Sparse Representations of Multiple Signals

We discuss the problem of finding sparse representations of a class of signals. We formalize the problem and prove it is NP-complete both in the case of a single signal and that of multiple ones. Next we develop a simple approximation method to the problem and we show experimental results using artificially generated signals. Furthermore,we use our approximation method to find sparse representations of classes of real signals, specifically of images of pedestrians. We discuss the relation between our formulation of the sparsity problem and the problem of finding representations of objects that are compact and appropriate for detection and classification.

The multiple signals assessed by female satin bowerbirds: could they be used to narrow down females' choices of mates?

Female choice based on multiple male traits has been documented in many species but the functions of such multiple traits are still under debate. The satin bowerbird has a polygynous mating system in which males attract females to bowers for mating; females choose mates based on multiple aspects of males and their bowers. In this paper, we demonstrate that females use some cues to decide which males to examine closely and other cues to decide which males to mate with. Female visitation rates to bowers were significantly related to male size and the males' 'solitary' display rates, and, to a lesser extent, to the numbers of bower decorations. After controlling for female visitation rates, it was found that a male's mating success was significantly related to his size and the rate at which he 'painted' his bower with saliva and chewed up plant material.

Independent sources of condition dependency and multiple pathways determine a composite trait: lessons from carotenoid-based plumage colouration.

Many colour ornaments are composite traits consisting of at least four components, which themselves may be more complex, determined by independent evolutionary pathways, and potentially being under different environmental control. To date, little evidence exists that several different components of colour elaboration are condition dependent and no direct evidence exists that different ornamental components are affected by different sources of variation. For example, in carotenoid-based plumage colouration, one of the best-known condition-dependent ornaments, colour elaboration stems from both condition-dependent pigment concentration and structural components. Some environmental flexibility of these components has been suggested, but specifically which and how they are affected remains unknown. Here, we tested whether multiple colour components may be condition dependent, by using a comprehensive 3 × 2 experimental design, in which we carotenoid supplemented and immune challenged great tit nestlings (Parus major) and quantified effects on different components of colouration. Plumage colouration was affected by an interaction between carotenoid availability and immune challenge. Path analyses showed that carotenoid supplementation increased plumage saturation via feather carotenoid concentration and via mechanisms unrelated to carotenoid deposition, while immune challenge affected feather length, but not carotenoid concentration. Thus, independent condition-dependent pathways, affected by different sources of variation, determine colour elaboration. This provides opportunities for the evolution of multiple signals within components of ornamental traits. This finding indicates that the selective forces shaping the evolution of different components of a composite trait and the trait's signal content may be more complex than believed so far, and that holistic approaches are required for drawing comprehensive evolutionary conclusions.

Integration of multiple instructive cues by neural crest stem cells reveals cell-intrinsic biases in relative growth factor responsiveness

Growth factors can influence lineage determination of neural crest stem cells (NCSCs) in an instructive manner, in vitro. Because NCSCs are likely exposed to multiple signals in vivo, these findings raise the question of how stem cells would integrate such combined influences. Bone morphogenetic protein 2 (BMP2) promotes neuronal differentiation and glial growth factor 2 (GGF2) promotes glial differentiation; if NCSCs are exposed to saturating concentrations of both factors, BMP2 appears dominant. By contrast, if the cells are exposed to saturating concentrations of both BMP2 and transforming growth factor β1 (which promotes smooth muscle differentiation), the two factors appear codominant. Sequential addition experiments indicate that NCSCs require 48–96 hrs in GGF2 before they commit to a glial fate, whereas the cells commit to a smooth muscle fate within 24 hr in transforming growth factor β1. The delayed response to GGF2 does not reflect a lack of functional receptors; however, because the growth factor induces rapid mitogen-activated protein kinase phosphorylation in naive cells. Furthermore, GGF2 can attenuate induction of the neurogenic transcription factor mammalian achaete-scute homolog 1, by low doses of BMP2. This short-term antineurogenic influence of GGF2 is not sufficient for glial lineage commitment, however. These data imply that NCSCs exhibit cell-intrinsic biases in the timing and relative dosage sensitivity of their responses to instructive factors that influence the outcome of lineage decisions in the presence of multiple factors. The relative delay in glial lineage commitment, moreover, apparently reflects successive short-term and longer-term actions of GGF2. Such a delay may help to explain why glia normally differentiate after neurons, in vivo.

