Molecular interactions involved in the transactivation of the human T-cell leukemia virus type 1 promoter mediated by Tax and CREB-2 (ATF-4).

The human T-cell leukemia virus type 1 (HTLV-1) Tax protein activates viral transcription through three 21-bp repeats located in the U3 region of the HTLV-1 long terminal repeat and called Tax-responsive elements (TxREs). Each TxRE contains nucleotide sequences corresponding to imperfect cyclic AMP response elements (CRE). In this study, we demonstrate that the bZIP transcriptional factor CREB-2 is able to bind in vitro to the TxREs and that CREB-2 binding to each of the 21-bp motifs is enhanced by Tax. We also demonstrate that Tax can weakly interact with CREB-2 bound to a cellular palindromic CRE motif such as that found in the somatostatin promoter. Mutagenesis of Tax and CREB-2 demonstrates that both N- and C-terminal domains of Tax and the C-terminal region of CREB-2 are required for direct interaction between the two proteins. In addition, the Tax mutant M47, defective for HTLV-1 activation, is unable to form in vitro a ternary complex with CREB-2 and TxRE. In agreement with recent results suggesting that Tax can recruit the coactivator CREB-binding protein (CBP) on the HTLV-1 promoter, we provide evidence that Tax, CREB-2, and CBP are capable of cooperating to stimulate viral transcription. Taken together, our data highlight the major role played by CREB-2 in Tax-mediated transactivation.

Long sequence duplications, repeats, and palindromes in HIV-1 gp120: length variation in V4 as the product of misalignment mechanism.

We have shown that indels in gp120 V4 are associated to the presence of duplicated and palindromic sequences, suggesting that they may be produced by strand-slippage misalignment mechanism. Indels in V4 involved region-specific duplications 9 to 15 bp long, and repeats of various lengths, associated to trinucleotides AAT. No duplications were found in V3 and C3. The frequency of palindromic sequences in individual genes was found to be significantly higher in gp120 (p < or = 3.00E-7), and significantly lower in Tat (p < or = 9.00E-7) than the average frequency calculated over the full genome. The finding of elements of misalignment in association with indels in V4 suggests that these mutations may occur in proviral DNA after integration of HIV into the host genome. It also implies that occurrence of large indels in gp120 is not random but is directed by the presence and distribution of elements of misalignment in the HIV genome.

J-shaped association between serum glucose and functional outcome in acute ischemic stroke.

BACKGROUND AND PURPOSE: Hyperglycemia after stroke is associated with larger infarct volume and poorer functional outcome. In an animal stroke model, the association between serum glucose and infarct volume is described by a U-shaped curve with a nadir ≈7 mmol/L. However, a similar curve in human studies was never reported. The objective of the present study is to investigate the association between serum glucose levels and functional outcome in patients with acute ischemic stroke. METHODS: We analyzed 1446 consecutive patients with acute ischemic stroke. Serum glucose was measured on admission at the emergency department together with multiple other metabolic, clinical, and radiological parameters. National Institutes of Health Stroke Scale (NIHSS) score was recorded at 24 hours, and Rankin score was recorded at 3 and 12 months. The association between serum glucose and favorable outcome (Rankin score ≤2) was explored in univariate and multivariate analysis. The model was further analyzed in a robust regression model based on fractional polynomial (-2-2) functions. RESULTS: Serum glucose is independently correlated with functional outcome at 12 months (OR, 1.15; P=0.01). Other predictors of outcome include admission NIHSS score (OR, 1.18; P<0001), age (OR, 1.06; P<0.001), prestroke Rankin score (OR, 20.8; P=0.004), and leukoaraiosis (OR, 2.21; P=0.016). Using these factors in multiple logistic regression analysis, the area under the receiver-operator characteristic curve is 0.869. The association between serum glucose and Rankin score at 12 months is described by a J-shaped curve with a nadir of 5 mmol/L. Glucose values between 3.7 and 7.3 mmol/L are associated with favorable outcome. A similar curve was generated for the association of glucose and 24-hour NIHSS score, for which glucose values between 4.0 and 7.2 mmol/L are associated with a NIHSS score <7. Discussion-Both hypoglycemia and hyperglycemia are dangerous in acute ischemic stroke as shown by a J-shaped association between serum glucose and 24-hour and 12-month outcome. Initial serum glucose values between 3.7 and 7.3 mmol/L are associated with favorable outcome.

