Gain modulation and odor concentration invariance in early olfactory networks.

The broad receptive field of the olfactory receptors constitutes the basis of a combinatorial code that allows animals to detect and discriminate many more odorants than the actual number of receptor types that they express. One drawback is that high odor concentrations recruit lower affinity receptors which can lead to the perception of qualitatively different odors. Here we addressed the contribution that signal-processing in the antennal lobe makes to reduce concentration dependence in odor representation. By means of calcium imaging and pharmacological approach we describe the contribution that GABA receptors play in terms of the amplitude and temporal profiles of the signals that convey odor information from the antennal lobes to higher brain centers. We found that GABA reduces the amplitude of odor elicited signals and the number of glomeruli that are recruited in an odor-concentration-dependent manner. Blocking GABA receptors decreases the correlation among glomerular activity patterns elicited by different concentrations of the same odor. In addition, we built a realistic mathematical model of the antennal lobe that was used to test the viability of the proposed mechanisms and to evaluate the processing properties of the AL network under conditions that cannot be achieved in physiology experiments. Interestingly, even though based on a rather simple topology and cell interactions solely mediated by GABAergic lateral inhibitions, the AL model reproduced key features of the AL response upon different odor concentrations and provides plausible solutions for concentration invariant recognition of odors by artificial sensors.

Frequency-dependent regulation of intrinsic excitability by voltage-activated membrane conductances, computational modeling and dynamic clamp.

As one of the most unique properties of nerve cells, their intrinsic excitability allows them to transform synaptic inputs into action potentials. This process reflects a complex interplay between the synaptic inputs and the voltage-dependent membrane currents of the postsynaptic neuron. While neurons in natural conditions mostly fire under the action of intense synaptic bombardment and receive fluctuating patterns of excitation and inhibition, conventional techniques to characterize intrinsic excitability mainly utilize static means of stimulation. Recently, we have shown that voltage-gated membrane currents regulate the firing responses under current step stimulation and under physiologically more realistic inputs in a differential manner. At the same time, a multitude of neuron types have been shown to exhibit some form of subthreshold resonance that potentially allows them to respond to synaptic inputs in a frequency-selective manner. In this study, we performed virtual experiments in computational models of neurons to examine how specific voltage-gated currents regulate their excitability under simulated frequency-modulated synaptic inputs. The model simulations and subsequent dynamic clamp experiments on mouse hippocampal pyramidal neurons revealed that the impact of voltage-gated currents in regulating the firing output is strongly frequency-dependent and mostly affecting the synaptic integration at theta frequencies. Notably, robust frequency-dependent regulation of intrinsic excitability was observed even when conventional analysis of membrane impedance suggested no such tendency. Consequently, plastic or homeostatic regulation of intrinsic membrane properties can tune the frequency selectivity of neuron populations in a way that is not readily expected from subthreshold impedance measurements.

Task allocation and site fidelity jointly influence foraging regulation in honeybee colonies.

Variation in behaviour among group members often impacts collective outcomes. Individuals may vary both in the task that they perform and in the persistence with which they perform each task. Although both the distribution of individuals among tasks and differences among individuals in behavioural persistence can each impact collective behaviour, we do not know if and how they jointly affect collective outcomes. Here, we use a detailed computational model to examine the joint impact of colony-level distribution among tasks and behavioural persistence of individuals, specifically their fidelity to particular resource sites, on the collective trade-off between exploring for new resources and exploiting familiar ones. We developed an agent-based model of foraging honeybees, parametrized by data from five colonies, in which we simulated scouts, who search the environment for new resources, and individuals who are recruited by the scouts to the newly found resources, i.e. recruits. We varied the persistence of returning to a particular food source of both scouts and recruits and found that, for each value of persistence, there is a different optimal ratio of scouts to recruits that maximizes resource collection by the colony. Furthermore, changes to the persistence of scouts induced opposite effects from changes to the persistence of recruits on the collective foraging of the colony. The proportion of scouts that resulted in the most resources collected by the colony decreased as the persistence of recruits increased. However, this optimal proportion of scouts increased as the persistence of scouts increased. Thus, behavioural persistence and task participation can interact to impact a colony's collective behaviour in orthogonal directions. Our work provides new insights and generates new hypotheses into how variations in behaviour at both the individual and colony levels jointly impact the trade-off between exploring for new resources and exploiting familiar ones.

FBB: a fast Bayesian-bound tool to calibrate RNA-seq aligners.

