Vector Boolean Functions: Applications in Symmetric Cryptography

Esta tesis establece los fundamentos teóricos y diseña una colección abierta de clases C++ denominada VBF (Vector Boolean Functions) para analizar funciones booleanas vectoriales (funciones que asocian un vector booleano a otro vector booleano) desde una perspectiva criptográfica. Esta nueva implementación emplea la librería NTL de Victor Shoup, incorporando nuevos módulos que complementan a las funciones de NTL, adecuándolas para el análisis criptográfico. La clase fundamental que representa una función booleana vectorial se puede inicializar de manera muy flexible mediante diferentes estructuras de datas tales como la Tabla de verdad, la Representación de traza y la Forma algebraica normal entre otras. De esta manera VBF permite evaluar los criterios criptográficos más relevantes de los algoritmos de cifra en bloque y de stream, así como funciones hash: por ejemplo, proporciona la no-linealidad, la distancia lineal, el grado algebraico, las estructuras lineales, la distribución de frecuencias de los valores absolutos del espectro Walsh o del espectro de autocorrelación, entre otros criterios. Adicionalmente, VBF puede llevar a cabo operaciones entre funciones booleanas vectoriales tales como la comprobación de igualdad, la composición, la inversión, la suma, la suma directa, el bricklayering (aplicación paralela de funciones booleanas vectoriales como la empleada en el algoritmo de cifra Rijndael), y la adición de funciones coordenada. La tesis también muestra el empleo de la librería VBF en dos aplicaciones prácticas. Por un lado, se han analizado las características más relevantes de los sistemas de cifra en bloque. Por otro lado, combinando VBF con algoritmos de optimización, se han diseñado funciones booleanas cuyas propiedades criptográficas son las mejores conocidas hasta la fecha. ABSTRACT This thesis develops the theoretical foundations and designs an open collection of C++ classes, called VBF, designed for analyzing vector Boolean functions (functions that map a Boolean vector to another Boolean vector) from a cryptographic perspective. This new implementation uses the NTL library from Victor Shoup, adding new modules which complement the existing ones making VBF better suited for cryptography. The fundamental class representing a vector Boolean function can be initialized in a flexible way via several alternative types of data structures such as Truth Table, Trace Representation, Algebraic Normal Form (ANF) among others. This way, VBF allows the evaluation of the most relevant cryptographic criteria for block and stream ciphers as well as for hash functions: for instance, it provides the nonlinearity, the linearity distance, the algebraic degree, the linear structures, the frequency distribution of the absolute values of the Walsh Spectrum or the Autocorrelation Spectrum, among others. In addition, VBF can perform operations such as equality testing, composition, inversion, sum, direct sum, bricklayering (parallel application of vector Boolean functions as employed in Rijndael cipher), and adding coordinate functions of two vector Boolean functions. This thesis also illustrates the use of VBF in two practical applications. On the one hand, the most relevant properties of the existing block ciphers have been analysed. On the other hand, by combining VBF with optimization algorithms, new Boolean functions have been designed which have the best known cryptographic properties up-to-date.

Functions of the two glutamate transporters GLAST and GLT-1 in the retina

In the retina, the glutamate transporter GLAST is expressed in Müller cells, whereas the glutamate transporter GLT-1 is found only in cones and various types of bipolar cells. To investigate the functional role of this differential distribution of glutamate transporters, we have analyzed GLAST and GLT-1 mutant mice. In GLAST-deficient mice, the electroretinogram b-wave and oscillatory potentials are reduced and retinal damage after ischemia is exacerbated, whereas GLT-1-deficient mice show almost normal electroretinograms and mild increased retinal damage after ischemia. These results demonstrate that GLAST is required for normal signal transmission between photoreceptors and bipolar cells and that both GLAST and GLT-1 play a neuroprotective role during ischemia in the retina.

A rhodopsin-guanylyl cyclase gene fusion functions in visual perception in a fungus

Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Fluorescence-intensity distribution analysis and its application in biomolecular detection technology

A methodology, fluorescence-intensity distribution analysis, has been developed for confocal microscopy studies in which the fluorescence intensity of a sample with a heterogeneous brightness profile is monitored. An adjustable formula, modeling the spatial brightness distribution, and the technique of generating functions for calculation of theoretical photon count number distributions serve as the two cornerstones of the methodology. The method permits the simultaneous determination of concentrations and specific brightness values of a number of individual fluorescent species in solution. Accordingly, we present an extremely sensitive tool to monitor the interaction of fluorescently labeled molecules or other microparticles with their respective biological counterparts that should find a wide application in life sciences, medicine, and drug discovery. Its potential is demonstrated by studying the hybridization of 5′-(6-carboxytetramethylrhodamine)-labeled and nonlabeled complementary oligonucleotides and the subsequent cleavage of the DNA hybrids by restriction enzymes.

