Efficient random variable generation: ratio of uniforms and polar rejection sampling

Monte Carlo techniques, which require the generation of samples from some target density, are often the only alternative for performing Bayesian inference. Two classic sampling techniques to draw independent samples are the ratio of uniforms (RoU) and rejection sampling (RS). An efficient sampling algorithm is proposed combining the RoU and polar RS (i.e. RS inside a sector of a circle using polar coordinates). Its efficiency is shown in drawing samples from truncated Cauchy and Gaussian random variables, which have many important applications in signal processing and communications. RESUMEN. Método eficiente para generar algunas variables aleatorias de uso común en procesado de señal y comunicaciones (por ejemplo, Gaussianas o Cauchy truncadas) mediante la combinación de dos técnicas: "ratio of uniforms" y "rejection sampling".

UWB doublet generation employing non-linear effects of a Semiconductor Optical Amplifier Mach-Zehnder inteferometer

In this article, a novel method to generate an ultra-wideband (UWB) doublet using the cross-phase modulation (XPM) effect is proposed and experimentally demonstrated. The main component of the submitted architecture is a SOA-Mach-Zehnder interferometer (MZI) pumped with a modulated Gaussian pulse. Maximum and minimum conversion points are analyzed through the systems transfer function in order to determinate the most effective operation stage. By tuning different values for the SOAs currents, it is possible to identify a conversion step in which the input pulse is enough large to saturate the SOAMZI, leading to the generation of a UWB doublet pulse.

Methods and Techniques for the Generation and Eficient Exploitation of RDB2RDF Mappings

RDB to RDF Mapping Language (R2RML) es una recomendación del W3C que permite especificar reglas para transformar bases de datos relacionales a RDF. Estos datos en RDF se pueden materializar y almacenar en un sistema gestor de tripletas RDF (normalmente conocidos con el nombre triple store), en el cual se pueden evaluar consultas SPARQL. Sin embargo, hay casos en los cuales la materialización no es adecuada o posible, por ejemplo, cuando la base de datos se actualiza frecuentemente. En estos casos, lo mejor es considerar los datos en RDF como datos virtuales, de tal manera que las consultas SPARQL anteriormente mencionadas se traduzcan a consultas SQL que se pueden evaluar sobre los sistemas gestores de bases de datos relacionales (SGBD) originales. Para esta traducción se tienen en cuenta los mapeos R2RML. La primera parte de esta tesis se centra en la traducción de consultas. Se propone una formalización de la traducción de SPARQL a SQL utilizando mapeos R2RML. Además se proponen varias técnicas de optimización para generar consultas SQL que son más eficientes cuando son evaluadas en sistemas gestores de bases de datos relacionales. Este enfoque se evalúa mediante un benchmark sintético y varios casos reales. Otra recomendación relacionada con R2RML es la conocida como Direct Mapping (DM), que establece reglas fijas para la transformación de datos relacionales a RDF. A pesar de que ambas recomendaciones se publicaron al mismo tiempo, en septiembre de 2012, todavía no se ha realizado un estudio formal sobre la relación entre ellas. Por tanto, la segunda parte de esta tesis se centra en el estudio de la relación entre R2RML y DM. Se divide este estudio en dos partes: de R2RML a DM, y de DM a R2RML. En el primer caso, se estudia un fragmento de R2RML que tiene la misma expresividad que DM. En el segundo caso, se representan las reglas de DM como mapeos R2RML, y también se añade la semántica implícita (relaciones de subclase, 1-N y M-N) que se puede encontrar codificada en la base de datos. Esta tesis muestra que es posible usar R2RML en casos reales, sin necesidad de realizar materializaciones de los datos, puesto que las consultas SQL generadas son suficientemente eficientes cuando son evaluadas en el sistema gestor de base de datos relacional. Asimismo, esta tesis profundiza en el entendimiento de la relación existente entre las dos recomendaciones del W3C, algo que no había sido estudiado con anterioridad. ABSTRACT. RDB to RDF Mapping Language (R2RML) is a W3C recommendation that allows specifying rules for transforming relational databases into RDF. This RDF data can be materialized and stored in a triple store, so that SPARQL queries can be evaluated by the triple store. However, there are several cases where materialization is not adequate or possible, for example, if the underlying relational database is updated frequently. In those cases, RDF data is better kept virtual, and hence SPARQL queries over it have to be translated into SQL queries to the underlying relational database system considering that the translation process has to take into account the specified R2RML mappings. The first part of this thesis focuses on query translation. We discuss the formalization of the translation from SPARQL to SQL queries that takes into account R2RML mappings. Furthermore, we propose several optimization techniques so that the translation procedure generates SQL queries that can be evaluated more efficiently over the underlying databases. We evaluate our approach using a synthetic benchmark and several real cases, and show positive results that we obtained. Direct Mapping (DM) is another W3C recommendation for the generation of RDF data from relational databases. While R2RML allows users to specify their own transformation rules, DM establishes fixed transformation rules. Although both recommendations were published at the same time, September 2012, there has not been any study regarding the relationship between them. The second part of this thesis focuses on the study of the relationship between R2RML and DM. We divide this study into two directions: from R2RML to DM, and from DM to R2RML. From R2RML to DM, we study a fragment of R2RML having the same expressive power than DM. From DM to R2RML, we represent DM transformation rules as R2RML mappings, and also add the implicit semantics encoded in databases, such as subclass, 1-N and N-N relationships. This thesis shows that by formalizing and optimizing R2RML-based SPARQL to SQL query translation, it is possible to use R2RML engines in real cases as the resulting SQL is efficient enough to be evaluated by the underlying relational databases. In addition to that, this thesis facilitates the understanding of bidirectional relationship between the two W3C recommendations, something that had not been studied before.