Neutrophil Chemotaxis in Multiple Chemoattractant Gradients

Chemotaxis, the phenomenon in which cells move in response to extracellular chemical gradients, plays a prominent role in the mammalian immune response. During this process, a number of chemical signals, called chemoattractants, are produced at or proximal to sites of infection and diffuse into the surrounding tissue. Immune cells sense these chemoattractants and move in the direction where their concentration is greatest, thereby locating the source of attractants and their associated targets. Leading the assault against new infections is a specialized class of leukocytes (white blood cells) known as neutrophils, which normally circulate in the bloodstream. Upon activation, these cells emigrate out of the vasculature and navigate through interstitial tissues toward target sites. There they phagocytose bacteria and release a number of proteases and reactive oxygen intermediates with antimicrobial activity. Neutrophils recruited by infected tissue in vivo are likely confronted by complex chemical environments consisting of a number of different chemoattractant species. These signals may include end target chemicals produced in the vicinity of the infectious agents, and endogenous chemicals released by local host tissues during the inflammatory response. To successfully locate their pathogenic targets within these chemically diverse and heterogeneous settings, activated neutrophils must be capable of distinguishing between the different signals and employing some sort of logic to prioritize among them. This ability to simultaneously process and interpret mulitple signals is thought to be essential for efficient navigation of the cells to target areas. In particular, aberrant cell signaling and defects in this functionality are known to contribute to medical conditions such as chronic inflammation, asthma and rheumatoid arthritis. To elucidate the biomolecular mechanisms underlying the neutrophil response to different chemoattractants, a number of efforts have been made toward understanding how cells respond to different combinations of chemicals. Most notably, recent investigations have shown that in the presence of both end target and endogenous chemoattractant variants, the cells migrate preferentially toward the former type, even in very low relative concentrations of the latter. Interestingly, however, when the cells are exposed to two different endogenous chemical species, they exhibit a combinatorial response in which distant sources are favored over proximal sources. Some additional results also suggest that cells located between two endogenous chemoattractant sources will respond to the vectorial sum of the combined gradients. In the long run, this peculiar behavior could result in oscillatory cell trajectories between the two sources. To further explore the significance of these and other observations, particularly in the context of physiological conditions, we introduce in this work a simplified phenomenological model of neutrophil chemotaxis. In particular, this model incorporates a trait commonly known as directional persistence - the tendency for migrating neutrophils to continue moving in the same direction (much like momentum) - while also accounting for the dose-response characteristics of cells to different chemical species. Simulations based on this model suggest that the efficiency of cell migration in complex chemical environments depends significantly on the degree of directional persistence. In particular, with appropriate values for this parameter, cells can improve their odds of locating end targets by drifting through a network of attractant sources in a loosely-guided fashion. This corroborates the prediction that neutrophils randomly migrate from one chemoattractant source to the next while searching for their end targets. These cells may thus use persistence as a general mechanism to avoid being trapped near sources of endogenous chemoattractants - the mathematical analogue of local maxima in a global optimization problem. Moreover, this general foraging strategy may apply to other biological processes involving multiple signals and long-range navigation.

Optical demultiplexer device operating in the visible spectrum

In this paper, we present results on the use of multilayered a-SiC:H heterostructures as a device for wavelength-division demultiplexing of optical signals. These devices are useful in optical communications applications that use the wavelength division multiplexing technique to encode multiple signals into the same transmission medium. The device is composed of two stacked p-i-n photodiodes, both optimized for the selective collection of photo generated carriers. Band gap engineering was used to adjust the photogeneration and recombination rate profiles of the intrinsic absorber regions of each photodiode to short and long wavelength absorption in the visible spectrum. The photocurrent signal using different input optical channels was analyzed at reverse and forward bias and under steady state illumination. A demux algorithm based on the voltage controlled sensitivity of the device was proposed and tested. An electrical model of the WDM device is presented and supported by the solution of the respective circuit equations.

