Antonio Paiva

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Papers by Antonio Paiva

A Reproducing Kernel Hilbert Space Framework for ITL

Information Science and Statistics, 2010

This paper presents a general framework based on reproducing kernel Hilbert spaces (RKHS) to math... more This paper presents a general framework based on reproducing kernel Hilbert spaces (RKHS) to mathematically describe and manipulate spike trains. The main idea is the definition of inner products to allow spike train signal processing from basic principles while incorporating their statistical description as point processes. Moreover, because many inner products can be formulated, a particular definition can be crafted to best fit an application. These ideas are illustrated by the definition of a number of spike train inner products. To further elicit the advantages of the RKHS framework, a family of these inner products, called the cross-intensity (CI) kernels, is further analyzed in detail. This particular inner product family encapsulates the statistical description from conditional intensity functions of spike trains. The problem of their estimation is also addressed. The simplest of the spike train kernels in this family provides an interesting perspective to other works presented in the literature, as will be illustrated in terms of spike train distance measures. Finally, as an application example, the presented RKHS framework is used to derive from simple principles a clustering algorithm for spike trains.

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Optimization in Reproducing Kernel Hilbert Spaces of Spike Trains

Springer Optimization and Its Applications, 2010

This paper presents a framework based on reproducing kernel Hilbert spaces (RKHS) for optimizatio... more This paper presents a framework based on reproducing kernel Hilbert spaces (RKHS) for optimization with spike trains. To establish the RKHS for optimization we start by introducing kernels for spike trains. It is shown that spike train kernels can be built from ideas of kernel methods, or from the intensity functions underlying the spike trains. However, the later approach shall be the main focus of this study. We introduce the memoryless cross-intensity (mCI) kernel as an example of an inner product of spike trains, which defines the RKHS bottom-up as an inner product of intensity functions. Being defined in terms of the intensity functions, this approach towards defining spike train kernels has the advantage that points in the RKHS incorporate a statistical description of the spike trains, and the statistical model is explicitly stated. Some properties of the mCI kernel and the RKHS it induces will be given to show that this RKHS has the necessary structure for optimization. The issue of estimation from data is also addressed. We finalize with an example of optimization in the RKHS by deriving an algorithm for principal component analysis (PCA) of spike trains.

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Reproducing kernel Hilbert spaces for spike train analysis

2008 IEEE International Conference on Acoustics, Speech and Signal Processing, 2008

... methods, 2007, sub-mitted. [10] George L. Gerstein, Donald H. Perkel, and Judith E. Dayhoff, ... more

A Novel Weighted LBG Algorithm for Neural Spike Compression

2007 International Joint Conference on Neural Networks, 2007

In this paper, we present a weighted Linde-Buzo-Gray algorithm (WLBG) as a powerful and efficient... more In this paper, we present a weighted Linde-Buzo-Gray algorithm (WLBG) as a powerful and efficient technique for compressing neural spike data. We compare this technique with the recently proposed Self-Organizing Map with Dynamic Learning (SOM-DL) and the traditional SOM. A significant achievement of WLBG over SOM-DL is a 15dB increase in the SNR of the spike data apart from having a compression ratio of 150 : 1. Being simple and extremely fast, this algorithm allows real-time implementation on DSP chips opening new opportunities in BMI applications.

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Spectral Clustering of Synchronous Spike Trains

2007 International Joint Conference on Neural Networks, 2007

In this paper a clustering algorithm that learns the groups of synchronized spike trains directly... more In this paper a clustering algorithm that learns the groups of synchronized spike trains directly from data is proposed. Clustering of spike trains based on the presence of synchronous neural activity is of high relevance in neurophysiological studies. In this context such activity is thought to be associated with functional structures in the brain. In addition, clustering has the potential to analyze large volumes of data. The algorithm couples a distance between two spike trains recently proposed in the literature with spectral clustering. Finally, the algorithm is illustrated in sets of computer generated spike trains and analyzed for the dependence on its parameters and accuracy with respect to features of interest.

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A Reproducing Kernel Hilbert Space Framework for Information-Theoretic Learning

IEEE Transactions on Signal Processing, 2008

This paper provides a functional analysis perspective of information-theoretic learning (ITL) by ... more This paper provides a functional analysis perspective of information-theoretic learning (ITL) by defining bottom-up a reproducing kernel Hilbert space (RKHS) uniquely determined by the symmetric nonnegative definite kernel function known as the cross-information potential (CIP). The CIP as an integral of the product of two probability density functions characterizes similarity between two stochastic functions. We prove the existence of a one-to-one congruence mapping between the ITL RKHS and the Hilbert space spanned by square integrable probability density functions. Therefore, all the statistical descriptors in the original information-theoretic learning formulation can be rewritten as algebraic computations on deterministic functional vectors in the ITL RKHS, instead of limiting the functional view to the estimators as is commonly done in kernel methods. A connection between the ITL RKHS and kernel approaches interested in quantifying the statistics of the projected data is also established.

