Eukaryotic methionyl aminopeptidases: two classes of cobalt-dependent enzymes.

Using partial amino acid sequence data derived from porcine methionyl aminopeptidase (MetAP; methionine aminopeptidase, peptidase M; EC 3.4.11.18), a full-length clone of the homologous human enzyme has been obtained. The cDNA sequence contains 2569 nt with a single open reading frame corresponding to a protein of 478 amino acids. The C-terminal portion representing the catalytic domain shows limited identity with MetAP sequences from various prokaryotes and yeast, while the N terminus is rich in charged amino acids, including extended strings of basic and acidic residues. These highly polar stretches likely result in the spuriously high observed molecular mass (67 kDa). This cDNA sequence is highly similar to a rat protein, termed p67, which was identified as an inhibitor of phosphorylation of initiation factor eIF2 alpha and was previously predicted to be a metallopeptidase based on limited sequence homology. Model building established that human MetAP (p67) could be readily accommodated into the Escherichia coli MetAP structure and that the Co2+ ligands were fully preserved. However, human MetAP was found to be much more similar to a yeast open reading frame that differed markedly from the previously reported yeast MetAP. A similar partial sequence from Methanothermus fervidus suggests that this p67-like sequence is also found in prokaryotes. These findings suggest that there are two cobalt-dependent MetAP families, presently composed of the prokaryote and yeast sequences (and represented by the E. coli structure) (type I), on the one hand, and by human MetAP, the yeast open reading frame, and the partial prokaryotic sequence (type II), on the other.

Transplantation of a 17-amino acid alpha-helical DNA-binding domain into an antibody molecule confers sequence-dependent DNA recognition.

Recombinant antibodies capable of sequence-specific interactions with nucleic acids represent a class of DNA- and RNA-binding proteins with potential for broad application in basic research and medicine. We describe the rational design of a DNA-binding antibody, Fab-Ebox, by replacing a variable segment of the immunoglobulin heavy chain with a 17-amino acid domain derived from TFEB, a class B basic helix-loop-helix protein. DNA-binding activity was studied by electrophoretic mobility-shift assays in which Fab-Ebox was shown to form a specific complex with DNA containing the TFEB recognition motif (CACGTG). Similarities were found in the abilities of TFEB and Fab-Ebox to discriminate between oligodeoxyribonucleotides containing altered recognition sequences. Comparable interference of binding by methylation of cytosine residues indicated that Fab-Ebox and TFEB both contact DNA through interactions along the major groove of double-stranded DNA. The results of this study indicate that DNA-binding antibodies of high specificity can be developed by using the modular nature of both immunoglobulins and transcription factors.

Rescue, propagation, and partial purification of a helper virus-dependent adenovirus vector.

Adenoviral vectors are widely used as highly efficient gene transfer vehicles in a variety of biological research strategies including human gene therapy. One of the limitations of the currently available adenoviral vector system is the presence of the majority of the viral genome in the vector, resulting in leaky expression of viral genes particularly at high multiplicity of infection and limited cloning capacity of exogenous sequences. As a first step to overcome this problem, we attempted to rescue a defective human adenovirus serotype 5 DNA, which had an essential region of the viral genome (L1, L2, VAI + II, pTP) deleted and replaced with an indicator gene. In the presence of wild-type adenovirus as a helper, this DNA was packaged and propagated as transducing viral particles. After several rounds of amplification, the titer of the recombinant virus reached at least 4 x 10(6) transducing particles per ml. The recombinant virus could be partially purified from the helper virus by CsCl equilibrium density-gradient centrifugation. The structure of the recombinant virus around the marker gene remained intact after serial propagation, while the pBR sequence inserted in the E1 region was deleted from the recombinant virus. Our results suggest that it should be possible to develop a helper-dependent adenoviral vector, which does not encode any viral proteins, as an alternative to the currently available adenoviral vector systems.

