David N Olivieri

David N Olivieri
University of Vigo | UVIGO

PhD, Physics
Profesor Titular, UVigo

About

130
Publications
40,028
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1,130
Citations
Additional affiliations
January 1999 - February 2020
University of Vigo
Position
  • Professor (Associate)
June 1993 - June 1996
Fermi National Accelerator Laboratory (Fermilab)
Position
  • PhD Student

Publications

Publications (130)
Article
To allow inhalation exposure studies, with control of particulate matter (PM) concentration/dose, a low-cost aerosol generator with real-time continual monitoring was developed and tested. This device can be used for comparing controlled laboratory experiments with resuspension of dry ambient PM or dry powders/particles to model atmospheric PM conc...
Article
Context. The repetitive solution of Kepler’s equation (KE) is the slowest step for several highly demanding computational tasks in astrophysics. Moreover, a recent work demonstrated that the current solvers face an accuracy limit that becomes particularly stringent for high eccentricity orbits. Aims. Here we describe two routines, ENRKE and ENP5KE,...
Article
Full-text available
In a recent MNRAS article, Raposo-Pulido and Pelaez (RPP) designed a scheme for obtaining very close seeds for solving the elliptic Kepler Equation with the classical and the modified Newton-Rapshon methods. This implied an important reduction in the number of iterations needed to reach a given accuracy. However, RPP also made strong claims about t...
Article
Immunoglobulin (Ig) genes encode antibodies in jawed vertebrates. They are essential elements of the adaptive immune response. Ig exists in soluble form or as part of the B cell membrane antigen receptor (BCR). Studies of Ig genes in fish genomes reveal the absence of Ig genes in Gouania willdenowi by deletion of the entire Ig locus from the canoni...
Article
In teleost fishes, there are three immunoglobulin isotypes named immunoglobulin M (IgM), D (IgD), and T (IgT). IgT was the last to be described in teleost fishes, and it is specific to them. From recent fish genomes, we identified and studied the immunoglobulin heavy chain genes in Actinopterygii. For this analysis, a custom bioinformatics and mach...
Conference Paper
We provide a software package implementing the well-known beam propaga- tion method to integrate the 1+1 and 1+2 dimensional nonlinear Schrödinger equation. It is useful to simulate optical beam propagation in the spatial and temporal domains.
Article
In teleost fishes, there are three immunoglobulin isotypes named immunoglobulin M (IgM), D (IgD), and T (IgT). IgT was the last to be described in teleost fishes, and it is specific to them. From recent fish genomes, we identified and studied the immunoglobulin heavy chain genes in Actinopterygii. For this analysis, a custom bioinformatics and mach...
Article
Full-text available
Obtaining the inverse of a nonlinear monotonic function f(x) over a given interval is a common problem in pure and applied mathematics, the most famous example being Kepler’s description of orbital motion in the two-body approximation. In traditional numerical approaches, this problem is reduced to solving the nonlinear equation f(x)−y=0 in each po...
Article
Immunoglobulins are essential proteins of the immune system to neutralize pathogens. Gene encoding B cell receptors and antibodies (Ig genes) first appeared with the emergence of early vertebrates having a jaw, and are now present in all extant jawed vertebrates, or Gnathostomata. The genes have undergone evolutionary changes. In particular, genomi...
Article
Full-text available
Feline leukemia virus (FeLV) causes an infection in cats that, in some cases, can also be reported with other pathologies, such as infection with feline immunodeficiency virus (FIV), feline infectious peritonitis (FIP), and lymphoma. Although, a compromised immune response is reported in these animals, little is known about the immunological state...
Preprint
Full-text available
Genes of the major class I and II histocompatibility complex have been extensively studied in mammals. Studies of these antigens in reptiles are very scarce. Here we describe the characteristics of these genes in the suborder Serpentes. We identified the presence of a much larger number of molecules of class I and beta chains of class II than found...
Preprint
Full-text available
In teleost fishes there are three immunoglobulin isotypes named immunoglobulin M (IgM), D (IgD) and T (IgT). IgT has been the last to be described and is considered a teleosts-fish specific isotype. From the recent availability of genome sequences of fishes, an in-depth analysis of Actinopterygii immunoglobulin heavy chain genes was undertaken. Wit...
Article
Full-text available
Numerical simulation experiments are of great importance for research and education in Physics. They can be greatly aided by proper graphical representations, especially for spatio-temporal dynamics. In this contribution, we describe and provide a novel Javascript-based library and cloud microservice—QMwebJS—for the visualization of the temporal ev...
