Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes

Background: Several studies in Drosophila have shown excessive movement of retrogenes from the X chromosome to autosomes, and that these genes are frequently expressed in the testis. This phenomenon has led to several hypotheses invoking natural selection as the process driving male-biased genes to the autosomes. Metta and Schlotterer (BMC Evol Biol 2010, 10:114) analyzed a set of retrogenes where the parental gene has been subsequently lost. They assumed that this class of retrogenes replaced the ancestral functions of the parental gene, and reported that these retrogenes, although mostly originating from movement out of the X chromosome, showed female-biased or unbiased expression. These observations led the authors to suggest that selective forces (such as meiotic sex chromosome inactivation and sexual antagonism) were not responsible for the observed pattern of retrogene movement out of the X chromosome. Results: We reanalyzed the dataset published by Metta and Schlotterer and found several issues that led us to a different conclusion. In particular, Metta and Schlotterer used a dataset combined with expression data in which significant sex-biased expression is not detectable. First, the authors used a segmental dataset where the genes selected for analysis were less testis-biased in expression than those that were excluded from the study. Second, sex-biased expression was defined by comparing male and female whole-body data and not the expression of these genes in gonadal tissues. This approach significantly reduces the probability of detecting sex-biased expressed genes, which explains why the vast majority of the genes analyzed (parental and retrogenes) were equally expressed in both males and females. Third, the female-biased expression observed by Metta and Schltterer is mostly found for parental genes located on the X chromosome, which is known to be enriched with genes with female-biased expression. Fourth, using additional gonad expression data, we found that autosomal genes analyzed by Metta and Schlotterer are less up regulated in ovaries and have higher chance to be expressed in meiotic cells of spermatogenesis when compared to X-linked genes. Conclusions: The criteria used to select retrogenes and the sex-biased expression data based on whole adult flies generated a segmental dataset of female-biased and unbiased expressed genes that was unable to detect the higher propensity of autosomal retrogenes to be expressed in males. Thus, there is no support for the authors' view that the movement of new retrogenes, which originated from X-linked parental genes, was not driven by selection. Therefore, selection-based genetic models remain the most parsimonious explanations for the observed chromosomal distribution of retrogenes.

Superdiffusion in a non-Markovian random walk model with a Gaussian memory profile

Most superdiffusive Non-Markovian random walk models assume that correlations are maintained at all time scales, e. g., fractional Brownian motion, Levy walks, the Elephant walk and Alzheimer walk models. In the latter two models the random walker can always "remember" the initial times near t = 0. Assuming jump size distributions with finite variance, the question naturally arises: is superdiffusion possible if the walker is unable to recall the initial times? We give a conclusive answer to this general question, by studying a non-Markovian model in which the walker's memory of the past is weighted by a Gaussian centered at time t/2, at which time the walker had one half the present age, and with a standard deviation sigma t which grows linearly as the walker ages. For large widths we find that the model behaves similarly to the Elephant model, but for small widths this Gaussian memory profile model behaves like the Alzheimer walk model. We also report that the phenomenon of amnestically induced persistence, known to occur in the Alzheimer walk model, arises in the Gaussian memory profile model. We conclude that memory of the initial times is not a necessary condition for generating (log-periodic) superdiffusion. We show that the phenomenon of amnestically induced persistence extends to the case of a Gaussian memory profile.

Random regression analyses using B-spline functions to model growth of Nellore cattle

The objective of this study was to estimate (co)variance components using random regression on B-spline functions to weight records obtained from birth to adulthood. A total of 82 064 weight records of 8145 females obtained from the data bank of the Nellore Breeding Program (PMGRN/Nellore Brazil) which started in 1987, were used. The models included direct additive and maternal genetic effects and animal and maternal permanent environmental effects as random. Contemporary group and dam age at calving (linear and quadratic effect) were included as fixed effects, and orthogonal Legendre polynomials of age (cubic regression) were considered as random covariate. The random effects were modeled using B-spline functions considering linear, quadratic and cubic polynomials for each individual segment. Residual variances were grouped in five age classes. Direct additive genetic and animal permanent environmental effects were modeled using up to seven knots (six segments). A single segment with two knots at the end points of the curve was used for the estimation of maternal genetic and maternal permanent environmental effects. A total of 15 models were studied, with the number of parameters ranging from 17 to 81. The models that used B-splines were compared with multi-trait analyses with nine weight traits and to a random regression model that used orthogonal Legendre polynomials. A model fitting quadratic B-splines, with four knots or three segments for direct additive genetic effect and animal permanent environmental effect and two knots for maternal additive genetic effect and maternal permanent environmental effect, was the most appropriate and parsimonious model to describe the covariance structure of the data. Selection for higher weight, such as at young ages, should be performed taking into account an increase in mature cow weight. Particularly, this is important in most of Nellore beef cattle production systems, where the cow herd is maintained on range conditions. There is limited modification of the growth curve of Nellore cattle with respect to the aim of selecting them for rapid growth at young ages while maintaining constant adult weight.