Perceived sexism as a health determinant in Spain

OBJECTIVES: The goals of the present study are to explore the association between perceived sexism and self-perceived health, health-related behaviors, and unmet medical care needs among women in Spain; to analyze whether higher levels of discrimination are associated with higher prevalence of poor health indicators and to examine whether these relationships are modified by country of origin and social class. MATERIALS AND METHODS: The study is based on a cross-sectional design using data from the 2006 Spanish Health Interview Survey. We included women aged 20-64 years (n = 10,927). Six dependent variables were examined: four of health (self-perceived health, mental health, hypertension, and having had an injury during the previous year), one health behavior (smoking), and another related to the use of the health services (unmet need for medical care). Perceived sexism was the main independent variable. Social class and country of origin were considered as effect modifiers. We obtained the prevalence of perceived sexism. Logistic regression models, adjusted for potential confounders, were fitted to study the association between sexism and poor health outcomes. Results: The prevalence of perceived sexism was 3.4%. Perceived sexism showed positive and consistent associations with four poor health outcomes (poor self-perceived health, poor mental health, injuries in the last 12 months, and smoking). The strength of these associations increased with increased scores for perceived sexism, and the patterns were found to be modified by country of origin and social class. CONCLUSION: This study shows a consistent association between perceived sexism and poor health outcomes in a country of southern Europe with a strong patriarchal tradition.

Efficient sampling of band-limited signals from sine wave crossings

This correspondence presents an efficient method for reconstructing a band-limited signal in the discrete domain from its crossings with a sine wave. The method makes it possible to design A/D converters that only deliver the crossing timings, which are then used to interpolate the input signal at arbitrary instants. Potentially, it may allow for reductions in power consumption and complexity in these converters. The reconstruction in the discrete domain is based on a recently-proposed modification of the Lagrange interpolator, which is readily implementable with linear complexity and efficiently, given that it re-uses known schemes for variable fractional-delay (VFD) filters. As a spin-off, the method allows one to perform spectral analysis from sine wave crossings with the complexity of the FFT. Finally, the results in the correspondence are validated in several numerical examples.

Difference schemes for time-dependent heat conduction models with delay

Different non-Fourier models of heat conduction, that incorporate time lags in the heat flux and/or the temperature gradient, have been increasingly considered in the last years to model microscale heat transfer problems in engineering. Numerical schemes to obtain approximate solutions of constant coefficients lagging models of heat conduction have already been proposed. In this work, an explicit finite difference scheme for a model with coefficients variable in time is developed, and their properties of convergence and stability are studied. Numerical computations showing examples of applications of the scheme are presented.

Positional accommodative intraocular lens power error induced by the estimation of the corneal power and the effective lens position

Purpose: To evaluate the predictability of the refractive correction achieved with a positional accommodating intraocular lenses (IOL) and to develop a potential optimization of it by minimizing the error associated with the keratometric estimation of the corneal power and by developing a predictive formula for the effective lens position (ELP). Materials and Methods: Clinical data from 25 eyes of 14 patients (age range, 52–77 years) and undergoing cataract surgery with implantation of the accommodating IOL Crystalens HD (Bausch and Lomb) were retrospectively reviewed. In all cases, the calculation of an adjusted IOL power (PIOLadj) based on Gaussian optics considering the residual refractive error was done using a variable keratometric index value (nkadj) for corneal power estimation with and without using an estimation algorithm for ELP obtained by multiple regression analysis (ELPadj). PIOLadj was compared to the real IOL power implanted (PIOLReal, calculated with the SRK-T formula) and also to the values estimated by the Haigis, HofferQ, and Holladay I formulas. Results: No statistically significant differences were found between PIOLReal and PIOLadj when ELPadj was used (P = 0.10), with a range of agreement between calculations of 1.23 D. In contrast, PIOLReal was significantly higher when compared to PIOLadj without using ELPadj and also compared to the values estimated by the other formulas. Conclusions: Predictable refractive outcomes can be obtained with the accommodating IOL Crystalens HD using a variable keratometric index for corneal power estimation and by estimating ELP with an algorithm dependent on anatomical factors and age.