Article
We review recent progress in Schrödinger–Poisson systems in 1+2 and 1+3 dimensions in the presence of nonlinear terms. In a mean field approach, this mathematical model describes the semiclassical behavior of an N-body system of identical bosons with nonlocal interactions between them. The 1+2D model can be used to describe the nonlinear propagatio...
Article
Full-text available
Contribution: The goal of this study is to validate the results of a prior study on the educational value of systematic mapping studies (SMS) and evaluate the possibility of generalizing those results to similar contexts. Background: since the inception of the Evidence Based Software Engineering (EBSE) paradigm in 2004, few studies have aimed at ev...
Preprint
Full-text available
In the study of immunoglobulin V genes in fish genomes, we found that the species Gouania willdenowi does not possess any such regions, neither for the heavy chain nor for the light chains. Also, genes that code for the immunoglobulin constant regions were also not found. A detailed analysis of the chromosomal region of these genes revealed a delet...
Article
Numerically obtaining the inverse of a function is a common task for many scientific problems, often solved using a Newton iteration method. Here we describe an alternative scheme, based on switching variables followed by spline interpolation, which can be applied to monotonic functions under very general conditions. To optimize the algorithm, we d...
Article
Full-text available
We present a dataset obtained by extracting information from an extensive literature search of toxicological experiments using mice and rat animal models to study the effects of exposure to airborne particulate matter (PM). Our dataset covers results reported from 75 research articles considering paper published in 2017 and seminal papers from prev...
Article
We study the self-trapped vortex-ring eigenstates of the two-dimensional Schrödinger equation with focusing Poisson and cubic nonlinearities. For each value of the topological charge l, there is a family of solutions depending on a parameter that can be understood as the relative importance of the cubic term. We analyze the perturbative stability o...
Article
Simulated three-dimensional quantum wave functions (or probability density distributions, in general), Ψ(x, t), are often represented graphically as smooth isocontours or with 2-dimensional cross-sectional plots. As such, neither the full wave dynamics nor the true stochastic interpretation are captured adequately in a single representation. Moreov...
Article
Ecotoxicological studies that try to describe the effects of particulate matter (PM)on human health are important in order to gain a deeper understanding of their effects in disease outcomes. Because exposure protocols are not easily comparable, evaluating human PM exposure is a difficult task. Thus, interpreting ambiguous or conflicting results fr...
Article
Full-text available
In jawed vertebrates, variable (V) genes code for antigen-binding regions of B and T lymphocyte receptors, which generate a specific response to foreign pathogens. Obtaining the detailed repertoire of these genes across the jawed vertebrate kingdom would help to understand their evolution and function. However, annotations of V-genes are known for...
Preprint
Full-text available
Numerically obtaining the inverse of a function is a common task for many scientific problems, often solved using a Newton iteration method. Here we describe an alternative scheme, based on switching variables followed by spline interpolation, which can be applied to monotonic functions under very general conditions. To optimize the algorithm, we d...
Article
Full-text available
A simple Python-based open source software library for the numerical simulation of the linear or nonlinear time-dependent Schrodinger equation in one and two dimensions is presented. The integration is performed using a first order split-step pseudospectral method, relying on the fast Fourier transform. The software library could be useful for unde...
Article
Reuse has been a topic of interest in software engineering since 1968. Although many academic papers have been written about adopting software reuse in companies, such a process in practice has proven difficult, long and costly to implement. At present, rigorous studies on the current practice of reuse in industry are scarce. Objective: The aim of...
Preprint
Full-text available
The major histocompatibility complex (MHC) molecule plays a central role in the adaptive immunity of jawed vertebrates. Allelic variations have been studied extensively in some primate species, however a comprehensive description of the number of genes remains incomplete. Here, a bioinformatics program was developed to identify three MHC Class I ex...
Article
Full-text available
Background: Chronic kidney disease (CKD) is the convergent point of several pathological processes, and its evolution is insidious and characterized by a progressive and irreversible loss of kidney function. This impaired function induces the accumulation of uremic toxins and individuals with terminal CKD often have altered physiological responses...
Article
Full-text available
A complete understanding of the mechanisms underlying the acquisition of protective immunity is crucial to improve vaccine strategies to eradicate malaria. However, it is still unclear whether recognition of damage signals influences the immune response to Plasmodium infection. Adenosine triphosphate (ATP) accumulates in infected erythrocytes and i...