Equidistribution of Fekete Points on the Sphere

Fekete points are the points that maximize a Vandermonde-type determinant that appears in the polynomial Lagrange interpolation formula. They are well suited points for interpolation formulas and numerical integration. We prove the asymptotic equidistribution of Fekete points in the sphere. The way we proceed is by showing their connection to other arrays of points, the so-called Marcinkiewicz-Zygmund arrays and interpolating arrays, that have been studied recently.

Performance of juveniles of Pseudoplatystoma fasciatum fed graded levels of corn gluten meal

The objective of this work was to evaluate corn gluten meal (CGM) as a substitute for fish meal in diets for striped catfish (Pseudoplatystoma fasciatum) juveniles. Eight isonitrogenous (46% crude protein) and isoenergetic (3,450 kcal kg-1 digestible energy) diets, with increasing levels of CGM - 0, 6, 12, 18, 24, 30, 36, and 42% -, were fed to juvenile striped catfish (113.56±5.10 g) for seven weeks. Maximum values for weight gain, specific growth rate, protein efficiency ratio and feed conversion ratio, evaluated by polynomial quadratic regression, were observed with 10.4, 11.4, 15.4 and 15% of CGM inclusion, respectively. Feed intake decreased significantly from 0.8% CGM. Mesenteric fat index and body gross energy decreased linearly with increasing levels of CGM; minimum body protein contents were observed with 34.1% CGM. Yellow pigmentation of fillets significantly increased until 26.5% CGM, and decreased from this point forth. Both plasma glucose and protein concentrations decreased with increased CGM levels. The inclusion of 10-15% CGM promotes optimum of striped catfish juveniles depending on the parameter evaluated. Yellow coloration in fillets produced by CGM diets can have marketing implications.

Length variation in HIV-1 gp120 as the product of DNA misalignment mechanism

Background: To determine whether misalignment structures such as duplications, repeats, and palindromes are associated to insertions/deletions (indels) in gp120, indicating that indels are indeed frameshift mutations generated by DNA misalignment mechanism. Methods: Cloning and sequencing of a fragment of HIV-1 gp120 spanning C2-C4 derived from plasma RNA in 12 patients with early chronic disease and naïve to antiretroviral therapy. Results: Indels in V4 involved always insertion and deletion of duplicated nucleotide segments, and AAT repeats, and were associated to the presence of palindromic sequences. No duplications were detected in V3 and C3. Palindromic sequences occurred with similar frequencies in V3, C3 and V4; the frequency of palindromes in individual genes was found to be significantly higher in structural (gp120, p ≤ 3.00E-7) and significantly lower in regulatory (Tat, p ≤ 9.00E-7) genes, as compared to the average frequency calculated over the full genome. Discussion: Indels in V4 are associated to misalignment structures (i.e. duplications repeat and palindromes) indicating DNA misalignment as the mechanism underlying length variation in V4. The finding that indels in V4 are caused by DNA misalignment has some very important implications: 1) indels in V4 are likely to occur in proviral DNA (and not in RNA), after integration of HIV into the host genome; 2) they are likely to occur as progressive modifications of the early founder virus during chronic infection, as more and more cells get infected; 3) frameshift mutations involving any number of base pairs are likely to occur evenly across gp120; however, only those mutants carrying a functional gp120 (indels as multiples of three base pairs) will be able to perpetuate the virus cycle and to keep spreading through the population.

Random regression models to estimate genetic parameters for milk production of Guzerat cows using orthogonal Legendre polynomials

The objective of this work was to compare random regression models for the estimation of genetic parameters for Guzerat milk production, using orthogonal Legendre polynomials. Records (20,524) of test-day milk yield (TDMY) from 2,816 first-lactation Guzerat cows were used. TDMY grouped into 10-monthly classes were analyzed for additive genetic effect and for environmental and residual permanent effects (random effects), whereas the contemporary group, calving age (linear and quadratic effects) and mean lactation curve were analized as fixed effects. Trajectories for the additive genetic and permanent environmental effects were modeled by means of a covariance function employing orthogonal Legendre polynomials ranging from the second to the fifth order. Residual variances were considered in one, four, six, or ten variance classes. The best model had six residual variance classes. The heritability estimates for the TDMY records varied from 0.19 to 0.32. The random regression model that used a second-order Legendre polynomial for the additive genetic effect, and a fifth-order polynomial for the permanent environmental effect is adequate for comparison by the main employed criteria. The model with a second-order Legendre polynomial for the additive genetic effect, and that with a fourth-order for the permanent environmental effect could also be employed in these analyses.

cis- and trans-acting elements of the estrogen-regulated vitellogenin gene B1 of Xenopus laevis.