Measurement of Photo Capacitance in Amorphous Silicon Photodiodes

This paper discusses the photodiode capacitance dependence on imposed light and applied voltage using different devices. The first device is a double amorphous silicon pin-pin photodiode; the second one a crystalline pin diode and the last one a single pin amorphous silicon diode. Double amorphous silicon diodes can be used as (de)multiplexer devices for optical communications. For short range applications, using plastic optical fibres, the WDM (wavelength-division multiplexing) technique can be used in the visible light range to encode multiple signals. Experimental results consist on measurements of the photodiode capacitance under different conditions of imposed light and applied voltage. The relation between the capacitive effects of the double diode and the quality of the semiconductor internal junction will be analysed. The dynamics of charge accumulations will be measured when the photodiode is illuminated by a pulsed monochromatic light.

Capacitive effects in pinpin photodiodes

The application of a-SiC:H/a-Si:H pinpin photodiodes for optoelectronic applications as a WDM demultiplexer device has been demonstrated useful in optical communications that use the WDM technique to encode multiple signals in the visible light range. This is required in short range optical communication applications, where for costs reasons the link is provided by Plastic Optical Fibers. Characterization of these devices has shown the presence of large photocapacitive effects. By superimposing background illumination to the pulsed channel the device behaves as a filter, producing signal attenuation, or as an amplifier, producing signal gain, depending on the channel/background wavelength combination. We present here results, obtained by numerical simulations, about the internal electric configuration of a-SiC:H/a-Si:H pinpin photodiode. These results address the explanation of the device functioning in the frequency domain to a wavelength tunable photo-capacitance due to the accumulation of space charge localized at the bottom diode that, according to the Shockley-Read-Hall model, it is mainly due to defect trapping. Experimental result about measurement of the photodiode capacitance under different conditions of illumination and applied bias will be also presented. The combination of these analyses permits the description of a wavelength controlled photo-capacitance that combined with the series and parallel resistance of the diodes may result in the explicit definition of cut off frequencies for frequency capacitive filters activated by the light background or an oscillatory resonance of photogenerated carriers between the two diodes. (C) 2013 Elsevier B.V. All rights reserved.

Long-range heterogeneity at the 3' ends of human mRNAs.

The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In the work presented here, we have focused on mapping mRNA 3' ends onto the genome by use of the raw data generated by the expressed sequence tag (EST) sequencing projects. We find that at least half of the human genes encode multiple transcripts whose polyadenylation is driven by multiple signals. The corresponding transcript 3' ends are spread over distances in the kilobase range. This finding has profound implications for our understanding of gene expression regulation and of the diversity of human transcripts, for the design of cDNA microarray probes, and for the interpretation of gene expression profiling experiments.

Adaptive tracking of EEG oscillations.

Neuronal oscillations are an important aspect of EEG recordings. These oscillations are supposed to be involved in several cognitive mechanisms. For instance, oscillatory activity is considered a key component for the top-down control of perception. However, measuring this activity and its influence requires precise extraction of frequency components. This processing is not straightforward. Particularly, difficulties with extracting oscillations arise due to their time-varying characteristics. Moreover, when phase information is needed, it is of the utmost importance to extract narrow-band signals. This paper presents a novel method using adaptive filters for tracking and extracting these time-varying oscillations. This scheme is designed to maximize the oscillatory behavior at the output of the adaptive filter. It is then capable of tracking an oscillation and describing its temporal evolution even during low amplitude time segments. Moreover, this method can be extended in order to track several oscillations simultaneously and to use multiple signals. These two extensions are particularly relevant in the framework of EEG data processing, where oscillations are active at the same time in different frequency bands and signals are recorded with multiple sensors. The presented tracking scheme is first tested with synthetic signals in order to highlight its capabilities. Then it is applied to data recorded during a visual shape discrimination experiment for assessing its usefulness during EEG processing and in detecting functionally relevant changes. This method is an interesting additional processing step for providing alternative information compared to classical time-frequency analyses and for improving the detection and analysis of cross-frequency couplings.