Cysteine String Protein Functions Directly in Regulated Exocytosis

Cysteine string protein (Csp) is essential for neurotransmitter release in Drosophila. It has been suggested that Csp functions by regulating the activity of presynaptic Ca2+ channels, thus controlling exocytosis. We have examined the effect of overexpressing Csp1 in PC12 cells, a neuroendocrine cell line. PC12 cell clones overexpressing Csp1 did not show any changes in morphology, granule number or distribution, or in the levels of other key exocytotic proteins. This overexpression did not affect intracellular Ca2+ signals after depolarization, suggesting that Csp1 has no gross effect on Ca2+ channel activity in PC12 cells. In contrast, we show that Csp1 overexpression enhances the extent of exocytosis from permeabilized cells in response to Ca2+ or GTPγS in the absence of Ca2+. Because secretion from permeabilized cells is not influenced by Ca2+ channel activity, this represents the first demonstration that Csp has a direct role in regulated exocytosis.

Differential Distribution of Dynamin Isoforms in Mammalian Cells

Dynamins are 100-kDa GTPases that are essential for clathrin-coated vesicle formation during receptor-mediated endocytosis. To date, three different dynamin genes have been identified, with each gene expressing at least four different alternatively spliced forms. Currently, it is unclear whether these different dynamin gene products perform distinct or redundant cellular functions. Therefore, the focus of this study was to identify additional spliced variants of dynamin from rat tissues and to define the distribution of the dynamin family members in a cultured rat epithelial cell model (Clone 9 cells). After long-distance reverse transcription (RT)-PCR of mRNA from different rat tissues, the full-length cDNAs encoding the different dynamin isoforms were sequenced and revealed four additional spliced variants for dynamin I and nine for dynamin III. Thus, in rat tissues there are a total of at least 25 different mRNAs produced from the three dynamin genes. Subsequently, we generated stably transfected Clone 9 cells expressing full-length cDNAs of six different spliced forms tagged with green fluorescent protein. Confocal or fluorescence microscopy of these transfected cells revealed that many of the dynamin proteins associate with distinct membrane compartments, which include clathrin-coated pits at the plasma membrane and the Golgi apparatus, and several undefined vesicle populations. These results indicate that the dynamin family is more extensive than was originally predicted and suggest that the different dynamin proteins are localized to distinct cytoplasmic or membrane compartments.

Occurrence of two somatostatin variants in the frog brain: characterization of the cDNAs, distribution of the mRNAs, and receptor-binding affinities of the peptides.

In tetrapods, only one gene encoding a somatostatin precursor has been identified so far. The present study reports the characterization of the cDNA clones that encode two distinct somatostatin precursors in the brain of the frog Rana ridibunda. The cDNAs were isolated by using degenerate oligonucleotides based on the sequence of the central region of somatostatin to screen a frog brain cDNA library. One of the cDNAs encodes a 115-amino acid protein (prepro-somatostatin-14; PSS1) that exhibits a high degree of structural similarity with the mammalian somatostatin precursor. The other cDNA encodes a 103-amino acid protein (prepro-[Pro2, Met13]somatostatin-14; PSS2) that contains the sequence of the somatostatin analog (peptide SS2) at its C terminus, but does not exhibit appreciable sequence similarity with PSS1 in the remaining region. In situ hybridization studies indicate differential expression of the PSS1 and PSS2 genes in the septum, the lateral part of the pallium, the amygdaloid complex, the posterior nuclei of the thalamus, the ventral hypothalamic nucleus, the torus semicircularis and the optic tectum. The somatostatin variant SS2 was significantly more potent (4-6 fold) than somatostatin itself in displacing [125I-Tyr0, D-Trp8] somatostatin-14 from its specific binding sites. The present study indicates that the two somatostatin variants could exert different functions in the frog brain and pituitary. These data also suggest that distinct genes encoding somatostatin variants may be expressed in the brain of other tetrapods.

cDNA structure, tissue distribution, and chromosomal localization of rat PC7, a novel mammalian proprotein convertase closest to yeast kexin-like proteinases.