Exports and Capacity Constraints: A smooth transition regression model for six euro-area countries. CEPS Working Document No. 395/May 2014

The significant gains in export market shares made in a number of vulnerable euro-area crisis countries have not been accompanied by an appropriate improvement in price competitiveness. This paper argues that, under certain conditions, firms consider export activity as a substitute for serving domestic demand. The strength of the link between domestic demand and exports is dependent on capacity constraints. Our econometric model for six euro-area countries suggests domestic demand pressure and capacity-constraint restrictions as additional variables of a properly specified export equation. As an innovation to the literature, we assess the empirical significance through the logistic and the exponential variant of the non-linear smooth transition regression model. We find that domestic demand developments are relevant for the short-run dynamics of exports in particular during more extreme stages of the business cycle. A strong substitutive relationship between domestic and foreign sales can most clearly be found for Spain, Portugal and Italy, providing evidence of the importance of sunk costs and hysteresis in international trade.

The European Power Hierarchy, Member State Trust, and Public Support for the Common Security and Defense Policy. Jean Monnet/Robert Schuman Paper Series Vol. 15 No. 2, August 2015

Existing studies focus on overall support for European integration while less work has been done on explaining public opinion on specific policy areas, such as the development of the Common Security and Defense Policy (CSDP). We hypothesize that the probability of supporting a CSDP increases with greater levels of trust in the European Union member states, most notably the more powerful members. This variable is critical since integration’s development is influenced strongly by, and dependent on, the resources of the relatively more powerful European member states. Binary logistic regression analyses using pooled repeated cross-sectional data from the Eurobarometer surveys conducted from 1992 to 1997 among individuals of 11 member states largely support these claims.

LOGITCPRPLOT: Stata module to graph component-plus-residual plot for logistic regression

logitcprplot can be used after logistic regression for graphing a component-plus-residual plot (a.k.a. partial residual plot) for a given predictor, including a lowess, local polynomial, restricted cubic spline, fractional polynomial, penalized spline, regression spline, running line, or adaptive variable span running line smooth

Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation

The South African Boer goat displays a characteristic white spotting phenotype, in which the pigment is limited to the head. Exploiting the existing phenotype variation within the breed, we mapped the locus causing this white spotting phenotype to chromosome 17 by genome wide association. Subsequent whole genome sequencing identified a 1 Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats. We propose a hypothesis that ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely lead to an absence of melanocytes in the non-pigmented body areas of Boer goats. Our findings demonstrate the value of domestic animals as reservoir of unique mutants and for identifying a precisely defined functional CNV.

Governança corporativa e custo de agência: uma visão do mercado brasileiro

Esse trabalho investiga empiricamente a relação entre custo de agência e as medidas de monitoramento interno disponíveis aos investidores brasileiros nas empresas nacionais, utilizando amostras de companhias abertas entre os anos de 2010 e 2014, totalizando 134 empresas analisadas e 536 observações. Para medir tal relação, foram utilizadas, como variáveis de monitoramento interno, informações sobre a remuneração variável dos executivos, entre elas o uso de outorgas de opções de compra de ações, a composição do conselho de administração, dando ênfase à representatividade dos conselheiros independentes e à dualidade entre Chairman e CEO, e o percentual do capital social das companhias que está sob propriedade dos executivos. Como proxy para custo de agência, foram utilizados os indicadores Asset Turnover Ratio e General & Administrative Expenses (G&A) como percentual da Receita Líquida. Neste contexto, foram estabelecidas duas hipóteses de pesquisa e estimados modelos de regressão em painel controlados por efeitos fixos de tempo e empresa, empregando como variável dependente as variáveis proxy do custo de agência e utilizando as variáveis endividamento e tamanho das empresas como variáveis de controle. Os resultados dos modelos demonstram que, na amostra selecionada, há uma relação positiva e significativa entre o percentual da remuneração variável e as proxies de custo de agência, comportamento este contrário ao esperado originalmente. Conclui-se assim que as empresas que apresentam uma maior composição variável no total remunerado ao executivo, incorrem em um maior custo de agência, o que leva à conclusão de que tais ferramentas não são boas estratégias de alinhamento de interesses entre executivos e acionistas. As demais variáveis de monitoramento interno não apresentaram significância.

Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae

To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50-80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in F-ST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (F-ST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low.

Impact of pre-existing sulfate on retention of imported chloride and nitrate in variable charge soil profiles

In variable charge soils, anion retention and accumulation through adsorption at exchange sites is a competitive process. The objectives of this study in the wet tropics of far north Queensland were to investigate (i) whether the pre-existing high sulphate in variable charge soils had any impact on the retention of chloride and nitrate, derived mostly from the applied fertilizer; and (ii) whether chloride competed with nitrate during the adsorption processes. Soil cores up to 12.5 m depth were taken from seven sites, representing four soil types, in the Johnstone River Catchment. Six of these sites had been under sugarcane (Saccharum officinarum-S) cultivation for at least 50 years and one was an undisturbed rainforest. The cores were segmented at 1.0 m depth increments, and subsamples were analysed for nitrate-N, cation (CEC)- and anion-exchange capacities (AEC), pH, exchangeable cations (Ca, Mg, K, Na), soil organic C (SOC), electrical conductivity (EC), sulphate-S, and chloride. Sulphate-S load in 1-12 m depth under cropping ranged from 9.4 to 73.9 t ha(-1) (mean= 40 t ha(-1)) compared with 74.4 t ha(-1) in the rainforest. Chloride load under cropping ranged from 1.5 to 9.6 t ha(-1) (mean= 4.9 t ha(-1)) compared to 0.9 t ha(-1) in the rainforest, and the nitrate-N load from 113 to 2760 kg ha(-1) (mean = 910 kg ha(-1)) under cropping compared to 12 kg ha(-1) in the rainforest. Regardless of the soil type, the total chloride or nitrate-N input in fertilisers was 7.5 t ha(-1), during the last 50 years. Sulphate-S distribution in soil profiles decreased with depth at >2 m, whereas bulges of chloride or nitrate-N were observed at depths >2 m. This suggests that chloride or nitrate adsorption and retention increased with decreasing sulphate dominance. Abrupt decreases in equivalent fraction of sulphate (EFSO4), at depths >2 m, were accompanied by rapid increases in equivalent fraction of chloride (EFCl), followed by nitrate (EFNO3). The stepwise regression for EFCl and EFNO3 indicated that nitrate retention was reduced by the pre-existing sulphate and imported chloride, whereas only sulphate reduced chloride adsorption. The results indicate that chloride and nitrate adsorption and retention occurred, in the order chloride>nitrate, in soils containing large amounts of sulphate under approximately similar total inputs of N- and Cl-fertilisers. (C) 2004 Elsevier B.V. All rights reserved.

A review of two journals found that articles using multivariable logistic regression frequently did not report commonly recommended assumptions

Background and Objective: To examine if commonly recommended assumptions for multivariable logistic regression are addressed in two major epidemiological journals. Methods: Ninety-nine articles from the Journal of Clinical Epidemiology and the American Journal of Epidemiology were surveyed for 10 criteria: six dealing with computation and four with reporting multivariable logistic regression results. Results: Three of the 10 criteria were addressed in 50% or more of the articles. Statistical significance testing or confidence intervals were reported in all articles. Methods for selecting independent variables were described in 82%, and specific procedures used to generate the models were discussed in 65%. Fewer than 50% of the articles indicated if interactions were tested or met the recommended events per independent variable ratio of 10: 1. Fewer than 20% of the articles described conformity to a linear gradient, examined collinearity, reported information on validation procedures, goodness-of-fit, discrimination statistics, or provided complete information on variable coding. There was no significant difference (P >.05) in the proportion of articles meeting the criteria across the two journals. Conclusion: Articles reviewed frequently did not report commonly recommended assumptions for using multivariable logistic regression. (C) 2004 Elsevier Inc. All rights reserved.