Vitellogenin genes are expressed under strict estrogen control in the liver of female oviparous vertebrates. Gene transfer experiments using estrogen-responsive cells have shown that the 13 bp perfect palindromic element GGTCACTGTGACC found upstream of the Xenopus laevis vitellogenin gene A2 promoter mediates hormonal stimulation and thus, was called the estrogen-responsive element (ERE). In the Xenopus vitellogenin genes B1 and B2 there are two closely adjacent EREs with one or more base substitutions when compared to the consensus ERE GGTCANNNTGACC. On their own, these degenerated elements have only a low or no regulatory capacity at all but act together synergistically to form an estrogen-responsive unit (ERU) with the same strength as the perfect palindromic 13 bp element. Analysis of estrogen receptor binding to the gene B1 ERU revealed a cooperative interaction of receptor dimers to the two adjacent imperfect EREs which most likely explains the synergistic stimulation observed in vivo. Furthermore, a promoter activator element located between positions --113 and --42 of the gene B1 and functional in the human MCF-7 and the Xenopus B3.2 cells has been identified and shown to be involved in the high level of induced transcription activity when the ERE is placed at a distance from the promoter. Finally, a hormone-controlled in vitro transcription system derived from Xenopus liver nuclear extracts was exploited to characterize two additional novel cis-acting elements within the vitellogenin gene B1 promoter. One of them, a negative regulatory element (NRE), is responsible for repression of promoter activity in the absence of hormone. The second is related to the NF-I binding site and is required, together with the ERE, to mediate hormonal induction. Moreover, we detected three trans-acting activities in Xenopus liver nuclear extracts that interact with these regions and demonstrated that they participate in the regulation of the expression of the vitellogenin promoter in vitro.

Studies on integrating kinematic design method with mechanical systems simulation techniques