Data
Malaria parasite development and ATP serum levels in acutely infected B6 mice. (A) The percentages of trophozoites, shizonts and ring stages were determined at 5 days p.i. with 1 × 106 iRBCs (n = 3). Arrows indicate the time at which blood samples were collected. (B) B6 and P2rx7-/- female mice were analyzed at 4 and 5 days p.i. with 1 × 106 iRBCs....
Data
Effects of apyrase and BBG in splenic B6 CD4 T cell responses to iRBCs. (A-B) B6 mice were analyzed at 4 days p.i. with 1 × 106 Pc-iRBCs. The data were expressed as means ± SD (n = 3) of one representative experiment out of three. Significant differences were observed for the (*) indicated groups with p < 0.05, using the Mann Whitney U test (NS, no...
Data
Phenotypic characterization of splenic CD4 T cells in acutely infected B6 and P2rx7-/- mice. (A-F) B6 and P2rx7-/- female mice were analyzed at 4, 7 and 20 days p.i. with 1 × 106 iRBCs. Naïve mice were used as controls (day 0). The data were expressed as means ± SD (n = 3–5) of one representative experiment out of three. Significant differences wer...
Data
CD4 TE, TEM and TCM cell numbers per spleen and phenotypic characterization of IFNγ- and IL-10-producing cells in chronically infected B6 and P2rx7-/- mice. (A-B) B6 and P2rx7-/- female mice were analyzed at 20 and 30 days p.i. with 1 × 106 Pc-iRBCs. Naïve mice were used as controls (day 0). The data were expressed as means ± SD (n = 3) of one repr...
Data
Splenic CD4 T cell populations in Cd4-/- mice adoptively transferred with B6 or P2rx7-/- CD4 cells and infected with Pc parasites. (A-B) Naïve CD4+ cells from B6 and P2rx7-/- mice were transferred into Cd4-/- mice that were infected with 1 × 106 iRBCs 7 days later. Splenic CD4+ cells were analyzed at 7 and 30 days p.i. Naïve mice were used as contr...
Data
Characterization of splenic CD4 TE/EM and TCM cells from chronically infected B6 and P2rx7-/- mice. (A-C) B6 and P2rx7-/- female mice were analyzed at 20 and 30 days p.i. with 1 × 106 Pc-iRBCs. Naïve mice were used as controls (day 0). The data were expressed as means ± SD (n = 3–4) of one representative experiment out of three. Significant differe...
Article
Tissue membranes are boundaries that isolate organs or cavities in the body. These semi-permeable membranes are responsible for passive protection that acts through the regulation of nutrient absorption, secretion and filtration of small molecules. These functions could be altered as a consequence of inflammation or trauma, which in turn could lead...
Article
Full-text available
Purpose Chronic myeloid leukemia (CML) is a clonal myeloproliferative disease, accounting for 15 to 20% of leukemias, with an incidence of one to two cases/100,000 inhabitants. In Brazil, the estimated incidence of leukemia is six cases/100,000 men and 4.28 cases/100,000 women. CML is characterized by the presence of the Philadelphia chromosome. At...
Article
Full-text available
This paper describes a novel software algorithm, called constrained Sequential Monte Carlo (SMC) clusters, for tracking a large collection of individual cells from intra-vital two-photon microscopy image sequences. We show how our method and software tool, implemented in python, is useful for quantifying the motility of T and B lymphocytes involved...
Article
Full-text available
The Squamata order represents a major evolutionary reptile lineage, yet the structure and expression of immunoglobulins in this order has been scarcely studied in detail. From the genome sequences of four Squamata species (Gekko japonicus, Ophisaurus gracilis, Pogona vitticeps and Ophiophagus hannah) and RNA-seq datasets from 18 other Squamata spec...
Article
We studied the immunoglobulin genes from either the genomes or RNAseq of amphibians. In particular, we obtained data from one frog genome (Nanorana parkeri) and three transcriptomes of the Caudata order (Andrias davidianus, Notophthalmus viridescens and Cynops pyrrhogaster). Apart from the immunoglobulins IgM and IgY previously described, we identi...
Article
We describe a new algorithm for distinguishing human actions in videos, called the differential geometric trajectory cloud (DGTC) method that captures both fine and large scale structure of the covariant transformed spatio-temporal optical flow field. We show the utility of our algorithm in the context of a content based video retrieval (CBVR) syst...
Article
We describe a set of new algorithms and a software tool, StabiTissue, for stabilizing in vivo intravital microscopy images that suffer from soft-tissue background movement. Because these images lack predetermined anchors and are dominated by noise, we use a pixel weighted image alignment together with a correction for nonlinear tissue deformations....