Studying the influence of a secondary variable in Collocated Cokriging estimates

In this paper the influence of a secondary variable as a function of the correlation with the primary variable for collocated cokriging is examined. For this study five exhaustive data sets were generated in computer, from which samples with 60 and 104 data points were drawn using the stratified random sampling method. These exhaustive data sets were generated departing from a pair of primary and secondary variables showing a good correlation. Then successive sets were generated by adding an amount of white noise in such a way that the correlation gets poorer. Using these samples, it was possible to find out how primary and secondary information is used to estimate an unsampled location according to the correlation level.

Pattern formation for a reaction-diffusion system: Catalytic-dependent diffusion coefficients

[ES]Se considera un modelo de reacción-difusión para dos reactantes en presencia de un tercero, que actúa de catalizador. La escala temporal para el catalizador se compara con la de los reactantes y los coeficientes de difusión dependen solamente de la concentración en el estado de equilibrio del catalizador. Se realizan experimentos para diferentes cinéticas

Elastic Propagation in random media: applications to the imaging of volcano structures

High-frequency seismograms contain features that reflect the random inhomogeneities of the earth. In this work I use an imaging method to locate the high contrast small- scale heterogeneity respect to the background earth medium. This method was first introduced by Nishigami (1991) and than applied to different volcanic and tectonically active areas (Nishigami, 1997, Nishigami, 2000, Nishigami, 2006). The scattering imaging method is applied to two volcanic areas: Campi Flegrei and Mt. Vesuvius. Volcanic and seismological active areas are often characterized by complex velocity structures, due to the presence of rocks with different elastic properties. I introduce some modifications to the original method in order to make it suitable for small and highly complex media. In particular, for very complex media the single scattering approximation assumed by Nishigami (1991) is not applicable as the mean free path becomes short. The multiple scattering or diffusive approximation become closer to the reality. In this thesis, differently from the ordinary Nishigami’s method (Nishigami, 1991), I use the mean of the recorded coda envelope as reference curve and calculate the variations from this average envelope. In this way I implicitly do not assume any particular scattering regime for the "average" scattered radiation, whereas I consider the variations as due to waves that are singularly scattered from the strongest heterogeneities. The imaging method is applied to a relatively small area (20 x 20 km), this choice being justified by the small length of the analyzed codas of the low magnitude earthquakes. I apply the unmodified Nishigami’s method to the volcanic area of Campi Flegrei and compare the results with the other tomographies done in the same area. The scattering images, obtained with frequency waves around 18 Hz, show the presence of high scatterers in correspondence with the submerged caldera rim in the southern part of the Pozzuoli bay. Strong scattering is also found below the Solfatara crater, characterized by the presence of densely fractured, fluid-filled rocks and by a strong thermal anomaly. The modified Nishigami’s technique is applied to the Mt. Vesuvius area. Results show a low scattering area just below the central cone and a high scattering area around it. The high scattering zone seems to be due to the contrast between the high rigidity body located beneath the crater and the low rigidity materials located around it. The central low scattering area overlaps the hydrothermal reservoirs located below the central cone. An interpretation of the results in terms of geological properties of the medium is also supplied, aiming to find a correspondence of the scattering properties and the geological nature of the material. A complementary result reported in this thesis is that the strong heterogeneity of the volcanic medium create a phenomenon called "coda localization". It has been verified that the shape of the seismograms recorded from the stations located at the top of the volcanic edifice of Mt. Vesuvius is different from the shape of the seismograms recorded at the bottom. This behavior is justified by the consideration that the coda energy is not uniformly distributed within a region surrounding the source for great lapse time.