Theultimate goal of any research in the mechanism/kinematic/design area may be called predictive design, ie the optimisation of mechanism proportions in the design stage without requiring extensive life and wear testing. This is an ambitious goal and can be realised through development and refinement of numerical (computational) technology in order to facilitate the design analysis and optimisation of complex mechanisms, mechanical components and systems. As a part of the systematic design methodology this thesis concentrates on kinematic synthesis (kinematic design and analysis) methods in the mechanism synthesis process. The main task of kinematic design is to find all possible solutions in the form of structural parameters to accomplish the desired requirements of motion. Main formulations of kinematic design can be broadly divided to exact synthesis and approximate synthesis formulations. The exact synthesis formulation is based in solving n linear or nonlinear equations in n variables and the solutions for the problem areget by adopting closed form classical or modern algebraic solution methods or using numerical solution methods based on the polynomial continuation or homotopy. The approximate synthesis formulations is based on minimising the approximation error by direct optimisation The main drawbacks of exact synthesis formulationare: (ia) limitations of number of design specifications and (iia) failure in handling design constraints- especially inequality constraints. The main drawbacks of approximate synthesis formulations are: (ib) it is difficult to choose a proper initial linkage and (iib) it is hard to find more than one solution. Recentformulations in solving the approximate synthesis problem adopts polynomial continuation providing several solutions, but it can not handle inequality const-raints. Based on the practical design needs the mixed exact-approximate position synthesis with two exact and an unlimited number of approximate positions has also been developed. The solutions space is presented as a ground pivot map but thepole between the exact positions cannot be selected as a ground pivot. In this thesis the exact synthesis problem of planar mechanism is solved by generating all possible solutions for the optimisation process ¿ including solutions in positive dimensional solution sets - within inequality constraints of structural parameters. Through the literature research it is first shown that the algebraic and numerical solution methods ¿ used in the research area of computational kinematics ¿ are capable of solving non-parametric algebraic systems of n equations inn variables and cannot handle the singularities associated with positive-dimensional solution sets. In this thesis the problem of positive-dimensional solutionsets is solved adopting the main principles from mathematical research area of algebraic geometry in solving parametric ( in the mathematical sense that all parameter values are considered ¿ including the degenerate cases ¿ for which the system is solvable ) algebraic systems of n equations and at least n+1 variables.Adopting the developed solution method in solving the dyadic equations in direct polynomial form in two- to three-precision-points it has been algebraically proved and numerically demonstrated that the map of the ground pivots is ambiguousand that the singularities associated with positive-dimensional solution sets can be solved. The positive-dimensional solution sets associated with the poles might contain physically meaningful solutions in the form of optimal defectfree mechanisms. Traditionally the mechanism optimisation of hydraulically driven boommechanisms is done at early state of the design process. This will result in optimal component design rather than optimal system level design. Modern mechanismoptimisation at system level demands integration of kinematic design methods with mechanical system simulation techniques. In this thesis a new kinematic design method for hydraulically driven boom mechanism is developed and integrated in mechanical system simulation techniques. The developed kinematic design method is based on the combinations of two-precision-point formulation and on optimisation ( with mathematical programming techniques or adopting optimisation methods based on probability and statistics ) of substructures using calculated criteria from the system level response of multidegree-of-freedom mechanisms. Eg. by adopting the mixed exact-approximate position synthesis in direct optimisation (using mathematical programming techniques) with two exact positions and an unlimitednumber of approximate positions the drawbacks of (ia)-(iib) has been cancelled.The design principles of the developed method are based on the design-tree -approach of the mechanical systems and the design method ¿ in principle ¿ is capable of capturing the interrelationship between kinematic and dynamic synthesis simultaneously when the developed kinematic design method is integrated with the mechanical system simulation techniques.

Dynamic Model of a Small Once-Through Boiler

In this study, a model for the unsteady dynamic behaviour of a once-through counter flow boiler that uses an organic working fluid is presented. The boiler is a compact waste-heat boiler without a furnace and it has a preheater, a vaporiser and a superheater. The relative lengths of the boiler parts vary with the operating conditions since they are all parts of a single tube. The present research is a part of a study on the unsteady dynamics of an organic Rankine cycle power plant and it will be a part of a dynamic process model. The boiler model is presented using a selected example case that uses toluene as the process fluid and flue gas from natural gas combustion as the heat source. The dynamic behaviour of the boiler means transition from the steady initial state towards another steady state that corresponds to the changed process conditions. The solution method chosen was to find such a pressure of the process fluid that the mass of the process fluid in the boiler equals the mass calculated using the mass flows into and out of the boiler during a time step, using the finite difference method. A special method of fast calculation of the thermal properties has been used, because most of the calculation time is spent in calculating the fluid properties. The boiler was divided into elements. The values of the thermodynamic properties and mass flows were calculated in the nodes that connect the elements. Dynamic behaviour was limited to the process fluid and tube wall, and the heat source was regarded as to be steady. The elements that connect the preheater to thevaporiser and the vaporiser to the superheater were treated in a special way that takes into account a flexible change from one part to the other. The model consists of the calculation of the steady state initial distribution of the variables in the nodes, and the calculation of these nodal values in a dynamic state. The initial state of the boiler was received from a steady process model that isnot a part of the boiler model. The known boundary values that may vary during the dynamic calculation were the inlet temperature and mass flow rates of both the heat source and the process fluid. A brief examination of the oscillation around a steady state, the so-called Ledinegg instability, was done. This examination showed that the pressure drop in the boiler is a third degree polynomial of the mass flow rate, and the stability criterion is a second degree polynomial of the enthalpy change in the preheater. The numerical examination showed that oscillations did not exist in the example case. The dynamic boiler model was analysed for linear and step changes of the entering fluid temperatures and flow rates.The problem for verifying the correctness of the achieved results was that there was no possibility o compare them with measurements. This is why the only way was to determine whether the obtained results were intuitively reasonable and the results changed logically when the boundary conditions were changed. The numerical stability was checked in a test run in which there was no change in input values. The differences compared with the initial values were so small that the effects of numerical oscillations were negligible. The heat source side tests showed that the model gives results that are logical in the directions of the changes, and the order of magnitude of the timescale of changes is also as expected. The results of the tests on the process fluid side showed that the model gives reasonable results both on the temperature changes that cause small alterations in the process state and on mass flow rate changes causing very great alterations. The test runs showed that the dynamic model has no problems in calculating cases in which temperature of the entering heat source suddenly goes below that of the tube wall or the process fluid.