Article
Full-text available
Information concerning the evolution of T lymphocyte receptors (TCR) can be deciphered from that part of the molecule that recognizes antigen presented by major histocompatibility complex (MHC), namely the variable (V) regions. The genes that code for these variable regions are found within the TCR loci. Here, we describe a study of the evolutionar...
Article
Full-text available
The adaptive immune system uses V genes for antigen recognition. However, the evolutionary diversification and selection processes within and across species and orders remain poorly understood. Here, we studied the amino acid (AA) sequences obtained from the translated in-frame V exons of immunoglobulins (IG) and T cell receptors (TR) from 16 prima...
Chapter
Observing the complex dynamics of cellular interactions and physiology in the uterus and placenta requires novel intravital imaging techniques, involving modern microscopy and surgical protocols. Here, we will briefly explain how two-photon microscopy with the development of new surgical tools and postprocessing image methods are advancing our unde...
Preprint
Full-text available
We studied the V exons of 14 rodent species obtained from whole genome sequencing (WGS) datasets. Compared to other mammals, we found an increase in the number of immunoglobulin (IG) V genes in the heavy (IGH) and kappa chain (IGK) loci. We provide evidence for a reduction genes in lambda chain (IGL) locus, disappearing entirely in one of the speci...
Preprint
The adaptive immune system uses V genes for antigen recognition. The evolutionary diversification and selection processes within and across species and orders are poorly understood. Here, we studied the amino acid (AA) sequences obtained of translated in-frame V exons of immunoglobulins (IG) and T cell receptors (TR) from 16 primate species whose g...
Article
Full-text available
Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole geno...
Article
Full-text available
We describe a content based video retrieval (CBVR) software system for identifying specific locations of a human action within a full length film, and retrieving similar video shots from a query. For this, we introduce the concept of a trajectory point cloud for classifying unique actions, encoded in a spatio-temporal covariant eigenspace, where ea...
Preprint
Full-text available
From recent whole genome shotgun data of 48 mammalian species, we have used our software VgenExtractor to obtain the functional V-gene sequence repertoire in order to conduct comparative phylogenetic studies. These studies reveal a large variation in the number of V-genes across mammalian species, ranging from a mere 36 V-genes in dolphins to nearl...
Preprint
Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged, one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia and birds. In this study, we determined the genomic variable (V)-gene repertoire in re...
Preprint
Full-text available
The VgeneRepertoire.org platform (http://vgenerepertoire.org) is a new public database repository for variable (V) gene sequences that encode immunoglobulin and T-cell receptor molecules. It identifies the nucleic and amino acid sequences of more than 20,000 genes, providing their exon location in either the contig, scaffold, or chromosome region,...
Article
Full-text available
Variable (V) domains of immunoglobulins (Ig) and T cell receptors (TCR) are generated from genomic V gene segments (V-genes). At present, such V-genes have been annotated only within the genome of a few species. We have developed a bioinformatics tool that accelerates the task of identifying functional V-genes from genome datasets. Automated recogn...
Article
Full-text available
Background Germinal Centers (GC) are short-lived micro-anatomical structures, within lymphoid organs, where affinity maturation is initiated. Theoretical modeling of the dynamics of the GC reaction including follicular CD4+ T helper and the recently described follicular regulatory CD4+ T cell populations, predicts that the intensity and life span o...
Article
Problem: Pregnancy is a challenge to the maternal immune system as it allows the growing of a semiallogeneic fetus within the uterus. Such tolerance suggests a set of complex cellular distributions and interactions inside the organ. Until now, direct observation of such processes was absent because proper intravital imaging techniques were not ava...
Article
Full-text available
Malaria in pregnancy is exquisitely aggressive, causing a range of adverse maternal and fetal outcomes prominently linked to Plasmodium-infected erythrocyte cytoadherence to fetal trophoblast. To elucidate the physiopathology of infected erythrocytes (IE) sequestration in the placenta we devised an experimental system for intravital placental exami...
Data
Diagram of the experimental procedure. BALB/c females were mated to B6-Cyan for 48 hours. Pregnant mice were infected with P. berghei-ANKA GFP+ IE on G13. On day 5 post-infection, mouse was anesthetized, placenta was exposed and maternal blood fluid was labeled (when applicable) with an i.v. injection of Dextran-Rhodamine immediately before imaging...
Data
IE movement in high and low blood flow regions. Images were acquired during 1.6 min and show stationary parasites (black arrow) only in low blood flow regions. Arrowhead points to IE that traverses maternal adjacent blood spaces. Placental tissue (blue), GFP+IE (green), Dextran-Rhodamine labeled maternal blood (red), FC (fetal capillary). Scale bar...