Probabilistic approaches in civil engineering: generation of random fields and structural identification with genetic algorithms

The inherent stochastic character of most of the physical quantities involved in engineering models has led to an always increasing interest for probabilistic analysis. Many approaches to stochastic analysis have been proposed. However, it is widely acknowledged that the only universal method available to solve accurately any kind of stochastic mechanics problem is Monte Carlo Simulation. One of the key parts in the implementation of this technique is the accurate and efficient generation of samples of the random processes and fields involved in the problem at hand. In the present thesis an original method for the simulation of homogeneous, multi-dimensional, multi-variate, non-Gaussian random fields is proposed. The algorithm has proved to be very accurate in matching both the target spectrum and the marginal probability. The computational efficiency and robustness are very good too, even when dealing with strongly non-Gaussian distributions. What is more, the resulting samples posses all the relevant, welldefined and desired properties of “translation fields”, including crossing rates and distributions of extremes. The topic of the second part of the thesis lies in the field of non-destructive parametric structural identification. Its objective is to evaluate the mechanical characteristics of constituent bars in existing truss structures, using static loads and strain measurements. In the cases of missing data and of damages that interest only a small portion of the bar, Genetic Algorithm have proved to be an effective tool to solve the problem.

Sulla progettazione in zona sismica di strutture dotate di dissipatori fluido-viscosi: proposta di una metodologia

CHAPTER 1:FLUID-VISCOUS DAMPERS In this chapter the fluid-viscous dampers are introduced. The first section is focused on the technical characteristics of these devices, their mechanical behavior and the latest evolution of the technology whose they are equipped. In the second section we report the definitions and the guide lines about the design of these devices included in some international codes. In the third section the results of some experimental tests carried out by some authors on the response of these devices to external forces are discussed. On this purpose we report some technical schedules that are usually enclosed to the devices now available on the international market. In the third section we show also some analytic models proposed by various authors, which are able to describe efficiently the physical behavior of the fluid-viscous dampers. In the last section we propose some cases of application of these devices on existing structures and on new-construction structures. We show also some cases in which these devices have been revealed good for aims that lies outside the reduction of seismic actions on the structures. CHAPTER 2:DESIGN METHODS PROPOSED IN LITERATURE In this chapter the more widespread design methods proposed in literature for structures equipped by fluid-viscous dampers are introduced. In the first part the response of sdf systems in the case of harmonic external force is studied, in the last part the response in the case of random external force is discussed. In the first section the equations of motion in the case of an elastic-linear sdf system equipped with a non-linear fluid-viscous damper undergoing a harmonic force are introduced. This differential problem is analytically quite complex and it’s not possible to be solved in a closed form. Therefore some authors have proposed approximate solution methods. The more widespread methods are based on equivalence principles between a non-linear device and an equivalent linear one. Operating in this way it is possible to define an equivalent damping ratio and the problem becomes linear; the solution of the equivalent problem is well-known. In the following section two techniques of linearization, proposed by some authors in literature, are described: the first technique is based on the equivalence of the energy dissipated by the two devices and the second one is based on the equivalence of power consumption. After that we compare these two techniques by studying the response of a sdf system undergoing a harmonic force. By introducing the equivalent damping ratio we can write the equation of motion of the non-linear differential problem in an implicit form, by dividing, as usual, for the mass of the system. In this way, we get a reduction of the number of variables, by introducing the natural frequency of the system. The equation of motion written in this form has two important properties: the response is linear dependent on the amplitude of the external force and the response is dependent on the ratio of the frequency of the external harmonic force and the natural frequency of the system only, and not on their single values. All these considerations, in the last section, are extended to the case of a random external force. CHAPTER 3: DESIGN METHOD PROPOSED In this chapter the theoretical basis of the design method proposed are introduced. The need to propose a new design method for structures equipped with fluid-viscous dampers arises from the observation that the methods reported in literature are always iterative, because the response affects some parameters included in the equation of motion (such as the equivalent damping ratio). In the first section the dimensionless parameterε is introduced. This parameter has been obtained from the definition of equivalent damping ratio. The implicit form of the equation of motion is written by introducing the parameter ε, instead of the equivalent damping ratio. This new implicit equation of motions has not any terms affected by the response, so that once ε is known the response can be evaluated directly. In the second section it is discussed how the parameter ε affects some characteristics of the response: drift, velocity and base shear. All the results described till this point have been obtained by keeping the non-linearity of the behavior of the dampers. In order to get a linear formulation of the problem, that is possible to solve by using the well-known methods of the dynamics of structures, as we did before for the iterative methods by introducing the equivalent damping ratio, it is shown how the equivalent damping ratio can be evaluated from knowing the value of ε. Operating in this way, once the parameter ε is known, it is quite easy to estimate the equivalent damping ratio and to proceed with a classic linear analysis. In the last section it is shown how the parameter ε could be taken as reference for the evaluation of the convenience of using non-linear dampers instead of linear ones on the basis of the type of external force and the characteristics of the system. CHAPTER 4: MULTI-DEGREE OF FREEDOM SYSTEMS In this chapter the design methods of a elastic-linear mdf system equipped with non-linear fluidviscous dampers are introduced. It has already been shown that, in the sdf systems, the response of the structure can be evaluated through the estimation of the equivalent damping ratio (ξsd) assuming the behavior of the structure elastic-linear. We would to mention that some adjusting coefficients, to be applied to the equivalent damping ratio in order to consider the actual behavior of the structure (that is non-linear), have already been proposed in literature; such coefficients are usually expressed in terms of ductility, but their treatment is over the aims of this thesis and we does not go into further. The method usually proposed in literature is based on energy equivalence: even though this procedure has solid theoretical basis, it must necessary include some iterative process, because the expression of the equivalent damping ratio contains a term of the response. This procedure has been introduced primarily by Ramirez, Constantinou et al. in 2000. This procedure is reported in the first section and it is defined “Iterative Method”. Following the guide lines about sdf systems reported in the previous chapters, it is introduced a procedure for the assessment of the parameter ε in the case of mdf systems. Operating in this way the evaluation of the equivalent damping ratio (ξsd) can be done directly without implementing iterative processes. This procedure is defined “Direct Method” and it is reported in the second section. In the third section the two methods are analyzed by studying 4 cases of two moment-resisting steel frames undergoing real accelerogramms: the response of the system calculated by using the two methods is compared with the numerical response obtained from the software called SAP2000-NL, CSI product. In the last section a procedure to create spectra of the equivalent damping ratio, affected by the parameter ε and the natural period of the system for a fixed value of exponent α, starting from the elasticresponse spectra provided by any international code, is introduced.