Weierstrass integrability of differential equations

The integrability problem consists in finding the class of functions a first integral of a given planar polynomial differential system must belong to. We recall the characterization of systems which admit an elementary or Liouvillian first integral. We define {\it Weierstrass integrability} and we determine which Weierstrass integrable systems are Liouvillian integrable. Inside this new class of integrable systems there are non--Liouvillian integrable systems.

Cyclicity versus center problem

We prove that there are one-parameter families of planar differential equations for which the center problem has a trivial solution and on the other hand the cyclicity of the weak focus is arbitrarily high. We illustrate this phenomenon in several examples for which this cyclicity is computed.

Generalization of Vélu’s formulae for isogenies between elliptic curves

Given an elliptic curve E and a finite subgroup G, V ́lu’s formulae concern to a separable isogeny IG : E → E ′ with kernel G. In particular, for a point P ∈ E these formulae express the first elementary symmetric polynomial on the abscissas of the points in the set P + G as the difference between the abscissa of IG (P ) and the first elementary symmetric polynomial on the abscissas of the nontrivial points of the kernel G. On the other hand, they express Weierstraß coefficients of E ′ as polynomials in the coefficients of E and two additional parameters: w0 = t and w1 = w. We generalize this by defining parameters wn for all n ≥ 0 and giving analogous formulae for all the elementary symmetric polynomials and the power sums on the abscissas of the points in P +G. Simultaneously, we obtain an efficient way of performing computations concerning the isogeny when G is a rational group.

Humeral development from neonatal period to skeletal maturity—application in age and sex assessment

The goal of the present study is to examine cross-sectional information on the growth of the humerus based on the analysis of four measurements, namely, diaphyseal length, transversal diameter of the proximal (metaphyseal) end of the shaft, epicondylar breadth and vertical diameter of the head. This analysis was performed in 181 individuals (90 ♂ and 91 ♀) ranging from birth to 25 years of age and belonging to three documented Western European skeletal collections (Coimbra, Lisbon and St. Bride). After testing the homogeneity of the sample, the existence of sexual differences (Student"s t- and Mann-Whitney U-test) and the growth of the variables (polynomial regression) were evaluated. The results showed the presence of sexual differences in epicondylar breadth above 20 years of age and vertical diameter of the head from 15 years of age, thus indicating that these two variables may be of use in determining sex from that age onward. The growth pattern of the variables showed a continuous increase and followed first- and second-degree polynomials. However, growth of the transversal diameter of the proximal end of the shaft followed a fourth-degree polynomial. Strong correlation coefficients were identified between humeral size and age for each of the four metric variables. These results indicate that any of the humeral measurements studied herein is likely to serve as a useful means of estimating sub-adult age in forensic samples.

Postnatal ontogenesis of the tibia. Implications for age and sex estimation

The growth of five variables of the tibia (diaphyseal length, diaphyseal length plus distal epiphysis, condylo-malleolar length, sagittal diameter of the proximal epiphysis, maximum breadth of the distal epiphysis) were analysed using polynomial regression in order to evaluate their significance and capacity for age and sex determination during and after growth. Data were collected from 181 (90♂ and 91♀) individuals ranging from birth to 25 years of age and belonging to three documented collections from Western Europe. Results indicate that all five variables exhibit linear behaviour during growth, which can be expressed by a first-degree polynomial function. Sexual significant differences were observed from age 15 onward in the two epiphysis measurements and condylo-malleolar length, suggesting that these three variables could be useful for sex determination in individuals older than 15 years. Strong correlation coefficients were identified between the five tibial variables and age. These results indicate that any of the studied tibial measurements is likely to serve as a useful source for estimating sub-adult age in both archaeological and forensic samples.