Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

La teoría aristotélica de la abstracción y su olvido moderno

Resumen: Este estudio analiza la teoría aristotélica de la abstracción, tratando de rescatar su sentido originario a partir de los textos del autor, así como los aportes de los aristotélicos medievales más relevantes, especialmente Tomás de Aquino. Y luego se pasa a describir algunos hitos fundamentales de la evolución posterior de dicha teoría en la historia de la Filosofía, como son: 1) La contraposición entre abstracción e intuición en Duns Escoto y Guillermo de Ockham. 2) el intuicionismo de Descartes 3) La reinterpretación empirista de la abstracción en J. Locke 4) La ausencia de la abstracción en el Espinoza, Leibniz y Kant, así como su sustitución por la “aufhebung” en Hegel. 5) La peculiar aproximación husserliana a la abstracción a partir de su método fenomenológico y 6) la relación de la teoría de la abstracción con el pensamiento de algunos autores contemporáneos como Zubiri, Polo y, especialmente, Heidegger.

The wave model of mesothermal plasma near wakes and Korteweg-de Vries equation

The stationary two-dimensional (x, z) near wakes behind a flat-based projectile which moves at a constant mesothermal speed (V∞) along a z-axis in a rarefied, fully ionized, plasma is studied using the wave model previously proposed by one of the authors (VCL). One-fluid theory is used to depict the free expansion of ambient plasma into the vacuum produced behind a fast-moving projectile. This nonstationary, one-dimensional (x, t) flow which is approximated by the K-dV equation can be transformed, through substitution, t=z/V∞, into a stationary two-dimensional (x, z) near wake flow seen by an observer moving with the body velocity (V∞). The initial value problem of the K-dV equation in (x, t) variables is solved by a specially devised numerical method. Comparisons of the present numerical solution for the asymptotically small and large times with available analytical solutions are made and found in satisfactory agreements.

R&D Policy in Economies with Endogenous Growth and Non-Renewable Resources

The aim of this paper is to analyze how active R&D policies affect the growth rate of an economy with endogenous growth and non-renewable resources. We know from Scholz and Ziemens (1999) and Groth (2006) that in infinitely lived agents (ILA) economies, any active R&D policy increases the growth rate of the economy. To see if this result also appears in economies with finite lifetime agents, we developed an endogenous growth overlapping generations (OLG) economy à la Diamond which uses non-renewable resources as essential inputs in final good’s production. We show analytically that any R&D policy that reduces the use of natural resources implies a raise in the growth rate of the economy. Numerically we show that in economies with low intertemporal elasticity of substitution (IES), active R&D policies lead the economy to increase the depletion of non-renewable resources. Nevertheless, we find that active R&D policies always imply increases in the endogenous growth rate, in both scenarios. Furthermore, when the IES coefficient is lower (greater) than one, active R&D policies affect the growth rate of the economy in the ILA more (less) than in OLG economies.

Entry into motherhood: The effect of wages

Using the ECHP, we explored the determinants of having the first child in Spain. Our main goal was to study the relation between female wages and the decision to enter motherhood. Since the offered wage of non-working women is not observed, we estimate it and impute a potential wage to each woman (working and non-working). This potential wage enable us to investigate the effect of wages (the opportunity cost of time non-worked and dedicated to children) on the decision to have the first child, for both workers and non-workers. Contrary to previous results, we found that female wages are positively related to the likelihood of having the first child. This result suggests that the income effect overcomes the substitution effect when non-participants opportunity cost is also taken into account.

Second-best tax policy in a growing economy with externalities

This paper investigates the exploitation of environmental resources in a growing economy within a second-best scal policy framework. Agents derive utility from two types of consumption goods one which relies on an environmental input and one which does not as well as from leisure and from environmental amenity values. Property rights for the environmental resource are potentially incomplete. We connect second best policy to essential components of utility by considering the elasticity of substitution among each of the four utility arguments. The results illustrate potentially important relationships between environmental amentity values and leisure. When amenity values are complementary with leisure, for instance when environmental amenities are used for recreation, taxes on extractive goods generally increase over time. On the other hand, optimal taxes on extractive goods generally decrease over time when leisure and environmental amenity values are substitutes. Unders some parameterizations, complex dynamics leading to nonmonotonic time paths for the state variables can emerge.