Traffic Signal Inventory Project, 2001

The Center for Transportation Research and Education performed a traffic signal inventory study for the Iowa Department of Transportation. The purpose of this study was to determine the level of compliance with the Manual on Uniform Traffic Control Devices (MUTCD) and other industry standards of traffic signals on the state highway system. Signals were randomly selected throughout the State of Iowa. Only signals in cities with a population less than 5,000 were considered. Several intersections need to be addressed immediately to correct clearance timing settings. Red clearance intervals were frequently too short. A handful of intersections had inadequate pedestrian clearance times. Six intersections had at least one yellow clearance interval that did not meet Institute of Transportation Engineers standards. Some of the intersections likely would not meet traffic signal warrants and should be investigated for possible removal. The most common problem found with traffic signals was a lack of maintenance. Many of the signals had at least one of the following problems: burned out lights (signals and/or pedestrian heads), pedestrian lenses in need of replacement, dirty cabinet/missing or poor filter, missing visors, or inoperative pedestrian push buttons. Timing sheets were frequently missing or out of date. Another frequent noncompliance issue was the use of backplates. The MUTCD states that backplates should be used on signals viewed against a bright sky. The majority of signals inventoried did not have backplates on the mast-arm mounted signals. The timing at some intersections could likely be improved by reducing the cycle length. Where there were multiple signals in close proximity rarely was there any attempt at signal coordination. Finally, a number of intersections had equipment that by today’s standards would be considered obsolete.

Dynamic single cell measurements of kinase activity by synthetic kinase activity relocation sensors.

BACKGROUND: Mitogen activated protein kinases (MAPK) play an essential role in integrating extra-cellular signals and intra-cellular cues to allow cells to grow, adapt to stresses, or undergo apoptosis. Budding yeast serves as a powerful system to understand the fundamental regulatory mechanisms that allow these pathways to combine multiple signals and deliver an appropriate response. To fully comprehend the variability and dynamics of these signaling cascades, dynamic and quantitative single cell measurements are required. Microscopy is an ideal technique to obtain these data; however, novel assays have to be developed to measure the activity of these cascades. RESULTS: We have generated fluorescent biosensors that allow the real-time measurement of kinase activity at the single cell level. Here, synthetic MAPK substrates were engineered to undergo nuclear-to-cytoplasmic relocation upon phosphorylation of a nuclear localization sequence. Combination of fluorescence microscopy and automated image analysis allows the quantification of the dynamics of kinase activity in hundreds of single cells. A large heterogeneity in the dynamics of MAPK activity between individual cells was measured. The variability in the mating pathway can be accounted for by differences in cell cycle stage, while, in the cell wall integrity pathway, the response to cell wall stress is independent of cell cycle stage. CONCLUSIONS: These synthetic kinase activity relocation sensors allow the quantification of kinase activity in live single cells. The modularity of the architecture of these reporters will allow their application in many other signaling cascades. These measurements will allow to uncover new dynamic behaviour that previously could not be observed in population level measurements.

Attractive silences in cricket courtship song : mate choice using a short-range signal /

Matings systems using signals for sexual communication have been studied extensively and results commonly suggest that females use these signals for locating males, species-identification, and mate choice. Although numerous mating systems employ multiple signals, research has generally focused on long-range signals perhaps due to their prominence and ease of study. This study focused on the short-range acoustic courtship song of crickets. The results presented here suggest this signal is under selection by female choice. Females mated preferentially with males having shorter silences between the two types of ticks within the song. The length of these silences (Gap 1) was correlated with male condition such that males having long silences were significantly lower in mass with respect to body size when compared to males having short silences. Both Gap 1 length and male condition were significantly repeatable within males over time suggesting the possibility these traits have a genetic basis. This study is the first empirical study to test female preferences within the natural variation of the courtship song. It now appears, at least in crickets, that both the longand short-range signals of a multi-signal mating system may contribute to male mating success.

