David N. Olivieri

Making optical vortices with computer-generated holograms

An optical vortex is a screw dislocation in a light field that carries quantized orbital angular momentum and, due to cancellations of the twisting along the propagation axis, experiences zero intensity at its center. When viewed in a perpendicular plane along the propagation axis, the vortex appears as a dark region in the center surrounded by a bright concentric ring of light. We give detailed instructions for generating optical vortices and optical vortex structures by computer-generated holograms and describe various methods for manipulating the resulting structures.

Eigenspace-based fall detection and activity recognition from motion templates and machine learning

Automatic recognition of anomalous human activities and falls in an indoor setting from video sequences could be an enabling technology for low-cost, home-based health care systems. Detection systems based upon intelligent computer vision software can greatly reduce the costs and inconveniences associated with sensor based systems. In this paper, we propose such a software based upon a spatio-temporal motion representation, called Motion Vector Flow Instance (MVFI) templates, that capture relevant velocity information by extracting the dense optical flow from video sequences of human actions. Automatic recognition is achieved by first projecting each human action video sequence, consisting of approximately 100 images, into a canonical eigenspace, and then performing supervised learning to train multiple actions from a large video database. We show that our representation together with a canonical transformation with PCA and LDA of image sequences provides excellent action discrimination. We also demonstrate that by including both the magnitude and direction of the velocity into the MVFI, sequences with abrupt velocities, such as falls, can be distinguished from other daily human action with both high accuracy and computational efficiency. As an added benefit, we demonstrate that, once trained, our method for detecting falls is robust and we can attain real-time performance.

Intravital Placenta Imaging Reveals Microcirculatory Dynamics Impact on Sequestration and Phagocytosis of Plasmodium-Infected Erythrocytes

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 examination of P. berghei-infected mice. BALB/c females were mated to C57Bl/6 CFP+ male mice and infected with GFP+ P. berghei IE, and at gestational day 18, placentas were exposed for time-lapse imaging acquisition under two-photon microscopy. Real-time images and quantitative measurements revealed that trophoblast conformational changes transiently restrain blood flow in the mouse placental labyrinth. The complex dynamics of placental microcirculation promotes IE accumulation in maternal blood spaces with low blood flow and allows the establishment of stable IE-trophoblast contacts. Further, we show that the fate of sequestered IE includes engulfment by both macrophagic and trophoblastic fetal-derived cells. These findings reinforce the current paradigm that IE interact with the trophoblast and provide definitive evidence on two novel pathogenesis mechanisms: (1) trophoblast layer controls placental microcirculation promoting IE sequestration; and (2) fetal-derived placental cells engulf sequestered IE.

Detecting Sleep Apnea by Heart Rate Variability Analysis: Assessing the Validity of Databases and Algorithms

Obstructive sleep apnea (OSA) is a serious disorder caused by intermittent airway obstruction which may have dangerous impact on daily living activities. Heart rate variability (HRV) analysis could be used for diagnosing OSA, since this disease affects HRV during sleep. In order to validate different algorithms developed for detecting OSA employing HRV analysis, several public or proprietary data collections have been employed for different research groups. However, for validation purposes, it is obvious and evident the lack of a common standard database, worldwide recognized and accepted by the scientific community. In this paper, different algorithms employing HRV analysis were applied over diverse public and proprietary databases for detecting OSA, and the outcomes were validated in terms of a statistical analysis. Results indicate that the use of a specific database may strongly affect the performance of the algorithms, due to differences in methodologies of processing. Our results suggest that researchers must strongly take into consideration the database used when quoting their results, since selected cases are highly database dependent and would bias conclusions.

In vivo Multiphoton Microscopy Technique to Reveal the Physiology of the Mouse Placenta

Pregnancy is a challenge to the maternal immune system as it must defend the body against pathogens while at the same time develop immune tolerance against the fetus growing inside the uterus. Despite ex vivo techniques being used to understand these processes, in vivo techniques are missing.

An automated algorithm for extracting functional immunologic V-genes from genomes in jawed vertebrates

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 recognition is accomplished by recognizing key V-gene signatures, such as recombination signal sequences, size of the exon region, and position of amino acid motifs within the translated exon. This algorithm also classifies extracted V-genes into either TCR or Ig loci. We describe the implementation of the algorithm and validate its accuracy by comparing V-genes identified from the human and mouse genomes with known V-gene annotations documented and available in public repositories. The advantages and utility of the algorithm are illustrated by using it to identify functional V-genes in the rat genome, where V-gene annotation is still incomplete. This allowed us to perform a comparative human–rodent phylogenetic analysis based on V-genes that supports the hypothesis that distinct evolutionary pressures shape the TCRs and Igs V-gene repertoires. Our program, together with a user graphical interface, is available as open-source software, downloadable at http://code.google.com/p/vgenextract/.

Early skin immunological disturbance after Plasmodium-infected mosquito bites.

Although the role of regulatory T cells (Tregs) during malaria infection has been studied extensively, such studies have focused exclusively on the role of Treg during the blood stage of infection; little is known about the detailed mechanisms of Tregs and sporozoite deposition in the dermis by mosquito bites. In this paper we show that sporozoites introduced into the skin by mosquito bites increase the mobility of skin Tregs and dendritic cells (DCs). We also show differences in MHC class II and/or CD86 expression on skin-resident dendritic cell subtypes and macrophages. From the observed decrease of the number of APCs into draining lymph nodes, suppression of CD28 expression in conventional CD4 T cells, and a low homeostatic proliferation of skin-migrated CD4 T found in nude mice indicate that Tregs may play a fundamental role during the initial phase of malaria parasite inoculation into the mammalian host.

Genomic V exons from whole genome shotgun data in reptiles

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 genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository (http://vgenerepertoire.org).

Controllable scattering of vector Bose-Einstein solitons

We show the possibility of producing matter-wave switching devices by using Manakov interactions between vector matter-wave solitons using two-species Bose-Einstein condensates (BECs). Our results establish the experimental parameters for three interaction regimes in two-species BECs: symmetric and asymmetric splitting, down-switching, and up-switching. We have studied the dependence upon the initial conditions and the kind of interaction between the two matter-wave solitons.

A KPCA spatio-temporal differential geometric trajectory cloud classifier for recognizing human actions in a CBVR system

A CBVR based upon spatio-temporal trajectories of human motion.Trajectories encode two motion scales: large (hyperplanes); small (local differential geometry).New fuzzy KNN classifies trajectories with proximity, orientation and approximate membership.Validation of video retrieval system from standard datasets and feature length films. 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) system, where specific frames from a full length video (or separate video shots in a database) are identified containing a queried human action. In the DGTC method, the local geometry of the spatio-temporal covariant eigenspace curves, unique to each human action, are characterized by the Frenet-Serret basis equations, thereby specifying the local time averaged curvature and torsion, as well as providing a means for defining a mean osculating hyperplane for the entire trajectory. To classify a human action from a query, our system uses an adaptive distance metric between the covariant transformed query trajectory and each of the trajectories from all of the actions in the training set. Based upon the separation of between the query and each class, the distance uses either large or small scale information about the trajectory: for large separations, the distance is the separation between trajectory cloud centroids, while for small and intermediate separations the distance is based upon the mean hyperplane orientation obtained from the time averaged curvature and torsion of the trajectory. Our system can function in real-time and has an accuracy greater than 93% for multiple action recognition within video repositories. We also demonstrate the use of our CBVR system locating specific frame positions of trained actions in two full featured films.