teo, 2000). It also gives customers greater control over managing their finances, as they are able to check their accounts easily. Besides, a customer’s Internet experience, his or her banking needs can affect his adoption. As there are more financial products and services, it is expected that individuals with many financial accounts and who subscribe to many banking services will be more inclined to adopt Internet banking. Tan and Teo (2000) has reported that potential adopters of Internet banking services are likely to own multiple banking accounts and subscribe to various banking services. Rogers argues that potential adapters, who are allowed to experiment with an innovation will feel more comfortable with the innovation and are more likely to adopt it. Thus, if customers have the opportunity to try the innovation, certain fears of the unknown may be minimized. Government policy could also aid or hinder Internet diffusion (Mbarika, 2002). This is consistent with the national systems of innovation theory that posits that government policies may encourage or mandate technology development and adoption (King et. al., 1994; Wolcott et. al., 2001). Tan and Teo (2000) suggest that the greater the extent of government support for Internet commerce, the more likely Internet banking will be adopted, thus, confirming Goh’s (1995) suggestion that governments can play an interventionist and leading role in the diffusion of innovation. Potential users in turn would view new applications such as Internet banking services more favorably and hence be more like to use them. Thus, the second alternative hypothesis is:
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Structure of X5CrNi18-10 and S355NL Steels after Remelting with the Electric Arc

Structure of X5CrNi18-10 and S355NL Steels after Remelting with the Electric Arc

The tested steels have wide application as a construction material, meeting particular conditions of loading during exploitation. Steel S355NL is often used in building constructions and machine construction, operating, among others areas in mining, drilling and motor industry. Steel X5CrNi18-10 according to the standard PN-EN 10088, is ranked as resistant to corrosion. It is used in many industrial branches such as in food and chemical industry, in devices used in medicine or households. The type is widely used due to its chemical capacity in contact with many types of chemical compounds.
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Teatro site specific

Teatro site specific

A segunda área desenrola-se na possibilidade de se criar dramaturgias em torno de espaços existentes, como é o caso de espectáculos site-specific. Estes são espectáculos que acontecem em espaços não teatrais, muitas vezes espaços/edifícios abandonados, fechados ou mesmo degradados. Estes espaços, geralmente, não obedecem à convenção arquitectónica da separação palco-plateia, tendo muitas vezes a cena aberta e o lugar do público indefinido e embebido no espaço cénico. Consequentemente, o envolvimento e aproximação do espectador é bastante potenciado. A criação site-specific de espectáculos ou instalações tem atenção de diversas formas, ao que o espaço nos diz à partida, desenvolvendo-se uma relação com a especificidade única desse. Geralmente estes são espaços com qualidades de ambiente únicas. Contudo o ambiente e funções dos espaços podem ser radicalmente alteradas, pelos acontecimentos ou tratamento plástico destes. Mike Pearson cita Simon Persighetti, do colectivo Wrights and Sights (Reino Unido) na questão do site-specific: “(...) site is frequently a scene of plenitude, its inherent characteristics, manifold effect and unruly elements always liable to leak, spill and diffuse into performance: site-specific work
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Braz. J. Phys.  vol.31 número4

Braz. J. Phys. vol.31 número4

temperature expansion of the grand potential per site of translationally invariant hain models,.. with periodi boundary onditions.[r]

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