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A Reproducing Kernel Hilbert Space Framework for ITL

During the last decade, research on Mercer kernel-based learning algorithms has flourished [294, ... more During the last decade, research on Mercer kernel-based learning algorithms has flourished [294, 226, 289]. These algorithms include, for example, the support vector machine (SVM) [63], kernel principal component analysis (KPCA) [289], and kernel Fisher discriminant analysis (KFDA) [219]. The common property of these methods is that they operate linearly, as they are explicitly expressed in terms of inner products in a transformed data space that is a reproducing kernel Hilbert space (RKHS). Most often they correspond to nonlinear operators in the data space, and they are still relatively easy to compute using the so-called “kernel-trick”. The kernel trick is no trick at all; it refers to a property of the RKHS that enables the computation of inner products in a potentially infinite-dimensional feature space, by a simple kernel evaluation in the input space. As we may expect, this is a computational saving step that is one of the big appeals of RKHS. At first glance one may even think that it defeats the “no free lunch theorem” (get something for nothing), but the fact of the matter is that the price of RKHS is the need for regularization and in the memory requirements as they are memory-intensive methods. Kernel-based methods (sometimes also called Mercer kernel methods) have been applied successfully in several applications, such as pattern and object recognition [194], time series prediction [225], and DNA and protein analysis [350], to name just a few.

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Alkylating analogs of peptide hormones. 2. Synthesis and properties of p-[N,N-bis(2-chloroethyl)amino]phenylbutyryl derivatives of angiotensin II

Journal of Medicinal Chemistry, 1972

... Therezinha B. Paiva, Antonio C. M. Paiva. Department of Biophysics and Physiology, Escola Pau... more

Endothelium-dependent inhibition of the use of extracellular calcium for the arterial response to vasoconstrictor agents

General Pharmacology: The Vascular System, 1985

1. The responses of rabbit mesenteric or coeliac artery rings to angiotensin II or adrenaline (bu... more

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Regions of G-Protein-Coupled Receptors Identified by Multiple Sequence Alignment

Peptides: The Wave of the Future, 2001

A common ligand-binding site in G-protein coupled receptors

American Peptide Symposia, 2002

... Laerte Oliveira,1 Gerrit Vriend,2 and Antonio CM Paiva1 1Department of Biophysics, Escola Pau... more

Effects of endothelin-1 on the isolated guinea-pig ileum: role of Na + ions

Naunyn-schmiedebergs Archives of Pharmacology, 1990

Endothelin-1 induced an unusual transient biphasic effect (relaxation followed by contraction) in... more Endothelin-1 induced an unusual transient biphasic effect (relaxation followed by contraction) in the isolated guinea-pig ileum. The contractile component of the response was concentration-dependent in the dose range studied, but the relaxant component was not. Neuronal mechanisms and cyclic GMP do not seem to be involved in the relaxing effect since this component was not affected by either tetrodotoxin, atropine or methylene blue. Endothelin-1 induced desensitization which was well characterized for the contractile component of the response, and was only partially reversed after a 3-h resting period. The effects of endothelin-1 were particularly sensitive to decreases in the Na+ gradient induced either by lowering the Na+ concentration in the medium or by treating the tissue with ouabain or by a previous treatment with acetylcholine. Amiloride partially inhibited the response induced by endothelin-1 indicating that Na+ channels and/or Na+/H+ exchange are probably involved in its action. Our results suggest that the contractile response induced by endothelin-1 in the isolated guinea-pig ileum depends greatly on Na+ ions, in contrast to the responses observed in vascular smooth muscle.

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Conformation of angiotensin II in aqueous solutions. Titration of several peptide analogs and homologs

Biochemistry, 1974

Fifteen analogs and homologs of [IIe5]angiotensin I1 (AII) were titrated electrometrically in the... more Fifteen analogs and homologs of [IIe5]angiotensin I1 (AII) were titrated electrometrically in the temperature range 15-40". A positive linear relationship between A H o and TAS", with slope near unity, was found for the dissociation of carboxyl, imidazole, amino, and phenoxy1 groups. The differences in pK, values for these groups in the series of AI1 analogs and homologs were interpreted as indicative of in-2 Abbreviations used are: AII, [Ile5]angiotensin 11; SUC, succinyl. Peptides were named according to the IUPAC tentative rules for naming synthetic modifications of natural peptides (1967).

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Spin-labeled extracellular loop from a seven-transmembrane helix receptor: Studies in solution and interaction with model membranes

Biopolymers, 1997

Alkylating analogs of peptide hormones. 2. Synthesis and properties of p-[N,Nbis(2-chloroethyl)amino]phenylbutyryl derivatives of angiotensin II

Journal of Medicinal Chemistry, 1972

... Therezinha B. Paiva, Antonio C. M. Paiva. Department of Biophysics and Physiology, Escola Pau... more

Transcriptional regulatory elements in the rat bradykinin B2 receptor gene

Immunopharmacology, 1996

In an attempt to elucidate the mechanisms underlying the regulation of bradykinin B2 receptor gen... more In an attempt to elucidate the mechanisms underlying the regulation of bradykinin B2 receptor gene expression, the molecular structure of the rat gene including the 5′-flanking region was characterized (itJ. Biol. Chem) 269: 26920–26925, 1994). In this study we show that the gene spans about 32 kb, including a long first intron of 25 kb. The promoter region drives reporter gene expression in NG108-15 neuroglioma cells, and its expression is upregulated by cAMP, bradykinin, phorbol esters and by coexpression of an activated ras oncogene but not by dexamethasone.