Impact de l'haploinsuffisance du gène Sim1 sur le développement et la fonction du noyau paraventriculaire de l'hypothalamus

L’obésité provient d’un déséquilibre de l’homéostasie énergétique, c’est-à-dire une augmentation des apports caloriques et/ou une diminution des dépenses énergétiques. Plusieurs données, autant anatomiques que physiologiques, démontrent que l’hypothalamus est un régulateur critique de l’appétit et des dépenses énergétiques. En particulier, le noyau paraventriculaire (noyau PV) de l’hypothalamus intègre plusieurs signaux provenant du système nerveux central (SNC) et/ou de la périphérie, afin de contrôler l’homéostasie énergétique via des projections axonales sur les neurones pré-ganglionnaires du système autonome situé dans le troc cérébral et la moelle épinière. Plusieurs facteurs de transcription, impliqués dans le développement du noyau PV, ont été identifiés. Le facteur de transcription SIM1, qui est produit par virtuellement tous les neurones du noyau PV, est requis pour le développement du noyau PV. En effet, lors d’une étude antérieure, nous avons montré que le noyau PV ne se développe pas chez les souris homozygotes pour un allèle nul de Sim1. Ces souris meurent à la naissance, probablement à cause des anomalies du noyau PV. Par contre, les souris hétérozygotes survivent, mais développent une obésité précoce. De façon intéressante, le noyau PV des souris Sim1+/- est hypodéveloppé, contenant 24% moins de cellules. Ces données suggèrent fortement que ces anomalies du développement pourraient perturber le fonctionnement du noyau PV et contribuer au développement du phénotype d’obésité. Dans ce contexte, nous avons entrepris des travaux expérimentaux ayant pour but d’étudier l’impact de l’haploinsuffisance de Sim1 sur : 1) le développement du noyau PV et de ses projections neuronales efférentes; 2) l’homéostasie énergétique; et 3) les voies neuronales physiologiques contrôlant l’homéostasie énergétique chez les souris Sim1+/-. A cette fin, nous avons utilisé : 1) des injections stéréotaxiques combinées à des techniques d’immunohistochimie afin de déterminer l’impact de l’haploinsuffisance de Sim1 sur le développement du noyau PV et de ses projections neuronales efférentes; 2) le paradigme des apports caloriques pairés, afin de déterminer l’impact de l’haploinsuffisance de Sim1 sur l’homéostasie énergétique; et 3) une approche pharmacologique, c’est-à-dire l’administration intra- cérébroventriculaire (i.c.v.) et/ou intra-péritonéale (i.p.) de peptides anorexigènes, la mélanotane II (MTII), la leptine et la cholécystokinine (CCK), afin de déterminer l’impact de l’haploinsuffisance de Sim1 sur les voies neuronales contrôlant l’homéostasie énergétique. Dans un premier temps, nous avons constaté une diminution de 61% et de 65% de l’expression de l’ARN messager (ARNm) de l’ocytocine (Ot) et de l’arginine-vasopressine (Vp), respectivement, chez les embryons Sim1+/- de 18.5 jours (E18.5). De plus, le nombre de cellules produisant l’OT et la VP est apparu diminué de 84% et 41%, respectivement, chez les souris Sim1+/- adultes. L’analyse du marquage axonal rétrograde des efférences du noyau PV vers le tronc cérébral, en particulier ses projections sur le noyau tractus solitaire (NTS) aussi que le noyau dorsal moteur du nerf vague (X) (DMV), a permis de démontrer une diminution de 74% de ces efférences. Cependant, la composition moléculaire de ces projections neuronales reste inconnue. Nos résultats indiquent que l’haploinsuffisance de Sim1 : i) perturbe spécifiquement le développement des cellules produisant l’OT et la VP; et ii) abolit le développement d’une portion importante des projections du noyau PV sur le tronc cérébral, et notamment ses projections sur le NTS et le DMV. Ces observations soulèvent donc la possibilité que ces anomalies du développement du noyau PV contribuent au phénotype d’hyperphagie des souris Sim1+/-. En second lieu, nous avons observé que la croissance pondérale des souris Sim1+/- et des souris Sim1+/+ n’était pas significativement différente lorsque la quantité de calories présentée aux souris Sim1+/- était la même que celle consommée par les souris Sim1+/+. De plus, l’analyse qualitative et quantitative des tissus adipeux blancs et des tissus adipeux bruns n’a démontré aucune différence significative en ce qui a trait à la taille et à la masse de ces tissus chez les deux groupes. Finalement, au terme de ces expériences, les souris Sim1+/--pairées n’étaient pas différentes des souris Sim1+/+ en ce qui a trait à leur insulinémie et leur contenu en triglycérides du foie et des masses adipeuses, alors que tous ces paramètres étaient augmentés chez les souris Sim1+/- nourries ad libitum. Ces résultats laissent croire que l’hyperphagie, et non une diminution des dépenses énergétiques, est la cause principale de l’obésité des souris Sim1+/-. Par conséquent, ces résultats suggèrent que : i) l’haploinsuffisance de Sim1 est associée à une augmentation de l’apport calorique sans toutefois moduler les dépenses énergétiques; ii) l’existence d’au moins deux voies neuronales issues du noyau PV : l’une qui régule la prise alimentaire et l’autre la thermogénèse; et iii) l’haploinsuffisance de Sim1 affecte spécifiquement la voie neuronale qui régule la prise alimentaire. En dernier lieu, nous avons montré que l’injection de MTII, de leptine ainsi que de CCK induit une diminution significative de la consommation calorique des souris des deux génotypes, Sim1+/+ et Sim1+/-. De fait, la consommation calorique cumulative des souris Sim1+/- et Sim1+/+ est diminuée de 37% et de 51%, respectivement, durant les 4 heures suivant l’administration i.p. de MTII comparativement à l’administration d’une solution saline. Lors de l’administration i.c.v. de la leptine, la consommation calorique cumulative des souris Sim1+/- et Sim1+/+ est diminuée de 47% et de 32%, respectivement. Finalement, l’injection i.p. de CCK diminue la consommation calorique des souris Sim1+/- et Sim1+/+ de 52% et de 36%, respectivement. L’ensemble des résultats suggère ici que l’haploinsuffisance de Sim1 diminue l’activité de certaines voies neuronales régulant l’homéostasie énergétique, et particulièrement de celles qui contrôlent la prise alimentaire. En résumé, ces travaux ont montré que l’haploinsuffisance de Sim1 affecte plusieurs processus du développement au sein du noyau PV. Ces anomalies du développement peuvent conduire à des dysfonctions de certains processus physiologiques distincts régulés par le noyau PV, et notamment de la prise alimentaire, et contribuer ainsi au phénotype d’obésité. Les souris hétérozygotes pour le gène Sim1 représentent donc un modèle animal unique, où l’hyperphagie, et non les dépenses énergétiques, est la principale cause de l’obésité. En conséquence, ces souris pourraient représenter un modèle expérimental intéressant pour l’étude des mécanismes cellulaires et moléculaires en contrôle de la prise alimentaire.