By using reverse transcription-coupled PCR on rat anterior pituitary RNA, we isolated a 285-bp cDNA coding for a novel subtilisin/kexin-like protein convertase (PC), called rat (r) PC7. By screening rat spleen and PC12 cell lambda gt11 cDNA libraries, we obtained a composite 3.5-kb full-length cDNA sequence of rPC7. The open reading frame codes for a prepro-PC with a 36-amino acid signal peptide, a 104-amino acid prosegment ending with a cleavable RAKR sequence, and a 747-amino acid type I membrane-bound glycoprotein, representing the mature form of this serine proteinase. Phylogenetic analysis suggests that PC7 represents the most divergent enzyme of the mammalian convertase family and that it is the closest member to the yeast convertases krp and kexin. Northern blot analyses demonstrated a widespread expression with the richest source of rPC7 mRNA being the colon and lymphoid-associated tissues. In situ hybridization revealed a distinctive tissue distribution that sometimes overlaps with that of furin, suggesting that PC7 has widespread proteolytic functions. The gene for PC7 (Pcsk7) was mapped to mouse chromosome 9 by linkage analysis of an interspecific backcross DNA panel.

The stem cell antigen CD34 functions as a regulator of hemopoietic cell adhesion.

Although the CD34 antigen is widely used in the identification and purification of hemopoietic stem and progenitor cells, its function within hemopoiesis is unknown. We have investigated this issue by ectopically expressing human (hu) CD34 on the surface of murine hemopoietic cells. Forced expression of hu-CD34 in the thymocytes of transgenic mice did not appear to affect the development, maturation, or distribution of murine T cells but did significantly increase their ability to adhere to bone marrow stromal layers of human but not mouse origin. Ectopic expression of hu-CD34 on murine 416B cells, a multipotential progenitor that expresses murine CD34, yielded similar results. In both cases hu-CD34-dependent adhesion was enhanced by molecular engagement of the hu-CD34 protein using anti-CD34 antibodies. These results provide evidence that CD34 promotes the adhesive interactions of hemopoietic cells with the stromal microenvironment of the bone marrow thereby implicating CD34 in regulation and compartmentalization of stem cells. We propose that CD34 regulates these processes in part via an indirect mechanism, signaling changes in cellular adhesion in response to molecular recognition of an as yet unidentified stromal CD34 counterreceptor or ligand.

The Gaia-ESO Survey: radial metallicity gradients and age-metallicity relation of stars in the Milky Way disk

We study the relationship between age, metallicity, and α-enhancement of FGK stars in the Galactic disk. The results are based upon the analysis of high-resolution UVES spectra from the Gaia-ESO large stellar survey. We explore the limitations of the observed dataset, i.e. the accuracy of stellar parameters and the selection effects that are caused by the photometric target preselection. We find that the colour and magnitude cuts in the survey suppress old metal-rich stars and young metal-poor stars. This suppression may be as high as 97% in some regions of the age-metallicity relationship. The dataset consists of 144 stars with a wide range of ages from 0.5 Gyr to 13.5 Gyr, Galactocentric distances from 6 kpcto 9.5 kpc, and vertical distances from the plane 0 < |Z| < 1.5 kpc. On this basis, we find that i) the observed age-metallicity relation is nearly flat in the range of ages between 0 Gyr and 8 Gyr; ii) at ages older than 9 Gyr, we see a decrease in [Fe/H] and a clear absence of metal-rich stars; this cannot be explained by the survey selection functions; iii) there is a significant scatter of [Fe/H] at any age; and iv) [Mg/Fe] increases with age, but the dispersion of [Mg/Fe] at ages >9 Gyr is not as small as advocated by some other studies. In agreement with earlier work, we find that radial abundance gradients change as a function of vertical distance from the plane. The [Mg/Fe] gradient steepens and becomes negative. In addition, we show that the inner disk is not only more α-rich compared to the outer disk, but also older, as traced independently by the ages and Mg abundances of stars.