Role of sodium ions in angiotensin tachyphylaxis in the guinea-pig ileum and taenia coli

Naunyn-schmiedebergs Archives of Pharmacology, 1988

We have examined the responsiveness of the guinea-pig ileum and taenia coli to angiotensin (ANG) ... more We have examined the responsiveness of the guinea-pig ileum and taenia coli to angiotensin (ANG) analogues that were previously shown to be either able (|1-sarcosine|-ANG, Sar1-ANG) or unable (|2-lysine|-ANG, Lys2-ANG) to induce tachyphylaxis in the ileum. The taenia coli, in which tachyphylaxis had not been previously shown to occur, was strongly tachyphylactic to Sar1-ANG, but not to Lys2-ANG. The contractile responses of the ileum, as well as the contractile and electrical (sucrose-gap) events in the taenia coli, in response to the two ANG analogues, were used to investigate the tachyphylactic phenomenon and the role of Na+ in the manifestation. Relaxation of the ileum and repolarizations of the taenia coli were faster after treatment with Lys2-ANG than after Sar1-ANG. In the tachyphylactic state, relaxation and repolarization after Sar1-ANG became as fast as after Lys2-ANG. In “low-Na+” (80 mmol/l) medium, as well as in ouabain-treated preparations, the responses of the ileum to ANG analogues were similar to those of tissues in the tachyphylactic state. Addition of Ca2+ to taenia coli preparations previously treated with the two ANG analogues in Ca+-free medium, caused contractile and electrical responses only in the case of Sar1-ANG. It is proposed that ANG tachyphylaxis is due to changes at the level of the receptor causing increased Na+ permeability which leads to a decreased Na+ gradient across the cell membrane.

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Identification of functionally conserved residues with the use of entropy–variability plots

Proteins-structure Function and Bioinformatics, 2003

We introduce sequence entropy–variability plots as a method of analyzing families of protein sequ... more We introduce sequence entropy–variability plots as a method of analyzing families of protein sequences, and demonstrate this for three well-known sequence families: globins, ras-like proteins, and serine-proteases. The location of an aligned residue position in the entropy–variability plot correlates with structural characteristics, and with known facts about the roles of individual amino acids in the function of these proteins. The large numbers of known sequences in these families allowed us to introduce new filtering methods for variability patterns. The results are discussed in terms of a simple evolutionary model for functional proteins. Proteins 2003;52:544–552. © 2003 Wiley-Liss, Inc.

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Synthesis and properties of new bradykinin potentiating peptides

Journal of Medicinal Chemistry, 1975

In a study of the relationship between structure and activity of bradykinin potentiating peptides... more In a study of the relationship between structure and activity of bradykinin potentiating peptides (BPP), six analogs and homologs of peptides occurring in the venoms of Bothrops jararaca and Agkistrodon halys blomhoffii were synthesized and assayed in the isolated guinea pig ileum and rat uterus. None of the peptides had bradykinin-like activity and their bradykinin potentiating activity was much greater in the guinea pig ileum than in the uterus. The following observations were made with the guinea pig ileum. The introduction of Gln as the eigth residue in potentiator B (pGlu-Gly-Leu-Pro-Pro-Arg-Pro-Lys-Ile-Pro-Pro) and potentiator C (pGlu-Gly-Leu-Pro-Pro-Gly-Pro-Pro-Ile-Pro-Pro) produced a small increase in their bradykinin potentiating activity. Removal of the two N-terminal residues of [Gln8]-potentiator B and [Gln8]-potentiator C led to alterations in activity that paralleled those described earlier for the parent compounds (potentiators B and C). The peptide with the sequence pGlu-Trp-Pro-Ary-Pro-Lys-Trp-Ala-Pro was seven times as active as BPP5a, while the most potent natural BPP, a nonapeptide from B. jararaca venom, is reported to be only four times as active as BPP5a. An analog of the above-mentioned nonapeptide containing Pro8 instead of Ala8 was only as active as BPPa. For all of the peptides, as well as for potentiatrs B and C and BPP5a, the concentration vs. potentiating activity curves had similar shapes, with a plateau at twofold potentiation and a maximum potentiation of 10- to 11-fold. A direct action on the bradykinin receptors may be responsible for the effects observed at lower BPP concentration while the effects at higher concentrations may be due to kininase inhibition. The potentiating activities of potentiator B and its Gln8 analog persisted after the peptides were removed from the medium. This &quot;sensitizing activity&quot; was not observed with any of the other peptides.

Conformational Studies of Angiotensin II Cyclic Analogues

Peptides: The Wave of the Future, 2001

Antonio Paiva

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