Generating multiple random exams using mathematica package and LATEX

[EN]In the framework of the European Higher Education Area, the assessment has been one of the most important aspects considered. In the Spanish Universities, one of the main differences with regard to the previous system is the incorporation of the continuous assessment to the evaluation process that is understood in several ways depending on the Universities, the courses and the lecturers. Focus on our context, a course of Mathematics of the first academic year in the Faculty of Business Administration at the University of Las Palmas de Gran Canaria (Spain), the continuous assessment has brought the preparation of a large amount of different tests to evaluate the students enrolled in it, therefore the incorporation of new tools and skills in order to make the teaching–learning process easier and more dynamic has become a need mainly in those degrees with a large number of students as the case we consider here. In this work we provide an efficient and effective way to elaborate random multiple-choice examina tion tests (although essay exams are also possible) by using Mathematica package and LATEXin order to make easier to the lectures the preparation of a large number of mid-term tests for a large number of students.

Valutazione del rapporto urinario proteine totali/creatinina e albumina/creatinina in cani affetti da iperadrenocorticismo e da diabete mellito

INTRODUCTION – In human medicine, diabetes mellitus (DM), hypertension, proteinuria and nephropathy are often associated although it is still not clear whether hypertension is the consequence or the cause of nephropathy and albuminuria. Microalbuminuria, in humans, is an early and sensitive marker which permits timely and effective therapy in the early phase of renal damage. Conversely, in dogs, these relationships were not fully investigated, even though hypertension has been associated with many diseases (Bodey and Michell, 1996). In a previous study, 20% of diabetic dogs were found proteinuric based on a U:P/C > 1 and 46% were hypertensive; this latter finding is similar to the prevalence of hypertension in diabetic people (40-80%) (Struble et al., 1998). In the same canine study, hypertension was also positively correlated with the duration of the disease, as is the case in human beings. Hypertension was also found to be a common complication of hypercortisolism (HC) in dogs, with a prevalence which varies from 50 (Goy-Thollot et al., 2002) to 80% (Danese and Aron, 1994).The aim of our study was to evaluate the urinary albumin to creatinine ratio (U:A/C) in dogs affected by Diabetes Mellitus and HC in order to ascertain if, as in human beings, it could represent an early and more sensitive marker of renal damage than U:P/C. Furthermore, the relationship between proteinuria and hypertension in DM and HC was also investigated. MATERIALS AND METHODS – Twenty dogs with DM, 14 with HC and 21 healthy dogs (control group) were included in the prospective case-control study. Inclusion criteria were hyperglycaemia, glicosuria and serum fructosamine above the reference range for DM dogs and a positive ACTH stimulation test and/or low-dose dexamethasone test and consistent findings of HC on abdominal ultrasonography in HC dogs. Dogs were excluded if affected by urinary tract infections and if the serum creatinine or urea values were above the reference range. At the moment of inclusion, an appropriate therapy had already been instituted less than 1 month earlier in 12 diabetic dogs. The control dogs were considered healthy based on clinical exam and clinicopathological findings. All dogs underwent urine sample collection by cystocentesis and systemic blood pressure measurement by means of either an oscillometric device (BP-88 Next, Colin Corporation, Japan) or by Doppler ultrasonic traducer (Minidop ES-100VX, Hadeco, Japan). The choice of method depended on the dog’s body weight: Doppler ultrasonography was employed in dogs < 20 kg