Fas-induced apoptosis of T cells occurs independently of ceramide generation

The Fas receptor is one of a number of important physiological inducers of programmed cell death (apoptosis). Current models for regulation of this process involve rapid conversion of sphingomyelin to ceramide by cellular sphingomyelinases. Induced changes in cellular levels of such sphingosine-based ceramides are normally extrapolated from measurements of sphingomyelinase activity or following their conversion to ceramide phosphate by treatment of cellular lipid extracts with bacterial diacylglycerol kinase (DAGK). To allow direct study of cellular sphingosine- and sphinganine-based ceramide levels, we developed a mass spectrometric technique capable of determining inducible changes in both overall ceramide levels and species distribution in cellular lipid preparations. Contrary to current models, we detected no changes in cellular ceramide levels up to 2 hr poststimulation of Jurkat T cells with an anti-Fas IgM, although this treatment did induce apoptosis. We also determined in the same system that, when utilizing the DAGK assay, increased phosphorylation of substrates that comigrated with ceramide standards was apparent but that this effect was due to an enhancement of DAGK activity rather than increases in levels of cellular ceramides as substrates per se. Thus, the first direct measurement of ceramides present in cells undergoing apoptosis indicates that, insofar as it can be measured, the induction of apoptosis does not involve the generation of sphingosine-based ceramides, contrary to many published accounts.

The prion model for [URE3] of yeast: Spontaneous generation and requirements for propagation

The genetic properties of the non-Mendelian element, [URE3], suggest that it is a prion (infectious protein) form of Ure2p, a mediator of nitrogen regulation in Saccharomyces cerevisiae. Into a ure2Δ strain (necessarily lacking [URE3]), we introduced a plasmid overproducing Ure2p. This induced the frequent “spontaneous generation” of [URE3], with properties identical to the original [URE3]. Altering the translational frame only in the prion-inducing domain of URE2 shows that it is Ure2 protein (and not URE2 RNA) that induces appearance of [URE3]. The proteinase K-resistance of Ure2p is unique to [URE3] strains and is not seen in nitrogen regulation of normal strains. The prion-inducing domain of Ure2p (residues 1–65) can propagate [URE3] in the absence of the C-terminal part of the molecule. In contrast, the C-terminal part of Ure2p cannot be converted to the prion (inactive) form without the prion-inducing domain covalently attached. These experiments support the prion model for [URE3] and extend our understanding of its propagation.

Generation and reproductive phenotypes of mice lacking estrogen receptor β

Estrogens influence the differentiation and maintenance of reproductive tissues and affect lipid metabolism and bone remodeling. Two estrogen receptors (ERs) have been identified to date, ERα and ERβ. We previously generated and studied knockout mice lacking estrogen receptor α and reported severe reproductive and behavioral phenotypes including complete infertility of both male and female mice and absence of breast tissue development. Here we describe the generation of mice lacking estrogen receptor β (ERβ −/−) by insertion of a neomycin resistance gene into exon 3 of the coding gene by using homologous recombination in embryonic stem cells. Mice lacking this receptor develop normally and are indistinguishable grossly and histologically as young adults from their littermates. RNA analysis and immunocytochemistry show that tissues from ERβ −/− mice lack normal ERβ RNA and protein. Breeding experiments with young, sexually mature females show that they are fertile and exhibit normal sexual behavior, but have fewer and smaller litters than wild-type mice. Superovulation experiments indicate that this reduction in fertility is the result of reduced ovarian efficiency. The mutant females have normal breast development and lactate normally. Young, sexually mature male mice show no overt abnormalities and reproduce normally. Older mutant males display signs of prostate and bladder hyperplasia. Our results indicate that ERβ is essential for normal ovulation efficiency but is not essential for female or male sexual differentiation, fertility, or lactation. Future experiments are required to determine the role of ERβ in bone and cardiovascular homeostasis.