MOREMATA: Stata module (Mata) to provide various functions

This package includes various Mata functions. kern(): various kernel functions; kint(): kernel integral functions; kdel0(): canonical bandwidth of kernel; quantile(): quantile function; median(): median; iqrange(): inter-quartile range; ecdf(): cumulative distribution function; relrank(): grade transformation; ranks(): ranks/cumulative frequencies; freq(): compute frequency counts; histogram(): produce histogram data; mgof(): multinomial goodness-of-fit tests; collapse(): summary statistics by subgroups; _collapse(): summary statistics by subgroups; gini(): Gini coefficient; sample(): draw random sample; srswr(): SRS with replacement; srswor(): SRS without replacement; upswr(): UPS with replacement; upswor(): UPS without replacement; bs(): bootstrap estimation; bs2(): bootstrap estimation; bs_report(): report bootstrap results; jk(): jackknife estimation; jk_report(): report jackknife results; subset(): obtain subsets, one at a time; composition(): obtain compositions, one by one; ncompositions(): determine number of compositions; partition(): obtain partitions, one at a time; npartitionss(): determine number of partitions; rsubset(): draw random subset; rcomposition(): draw random composition; colvar(): variance, by column; meancolvar(): mean and variance, by column; variance0(): population variance; meanvariance0(): mean and population variance; mse(): mean squared error; colmse(): mean squared error, by column; sse(): sum of squared errors; colsse(): sum of squared errors, by column; benford(): Benford distribution; cauchy(): cumulative Cauchy-Lorentz dist.; cauchyden(): Cauchy-Lorentz density; cauchytail(): reverse cumulative Cauchy-Lorentz; invcauchy(): inverse cumulative Cauchy-Lorentz; rbinomial(): generate binomial random numbers; cebinomial(): cond. expect. of binomial r.v.; root(): Brent's univariate zero finder; nrroot(): Newton-Raphson zero finder; finvert(): univariate function inverter; integrate_sr(): univariate function integration (Simpson's rule); integrate_38(): univariate function integration (Simpson's 3/8 rule); ipolate(): linear interpolation; polint(): polynomial inter-/extrapolation; plot(): Draw twoway plot; _plot(): Draw twoway plot; panels(): identify nested panel structure; _panels(): identify panel sizes; npanels(): identify number of panels; nunique(): count number of distinct values; nuniqrows(): count number of unique rows; isconstant(): whether matrix is constant; nobs(): number of observations; colrunsum(): running sum of each column; linbin(): linear binning; fastlinbin(): fast linear binning; exactbin(): exact binning; makegrid(): equally spaced grid points; cut(): categorize data vector; posof(): find element in vector; which(): positions of nonzero elements; locate(): search an ordered vector; hunt(): consecutive search; cond(): matrix conditional operator; expand(): duplicate single rows/columns; _expand(): duplicate rows/columns in place; repeat(): duplicate contents as a whole; _repeat(): duplicate contents in place; unorder2(): stable version of unorder(); jumble2(): stable version of jumble(); _jumble2(): stable version of _jumble(); pieces(): break string into pieces; npieces(): count number of pieces; _npieces(): count number of pieces; invtokens(): reverse of tokens(); realofstr(): convert string into real; strexpand(): expand string argument; matlist(): display a (real) matrix; insheet(): read spreadsheet file; infile(): read free-format file; outsheet(): write spreadsheet file; callf(): pass optional args to function; callf_setup(): setup for mm_callf().

A note on a gamma distribution computer program and computer produced graphs /

"NOAA--S/T 77-2535"

A note on a gamma distribution computer program /

Mode of access: Internet.

Beluga whale distribution, migration, and behavior in a changing Pacific Arctic

Thesis (Ph.D.)--University of Washington, 2016-06

Application of density functional theory to capillary phenomena in cylindrical mesopores with radial and longitudinal density distributions

In this paper, we applied a version of the nonlocal density functional theory (NLDFT) accounting radial and longitudinal density distributions to study the adsorption and desorption of argon in finite as well as infinite cylindrical nanopores at 87.3 K. Features that have not been observed before with one-dimensional NLDFT are observed in the analysis of an inhomogeneous fluid along the axis of a finite cylindrical pore using the two-dimensional version of the NLDFT. The phase transition in pore is not strictly vapor-liquid transition as assumed and observed in the conventional version, but rather it exhibits a much elaborated feature with phase transition being complicated by the formation of solid phase. Depending on the pore size, there are more than one phase transition in the adsorption-desorption isotherm. The solid formation in finite pore has been found to be initiated by the presence of the meniscus. Details of the analysis of the extended version of NLDFT will be discussed in the paper. (C) 2004 American Institute of Physics.