of body weight and the oscillometric method in the other subjects. Dogs were considered hypertensive whenever systemic blood pressure was found ≥ 160 mmHg. The urine was assayed for U:P/C and U:A/C (Gentilini et al., 2005). The data between groups were compared using the Mann-Whitney U test. The reference ranges for U:P/C and U:A/C had already been established by our laboratory as 0.6 and 0.05, respectively. U:P/C and U:A/C findings were correlated to systemic blood pressure and Spearman R correlation coefficients were calculated. In all cases, p < 0.05 was considered statistically significant. RESULTS – The mean ± sd urinary albumin concentration in the three groups was 1.79 mg/dl ± 2.18; 20.02 mg/dl ± 43.25; 52.02 mg/dl ± 98.27, in healthy, diabetic and hypercortisolemic dogs, respectively. The urine albumin concentration differed significantly between healthy and diabetic dogs (p = 0.008) and between healthy and HC dogs (p = 0.011). U:A/C values ranged from 0.00 to 0.34 (mean ± sd 0.02 ± 0.07), 0.00 to 6.72 (mean ± sd 0.62 ± 1.52) and 0.00 to 5.52 (mean ± sd 1.27 ± 1.70) in the control, DM and HC groups, respectively; U:P/C values ranged from 0.1 to 0.6 (mean ± sd 0.17 ± 0.15) 0.1 to 6.6 (mean ± sd 0.93 ± 1.15) and 0.2 to 7.1 (mean ± sd 1.90 ± 2.11) in the control, DM and HC groups, respectively. In diabetic dogs, U:A/C was above the reference range in 11 out of 20 dogs (55%). Among these, 5/20 (25%) showed an increase only in the U:A/C ratio while, in 6/20 (30%), both the U:P/C and the U:A/C were abnormal. Among the latter, 4 dogs had already undergone therapy. In subjects affected with HC, U:P/C and U:A/C were both increased in 10/14 (71%) while in 2/14 (14%) only U:A/C was above the reference range. Overall, by comparing U:P/C and U:A/C in the various groups, a significant increase in protein excretion in disease-affected animals compared to healthy dogs was found. Blood pressure (BP) in diabetic subjects ranged from 88 to 203 mmHg (mean ± sd 143 ± 33 mmHg) and 7/20 (35%) dogs were found to be hypertensive. In HC dogs, BP ranged from 116 to 200 mmHg (mean ± sd 167 ± 26 mmHg) and 9/14 (64%) dogs were hypertensive. Blood pressure and proteinuria were not significantly correlated. Furthermore, in the DM group, U:P/C and U:A/C were both increased in 3 hypertensive dogs and 2 normotensive dogs while the only increase of U:A/C was observed in 2 hypertensive and 3 normotensive dogs. In the HC group, the U:P/C and the U:A/C were both increased in 6 hypertensive and 2 normotensive dogs; the U:A/C was the sole increased parameter in 1 hypertensive dog and in 1 dog with normal pressure. DISCUSSION AND CONCLUSION- The findings of this study suggest that, in dogs affected by DM and HC, an increase in U:P/C, U:A/C and systemic hypertension is frequently present. Remarkably, some dogs affected by both DM and HC showed an U:A/C but not U:P/C above the reference range. In diabetic dogs, albuminuria was observed in 25% of the subjects, suggesting the possibility that this parameter could be employed for detecting renal damage at an early phase when common semiquantiative tests and even U:P/C fall inside the reference range. In HC dogs, a higher number of subjects with overt proteinuria was found while only 14% presented an increase only in the U:A/C. This fact, associated with a greater number of hypertensive dogs having HC rather than DM, could suggest a greater influence on renal function by the mechanisms involved in hypertension secondary to hypercortisolemia. Furthermore, it is possible that, in HC dogs, the diagnosis was more delayed than in DM dogs. However, the lack of a statistically significant correlation between hypertension and increased protein excretion as well as the apparently random distribution of proteinuric subjects in normotensive and hypertensive cases, imply that other factors besides hypertension are involved in causing proteinuria. Longitudinal studies are needed to further investigate the relationship between hypertension and proteinuria.