Verb generation in patients with focal frontal lesions: A neuropsychological test of neuroimaging findings

What are the neural bases of semantic memory? Traditional beliefs that the temporal lobes subserve the retrieval of semantic knowledge, arising from lesion studies, have been recently called into question by functional neuroimaging studies finding correlations between semantic retrieval and activity in left prefrontal cortex. Has neuroimaging taught us something new about the neural bases of cognition that older methods could not reveal or has it merely identified brain activity that is correlated with but not causally related to the process of semantic retrieval? We examined the ability of patients with focal frontal lesions to perform a task commonly used in neuroimaging experiments, the generation of semantically appropriate action words for concrete nouns, and found evidence of the necessity of the left inferior frontal gyrus for certain components of the verb generation task. Notably, these components did not include semantic retrieval per se.

Localized Changes in Peroxidase Activity Accompany Hydrogen Peroxide Generation during the Development of a Nonhost Hypersensitive Reaction in Lettuce1

Peroxidase activity was characterized in lettuce (Lactuca sativa L.) leaf tissue. Changes in the activity and distribution of the enzyme were examined during the development of a nonhost hypersensitive reaction (HR) induced by Pseudomonas syringae (P. s.) pv phaseolicola and in response to an hrp mutant of the bacterium. Assays of activity in tissue extracts revealed pH optima of 4.5, 6.0, 5.5 to 6.0, and 6.0 to 6.5 for the substrates tetramethylbenzidine, guaiacol, caffeic acid, and chlorogenic acid, respectively. Inoculation with water or with wild-type or hrp mutant strains of P. s. pv phaseolicola caused an initial decline in total peroxidase activity; subsequent increases depended on the hydrogen donor used in the assay. Guaiacol peroxidase recovered more rapidly in tissues undergoing the HR, whereas changes in tetramethylbenzidine peroxidase were generally similar in the two interactions. In contrast, increases in chlorogenic acid peroxidase were significantly higher in tissues inoculated with the hrp mutant. During the HR, increased levels of Mn2+/2,4-dichlorophenol-stimulated NADH and NADPH oxidase activities, characteristic of certain peroxidases, were found in intercellular fluids and closely matched the accumulation of H2O2 in the apoplast. Histochemical analysis of peroxidase distribution by electron microscopy revealed a striking, highly localized increase in activity within the endomembrane system and cell wall at the sites of bacterial attachment. However, no clear differences in peroxidase location were observed in tissue challenged by the wild-type strain or the hrp mutant. Our results highlight the significance of the subcellular control of oxidative reactions leading to the generation of reactive oxygen species, cell wall alterations, and the HR.

Source and Magnitude of Ammonium Generation in Maize Roots1

Studies with 15N indicate that appreciable generation of NH4+ from endogenous sources accompanies the uptake and assimilation of exogenous NH4+ by roots. To identify the source of NH4+ generation, maize (Zea mays L.) seedlings were grown on 14NH4+ and then exposed for 3 d to highly labeled 15NH4+. More of the entering 15NH4+ was incorporated into the protein-N fraction of roots in darkness (approximately 25%) than in the light (approximately 14%). Although the 14NH4+ content of roots declined rapidly to less than 1 μmol per plant, efflux of 14NH4+ continued throughout the 3-d period at an average daily rate of 14 μmol per plant. As a consequence, cumulative 14NH4+ efflux during the 3-d period accounted for 25% of the total 14N initially present in the root. Although soluble organic 14N in roots declined during the 3-d period, insoluble 14N remained relatively constant. In shoots both soluble organic 14N and 14NH4+ declined, but a comparable increase in insoluble 14N was noted. Thus, total 14N in shoots remained constant, reflecting little or no net redistribution of 14N between shoots and roots. Collectively, these observations reveal that catabolism of soluble organic N, not protein N, is the primary source of endogenous NH4+ generation in maize roots.

Role of cortical N-methyl-D-aspartate receptors in auditory sensory memory and mismatch negativity generation: implications for schizophrenia.