Medida provisória na Constituição de 1988 e a necessidade de sua limitação

As medidas provisórias passaram a integrar o processo legislativo brasileiro com o advento da Constituição de 1988. A previsão inicial das medidas provisórias no art. 62 da Constituição Federal foi se tornando insatisfatória por deficiências oriundas dos pressupostos de relevância e urgência, em razão dos mesmos terem sido aferidos como muito genéricos ou subjetivos, o que acarretou sua demasiada edição. Com o intuito de restringir o poder do chefe do Executivo, foi aprovada, a Emenda Constitucional n. 32/2002, regulamentada pela Resolução 01/2002 do Congresso Nacional. Há consenso geral sobre a afronta estabelecida ao processo legislativo em função da perda de competência do Congresso derivada da excessiva edição de medidas provisórias, sendo necessário limitar essa prejudicial atuação executiva que tem estabelecido o trancamento de pauta constante nas votações no Parlamento.

Automatismos y racionalidad en la toma de decisiones para sustituir a un deportista en momentos decisivos

[ES] Cada vez más el deporte-espectáculo se está abriendo paso como objeto de estudio en los centros de investigación avanzada, como consecuencia de la necesidad de gestionar los altos presupuestos de las entidades deportivas.

Discursos forales y fiscalidad real. Las provincias vascas ante el "crecimiento" de la sal de 1631

[ES]La sustitución de los millones por el crecimiento en el precio de la sal que Felipe IV estableció en 1631 provocó reacciones generalizadas en toda Castilla, y en particular entre las provincias que se hallaban exentas de pagarlos. Son conocidos los violentos disturbios de Vizcaya. En cambio, poco se sabe acerca de lo sucedido en las otras dos Provincias Exentas. El presente artículo analiza, en conjunto, la actitud que tanto Vizcaya como Guipúzcoa y Álava adoptaron ante el nuevo impuesto. Aunque las tres coincidieron en rechazarlo, lo hicieron mediante discursos y métodos bien diferentes. No en vano, lejos de lo que suele pensarse no gozaban de una plena equiparación fiscal ni jurídica.

Evaluation of wheat or corn dried distillers' grains with solubles on performance and carcass characteristics of feedlot steers

[EN]A study was conducted on crossbred steers (n=275; 376±924 kg) to evaluate performance and carcass quality of cattle fed wheat or corn dried distillers’ grains with solubles (DDGS). The control ration contained 86.6% rolled barley grain, 5.7% supplement and 7.7% barley silage (DM basis). The four treatments included replacement of barley grain at 20 or 40% of the diet (DM basis) with wheat or corn DDGS. Steers were slaughtered at a common end weight of 645 kg with 100 steers randomly (n=20 per treatment) selected for determination of the retail yield of sub-primal boneless boxed beef (SPBBB). Data were analyzed as a completely randomized design using pen as the experimental unit. Feeding increasing levels of wheat DDGS led to a quadratic increase in dry matter intake (DMI) (P<0.01), whereas increasing levels of corn DDGS led to a quadratic decrease in DMI (P=0.01). Average daily gain was not influenced (P=0.13) by feeding wheat or corn DDGS, but cattle fed corn DDGS exhibited a quadratic increase (P=0.01) in gain:feed. As a result, a quadratic increase (P<0.01) in calculated NEg of the diet was observed as corn DDGS levels increased. A linear decrease (P=0.04) in days on feed (169, 166 and 154 d) was noted when increasing levels of wheat DDGS (0, 20 and 40%) were fed. Dressing percentage increased in a linear fashion with wheat DDGS (P<0.01) inclusion level and in a quadratic fashion (P=0.01) as corn DDGS inclusion level increased although other carcass traits were not affected (P=0.10) by treatment. The results indicate that replacement of barley grain with corn or wheat DDGS up to 40% of the diet (DM) can lead to superior performance (improved gain:feed or reduced days on feed, respectively) with no detrimental effect on quality grade or carcass SPBBB yield.

Income Taxation and Growth in an OLG Economy: Does Aggregate Uncertainty Play any Role?

We analyze the effects of capital income taxation on long-run growth in a stochastic, two-period overlapping generations economy. Endogenous growth is driven by a positive externality of physical capital in the production sector that makes firms exhibit an aggregate technology in equilibrium. We distinguish between capital income and labor income, and between attitudes towards risk and intertemporal substitution of consumption. We show necessary and sufficient conditions such that i) increments in the capital income taxation lead to higher equilibrium growth rates, and ii) the effect of changes in the capital income tax rate on the equilibrium growth may be of opposite signs in stochastic and in deterministic economies. Such a sign reversal is shown to be more likely depending on i) how the intertemporal elasticity of substitution compares to one, and ii) the size of second- period labor supply. Numerical simulations show that for reasonable values of the intertemporal elasticity of substitution, a sign reversal shows up only for implausibly high values of the second- period’s labor supply. The conclusion is that deterministic OLG economies are a good approximation of the effect of taxes on the equilibrium growth rate as in Smith (1996).