Antipodal random sequences with prescribed second-order statistics: application to Compressive Sensing and UWB system based on DS-CDMA

It is usual to hear a strange short sentence: «Random is better than...». Why is randomness a good solution to a certain engineering problem? There are many possible answers, and all of them are related to the considered topic. In this thesis I will discuss about two crucial topics that take advantage by randomizing some waveforms involved in signals manipulations. In particular, advantages are guaranteed by shaping the second order statistic of antipodal sequences involved in an intermediate signal processing stages. The first topic is in the area of analog-to-digital conversion, and it is named Compressive Sensing (CS). CS is a novel paradigm in signal processing that tries to merge signal acquisition and compression at the same time. Consequently it allows to direct acquire a signal in a compressed form. In this thesis, after an ample description of the CS methodology and its related architectures, I will present a new approach that tries to achieve high compression by design the second order statistics of a set of additional waveforms involved in the signal acquisition/compression stage. The second topic addressed in this thesis is in the area of communication system, in particular I focused the attention on ultra-wideband (UWB) systems. An option to produce and decode UWB signals is direct-sequence spreading with multiple access based on code division (DS-CDMA). Focusing on this methodology, I will address the coexistence of a DS-CDMA system with a narrowband interferer. To do so, I minimize the joint effect of both multiple access (MAI) and narrowband (NBI) interference on a simple matched filter receiver. I will show that, when spreading sequence statistical properties are suitably designed, performance improvements are possible with respect to a system exploiting chaos-based sequences minimizing MAI only.

On the identification of bridge decks aeroelastic coefficients: the covariance block hankel matrix method

Il seguente elaborato si concentra sull'identifi�cazione strutturale di sistemi soggetti a sollecitazioni aeroelastiche e nello speci�fico l'attenzione viene rivolta ad impalcati da ponte. Si analizzano i concetti principali caratterizzanti il campo dell'aeroelasticità indagando i fattori dominanti che entrano in gioco sul piano teorico. In seguito, si considera il metodo di identifi�cazione strutturale chiamato Covariance Block Hankel Matrix (CBHM) utilizzato come strumento di derivazione dei coeffi�cienti aeroelastici propri della struttura. Infi�ne, si indaga il comportamento di questo metodo di identi�ficazione al variare di una serie di parametri chiave e all'interno di diversi scenari, visionando risultati ottenuti tramite una serie di test eff�ettuati per provare l'a�dattabilità del metodo stesso al variare delle condizioni che caratterizzano il sistema.