Data
Parasitized erythrocytes in the popliteal lymph-node blood circulation. Non-pregnant BALB/c female was infected with P. berghei-ANKAGFP+ and imaged 1 week after infection. Arrows point to infected cells. Green: IE; red: blood fluid. Scale bar: 20 µm; images are at 5 frames/s (1.5 min acquisition). (AVI)
Data
Intermittent blood flow in maternal space of infected placenta. Sequential images (4.3 min) show GFP+IE alternating between stationary and progressive movement. Placental tissue (blue), GFP+IE (green); maternal blood spaces (black). Arrow indicates region of the referred events. Scale bar: 50 µm; images are at 5 frames/s. (AVI)
Data
Stationary infected cells in a “niche” (arrows) away from blood flow. Placental tissue (blue), GFP+IE (green). Scale bar: 20 µm; images are at 10 frames/s (4.5 min acquisition). (AVI)
Data
Stationary cells are target of phagocytosis. Sequential images show fetal-derived phagocyte (arrow) migrating towards an IE (arrowhead) and engulfing the infected cell. Blue: placental tissue; green: IE. Scale bar: 20 µm; images are at 10 frames/s (6 min acquisition). (AVI)
Data
Deposition of amorfous eosinophilic fibrinoid material in the lumina of maternal blood space (MBS) (A), often associated with necrotic cell debris (B) (arrows). Thrombus formation was also registered (C). H&E sagittal section of P.berghei-infected placentas at G18. FC: fetal capillary; IM: interheamal membrane. (DOCX)
Data
Trophoblast can occlude blood space lumen. Intravital imaging (9 min) of infected placenta show gradual occlusion (white arrow) and opening of blood space areas (black regions; green arrow); blue: placental tissue. Scale bar: 20 µm; images are at 10 frames/s. (AVI)
Data
Blood flow pattern of non-infected placenta. Intravital imaging (5 min) of the placental labyrinth at G18 shows heterogeneous blood flow rates. Blood fluid was labeled with Dextran-Rhodamine (red); black regions inside blood spaces are erythrocytes. Scale bar: 30 µm; images are at 5 frames/s. (AVI)
Data
P. berghei-infected cell shows progressive stationary behavior. Five-minute imaging show parasitized cell moving towards the trophoblast with apparent contact and progressively acquiring stationary behavior (arrow). Placental tissue (blue), GFP+IE (green). Scale bar: 20 µm; images are at 10 frames/s. (AVI)
Data
Transient contact of parasitized cell with placental tissue. Sequential images show IE caught in a fetal-derived placental cell for approx 80 s followed by a possible escape behavior (arrow). Placental tissue (blue), GFP+IE (green). Scale bar: 20 µm; images are at 5 frames/s (2 min acquisition). (AVI)
Data
Parasitized erythrocytes in the periphery. Non-pregnant BALB/c female was infected with P. berghei-ANKA and imaged 1 week after infection. Sequential images of blood circulation inside the popliteal lymph-node show IE (indicated by arrows) travelling at speed over 20 µm/s (velocity was calculated by Fiji imageJ manual tracking plug-in; data not sho...
Data
Distinct blood flow rates in the infected placenta. Intravital acquisition of P. berghei-infected mouse at G18 showing fetal-derived CFP+ placental tissue (blue), GFP+ IE (green) and Dextran-Rhodamine+ labelled blood fluid (red). Images were acquired during 3 min with a 20X objective. Scale bar: 100 µm; images are at 5 frames/s. (AVI)
Data
Maternal blood flow is conditioned by trophoblast. Magnified area of the infected placenta (600X) at G18 shows blood flow interruption by emergence of a trophoblast bridge (arrow). Images were acquired during 6 min. Placental tissue (blue), GFP+IE (green); blood spaces (black). Scale bar: 50 µm; images are at 5 frames/s. (AVI)
Data
IE migrate across blood spaces. Sequential images (7.2 min) show stationary IE (arrows) that trasverse the “Coan-Burton bridge” (C-BB) and migrate to the adjacent maternal space (MBS) remaining stationary in that site. Placental tissue (blue), GFP+IE (green). Scale bar: 20 µm; images are at 5 frames/s. (AVI)
Article
Historically, several in vitro/ex vivo microscopy imaging techniques have been used to study cellular interactions within the uterus and the placenta. As these experimental methods have revealed compelling facts about the biologic phenomena of cell-cell contacts in these organs, they cannot be used to study complex dynamic behavior of living cells...