MOTIVATION: Despite RNA-seq reads provide quality scores that represent the probability of calling a correct base, these values are not probabilistically integrated in most alignment algorithms. Based on the quality scores of the reads, we propose to calculate a lower bound of the probability of alignment of any fast alignment algorithm that generates SAM files. This bound is called Fast Bayesian Bound (FBB) and serves as a canonical reference to compare alignment results across different algorithms. This Bayesian Bound intends to provide additional support to the current state-of-the-art aligners, not to replace them. RESULTS: We propose a feasible Bayesian bound that uses quality scores of the reads to align them to a genome of reference. Two theorems are provided to efficiently calculate the Bayesian bound that under some conditions becomes the equality. The algorithm reads the SAM files generated by the alignment algorithms using multiple command option values. The program options are mapped into the FBB reference values, and all the aligners can be compared respect to the same accuracy values provided by the FBB. Stranded paired read RNA-seq data was used for evaluation purposes. The errors of the alignments can be calculated based on the information contained in the distance between the pairs given by Theorem 2, and the alignments to the incorrect strand. Most of the algorithms (Bowtie, Bowtie 2, SHRiMP2, Soap 2, Novoalign) provide similar results with subtle variations. AVAILABILITY AND IMPLEMENTATION: Current version of the FBB software is provided at https://bitbucket.org/irenerodriguez/fbb CONTACT: rhuerta@ucsd.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Chemical gas sensor array dataset.

To address drift in chemical sensing, an extensive dataset was collected over a period of three years. An array of 16 metal-oxide gas sensors was exposed to six different volatile organic compounds at different concentration levels under tightly-controlled operating conditions. Moreover, the generated dataset is suitable to tackle a variety of challenges in chemical sensing such as sensor drift, sensor failure or system calibration. The data is related to "Chemical gas sensor drift compensation using classifier ensembles", by Vergara et al. [1], and "On the calibration of sensor arrays for pattern recognition using the minimal number of experiments", by Rodriguez-Lujan et al. [2] The dataset can be accessed publicly at the UCI repository upon citation of: http://archive.ics.uci.edu/ml/datasets/Gas+Sensor+Array+Drift+Dataset+at+Different+Concentrations.

Dataset from chemical gas sensor array in turbulent wind tunnel.

The dataset includes the acquired time series of a chemical detection platform exposed to different gas conditions in a turbulent wind tunnel. The chemo-sensory elements were sampling directly the environment. In contrast to traditional approaches that include measurement chambers, open sampling systems are sensitive to dispersion mechanisms of gaseous chemical analytes, namely diffusion, turbulence, and advection, making the identification and monitoring of chemical substances more challenging. The sensing platform included 72 metal-oxide gas sensors that were positioned at 6 different locations of the wind tunnel. At each location, 10 distinct chemical gases were released in the wind tunnel, the sensors were evaluated at 5 different operating temperatures, and 3 different wind speeds were generated in the wind tunnel to induce different levels of turbulence. Moreover, each configuration was repeated 20 times, yielding a dataset of 18,000 measurements. The dataset was collected over a period of 16 months. The data is related to "On the performance of gas sensor arrays in open sampling systems using Inhibitory Support Vector Machines", by Vergara et al.[1]. The dataset can be accessed publicly at the UCI repository upon citation of [1]: http://archive.ics.uci.edu/ml/datasets/Gas+sensor+arrays+in+open+sampling+settings.

Data set from chemical sensor array exposed to turbulent gas mixtures.

A chemical detection platform composed of 8 chemo-resistive gas sensors was exposed to turbulent gas mixtures generated naturally in a wind tunnel. The acquired time series of the sensors are provided. The experimental setup was designed to test gas sensors in realistic environments. Traditionally, chemical detection systems based on chemo-resistive sensors include a gas chamber to control the sample air flow and minimize turbulence. Instead, we utilized a wind tunnel with two independent gas sources that generate two gas plumes. The plumes get naturally mixed along a turbulent flow and reproduce the gas concentration fluctuations observed in natural environments. Hence, the gas sensors can capture the spatio-temporal information contained in the gas plumes. The sensor array was exposed to binary mixtures of ethylene with either methane or carbon monoxide. Volatiles were released at four different rates to induce different concentration levels in the vicinity of the sensor array. Each configuration was repeated 6 times, for a total of 180 measurements. The data is related to "Chemical Discrimination in Turbulent Gas Mixtures with MOX Sensors Validated by Gas Chromatography-Mass Spectrometry", by Fonollosa et al. [1]. The dataset can be accessed publicly at the UCI repository upon citation of [1]: http://archive.ics.uci.edu/ml/datasets/Gas+senso+rarray+exposed+to+turbulent+gas+mixtures.