Genetics of Type III Bartter Syndrome in Spain, Proposed Diagnostic Algorithm

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Molecular diagnosis of distal renal tubular acidosis in Tunisian patients: proposed algorithm for Northern Africa populations for the ATP6V1B1, ATP6V0A4 and SCL4A1 genes

Background: Primary distal renal tubular acidosis (dRTA) caused by mutations in the genes that codify for the H+ -ATPase pump subunits is a heterogeneous disease with a poor phenotype-genotype correlation. Up to now, large cohorts of dRTA Tunisian patients have not been analyzed, and molecular defects may differ from those described in other ethnicities. We aim to identify molecular defects present in the ATP6V1B1, ATP6V0A4 and SLC4A1 genes in a Tunisian cohort, according to the following algorithm: first, ATP6V1B1 gene analysis in dRTA patients with sensorineural hearing loss (SNHL) or unknown hearing status. Afterwards, ATP6V0A4 gene study in dRTA patients with normal hearing, and in those without any structural mutation in the ATP6V1B1 gene despite presenting SNHL. Finally, analysis of the SLC4A1 gene in those patients with a negative result for the previous studies. Methods: 25 children (19 boys) with dRTA from 20 families of Tunisian origin were studied. DNAs were extracted by the standard phenol/chloroform method. Molecular analysis was performed by PCR amplification and direct sequencing. Results: In the index cases, ATP6V1B1 gene screening resulted in a mutation detection rate of 81.25%, which increased up to 95% after ATP6V0A4 gene analysis. Three ATP6V1B1 mutations were observed: one frameshift mutation (c.1155dupC; p.Ile386fs), in exon 12; a G to C single nucleotide substitution, on the acceptor splicing site (c.175-1G > C; p.?) in intron 2, and one novel missense mutation (c. 1102G > A; p. Glu368Lys), in exon 11. We also report four mutations in the ATP6V0A4 gene: one single nucleotide deletion in exon 13 (c.1221delG; p. Met408Cysfs* 10); the nonsense c.16C > T; p.Arg6*, in exon 3; and the missense changes c.1739 T > C; p.Met580Thr, in exon 17 and c.2035G > T; p.Asp679Tyr, in exon 19. Conclusion: Molecular diagnosis of ATP6V1B1 and ATP6V0A4 genes was performed in a large Tunisian cohort with dRTA. We identified three different ATP6V1B1 and four different ATP6V0A4 mutations in 25 Tunisian children. One of them, c.1102G > A; p.Glu368Lys in the ATP6V1B1 gene, had not previously been described. Among deaf since childhood patients, 75% had the ATP6V1B1 gene c. 1155dupC mutation in homozygosis. Based on the results, we propose a new diagnostic strategy to facilitate the genetic testing in North Africans with dRTA and SNHL.

STM study on the self-assembly of oligothiophene-based organic semiconductors

The self-assembly properties of a series of functionalized regioregular oligo(3-alkylthiophenes) were investigated by using scanning tunneling microscopy (STM) at the liquid-solid interface under ambient conditions. The characteristics of the 2-D crystals formed on the (0001) plane of highly ordered pyrolitic graphite (HOPG) strongly depend on the length of the p-conjugated oligomer backbone, on the functional groups attached to it, and on the alkyl substitution pattern on the individual thiophene units. Theoretical calculations were performed to analyze the geometry and electronic density of the molecular orbitals as well as to analyze the intermolecular interactions, in order to obtain models of the 2-D molecular ordering on the substrate.

Alkene selenenylation: A comprehensive analysis of relative reactivities, stereochemistry and asymmetric induction, and their comparisons with sulfenylation

A broad perspective of various factors influencing alkene selenenylation has been developed by concurrent detailed analysis of key experimental and theoretical data, such as asymmetric induction, stereochemistry, relative reactivities, and comparison with that of alkene sulfenylation. Alkyl group branching a to the double bond was shown to have the greatest effect on alkene reactivity and the stereochemical outcome of corresponding addition reactions. This is in sharp contrast with other additions to alkenes, which depend more on the degree of substitution on C=C or upon substituent electronic effects. Electronic and steric effects influencing asymmetric induction, stereochemistry, regiochemistry, and relative reactivities in the addition of PhSeOTf to alkenes are compared and contrasted with those of PhSCl.