Modeling chemotaxis reveals the role of reversed phosphotransfer and a bi-functional kinase-phosphatase

Understanding how multiple signals are integrated in living cells to produce a balanced response is a major challenge in biology. Two-component signal transduction pathways, such as bacterial chemotaxis, comprise histidine protein kinases (HPKs) and response regulators (RRs). These are used to sense and respond to changes in the environment. Rhodobacter sphaeroides has a complex chemosensory network with two signaling clusters, each containing a HPK, CheA. Here we demonstrate, using a mathematical model, how the outputs of the two signaling clusters may be integrated. We use our mathematical model supported by experimental data to predict that: (1) the main RR controlling flagellar rotation, CheY6, aided by its specific phosphatase, the bifunctional kinase CheA3, acts as a phosphate sink for the other RRs; and (2) a phosphorelay pathway involving CheB2 connects the cytoplasmic cluster kinase CheA3 with the polar localised kinase CheA2, and allows CheA3-P to phosphorylate non-cognate chemotaxis RRs. These two mechanisms enable the bifunctional kinase/phosphatase activity of CheA3 to integrate and tune the sensory output of each signaling cluster to produce a balanced response. The signal integration mechanisms identified here may be widely used by other bacteria, since like R. sphaeroides, over 50% of chemotactic bacteria have multiple cheA homologues and need to integrate signals from different sources.