Working memory refers to the ability of the brain to store and manipulate information over brief time periods, ranging from seconds to minutes. As opposed to long-term memory, which is critically dependent upon hippocampal processing, critical substrates for working memory are distributed in a modality-specific fashion throughout cortex. N-methyl-D-aspartate (NMDA) receptors play a crucial role in the initiation of long-term memory. Neurochemical mechanisms underlying the transient memory storage required for working memory, however, remain obscure. Auditory sensory memory, which refers to the ability of the brain to retain transient representations of the physical features (e.g., pitch) of simple auditory stimuli for periods of up to approximately 30 sec, represents one of the simplest components of the brain working memory system. Functioning of the auditory sensory memory system is indexed by the generation of a well-defined event-related potential, termed mismatch negativity (MMN). MMN can thus be used as an objective index of auditory sensory memory functioning and a probe for investigating underlying neurochemical mechanisms. Monkeys generate cortical activity in response to deviant stimuli that closely resembles human MMN. This study uses a combination of intracortical recording and pharmacological micromanipulations in awake monkeys to demonstrate that both competitive and noncompetitive NMDA antagonists block the generation of MMN without affecting prior obligatory activity in primary auditory cortex. These findings suggest that, on a neurophysiological level, MMN represents selective current flow through open, unblocked NMDA channels. Furthermore, they suggest a crucial role of cortical NMDA receptors in the assessment of stimulus familiarity/unfamiliarity, which is a key process underlying working memory performance.

Enzyme-mediated spatial segregation on individual polymeric support beads: application to generation and screening of encoded combinatorial libraries.

Proteolysis of short N alpha-protected peptide substrates bound to polyoxyethylene-polystyrene beads releases selectively free amino sites in the enzyme-accessible "surface" area. The substantial majority of functional sites in the "interior" of the polymeric support are not reached by the enzyme and remain uncleaved (protected). Subsequent synthesis with two classes of orthogonal protecting groups-N alpha-tert-butyloxycarbonyl (Boc) and N alpha-9-fluorenylmethyloxy-carbonyl (Fmoc)-allows generation of two structures on the same bead. The surface structure is available for receptor interactions, whereas the corresponding interior structure is used for coding. Coding structures are usually readily sequenceable peptides. This "shaving" methodology was illustrated by the preparation of a peptide-encoded model peptide combinatorial library containing 1.0 x 10(5) members at approximately 6-fold degeneracy. From this single library, good ligands were selected for three different receptors: anti-beta-endorphin anti-body, streptavidin, and thrombin, and the binding structures were deduced correctly by sequencing the coding peptides present on the same beads.

Study of plutonium oxide heat generation in a wood moderated container /

The generation of heat due to the radioactive decay of plutonium in the form of plutonium dioxide stored in wooden containers is considered. The results of two experiments in which plutonium dioxide is placed inside wooden blocks and the temperature rise measured at various points is reported. Heat transfer calculations are then performed to show that the data obtained are those which would be expected, i.e., that Fourier's Law adequately describes the situation. The heat build up in a proposed wood moderated shipping container is calculated, using some of the assumptions verified in the described experiments.

Long wave generation by the shoaling and breaking of transient wave groups on a beach

This paper presents new laboratory data on the generation of long waves by the shoaling and breaking of transient-focused short-wave groups. Direct offshore radiation of long waves from the breakpoint is shown experimentally for the first time. High spatial resolution enables identification of the relationship between the spatial gradients of the short-wave envelope and the long-wave surface. This relationship is consistent with radiation stress theory even well inside the surf zone and appears as a result of the strong nonlinear forcing associated with the transient group. In shallow water, the change in depth across the group leads to asymmetry in the forcing which generates significant dynamic setup in front of the group during shoaling. Strong amplification of the incident dynamic setup occurs after short-wave breaking. The data show the radiation of a transient long wave dominated by a pulse of positive elevation, preceded and followed by weaker trailing waves with negative elevation. The instantaneous cross-shore structure of the long wave shows the mechanics of the reflection process and the formation of a transient node in the inner surf zone. The wave run-up and relative amplitude of the radiated and incident long waves suggests significant modification of the incident bound wave in the inner surf zone and, the dominance of long waves generated by the breaking process. It is proposed that these conditions occur when the primary short waves and bound wave are not shallow water waves at the breakpoint. A simple criterion is given to determine these conditions, which generally occur for the important case of storm waves.

Experimental optimization of triangular pulse generation in normal dispersion fiber for all optical processing applications

We experimentally investigate a multi-parameter optimization of conditions for generation of triangular pulses in normal dispersion fiber. We find that triangular pulses suitable for all optical processing applications can be generated for a wide range of input pulse chirps but that triangular pulse quality and stability is improved with increased input pulse chirp.

Comparison of frequency symmetric signal generation from a BPSK input using fiber and semiconductor-based nonlinear elements

This letter compares two nonlinear media for simultaneous carrier recovery and generation of frequency symmetric signals from a 42.7-Gb/s nonreturn-to-zero binary phase-shift-keyed input by exploiting four-wave mixing in a semiconductor optical amplifier and a highly nonlinear optical fiber for use in a phase-sensitive amplifier.