Multi-input distributed classifiers for synthetic genetic circuits.

For practical construction of complex synthetic genetic networks able to perform elaborate functions it is important to have a pool of relatively simple modules with different functionality which can be compounded together. To complement engineering of very different existing synthetic genetic devices such as switches, oscillators or logical gates, we propose and develop here a design of synthetic multi-input classifier based on a recently introduced distributed classifier concept. A heterogeneous population of cells acts as a single classifier, whose output is obtained by summarizing the outputs of individual cells. The learning ability is achieved by pruning the population, instead of tuning parameters of an individual cell. The present paper is focused on evaluating two possible schemes of multi-input gene classifier circuits. We demonstrate their suitability for implementing a multi-input distributed classifier capable of separating data which are inseparable for single-input classifiers, and characterize performance of the classifiers by analytical and numerical results. The simpler scheme implements a linear classifier in a single cell and is targeted at separable classification problems with simple class borders. A hard learning strategy is used to train a distributed classifier by removing from the population any cell answering incorrectly to at least one training example. The other scheme implements a circuit with a bell-shaped response in a single cell to allow potentially arbitrary shape of the classification border in the input space of a distributed classifier. Inseparable classification problems are addressed using soft learning strategy, characterized by probabilistic decision to keep or discard a cell at each training iteration. We expect that our classifier design contributes to the development of robust and predictable synthetic biosensors, which have the potential to affect applications in a lot of fields, including that of medicine and industry.

A Framework for Quantitative Modeling of Neural Circuits Involved in Sleep-to-Wake Transition.

Identifying the neuronal circuits and dynamics of sleep-to-wake transition is essential to understanding brain regulation of behavioral states, including sleep-wake cycles, arousal, and hyperarousal. Recent work by different laboratories has used optogenetics to determine the role of individual neuromodulators in state transitions. The optogenetically driven data do not yet provide a multi-dimensional schematic of the mechanisms underlying changes in vigilance states. This work presents a modeling framework to interpret, assist, and drive research on the sleep-regulatory network. We identify feedback, redundancy, and gating hierarchy as three fundamental aspects of this model. The presented model is expected to expand as additional data on the contribution of each transmitter to a vigilance state becomes available. Incorporation of conductance-based models of neuronal ensembles into this model and existing models of cortical excitability will provide more comprehensive insight into sleep dynamics as well as sleep and arousal-related disorders.

Learning modifies odor mixture processing to improve detection of relevant components.

Honey bees have a rich repertoire of olfactory learning behaviors, and they therefore are an excellent model to study plasticity in olfactory circuits. Recent behavioral, physiological, and molecular evidence suggested that the antennal lobe, the first relay of the olfactory system in insects and analog to the olfactory bulb in vertebrates, is involved in associative and nonassociative olfactory learning. Here we use calcium imaging to reveal how responses across antennal lobe projection neurons change after association of an input odor with appetitive reinforcement. After appetitive conditioning to 1-hexanol, the representation of an odor mixture containing 1-hexanol becomes more similar to this odor and less similar to the background odor acetophenone. We then apply computational modeling to investigate how changes in synaptic connectivity can account for the observed plasticity. Our study suggests that experience-dependent modulation of inhibitory interactions in the antennal lobe aids perception of salient odor components mixed with behaviorally irrelevant background odors.

Differential effects of static and dynamic inputs on neuronal excitability.

The intrinsic excitability of neurons is known to be dynamically regulated by activity-dependent plasticity and homeostatic mechanisms. Such processes are commonly analyzed in the context of input-output functions that describe how neurons fire in response to constant levels of current. However, it is not well understood how changes of excitability as observed under static inputs translate to the function of the same neurons in their natural synaptic environment. Here we performed a computational study and hybrid experiments on rat bed nucleus of stria terminalis neurons to compare the two scenarios. The inward rectifying Kir current (IKir) and the hyperpolarization-activated cation current (Ih) were found to be considerably more effective in regulating the firing under synaptic inputs than under static stimuli. This prediction was experimentally confirmed by dynamic-clamp insertion of a synthetic inwardly rectifying Kir current into the biological neurons. At the same time, ionic currents that activate with depolarization were more effective regulating the firing under static inputs. When two intrinsic currents are concurrently altered such as those under homeostatic regulation, the effects in firing responses under static vs. dynamic inputs can be even more contrasting. Our results show that plastic or homeostatic changes of intrinsic membrane currents can shape the current step responses of neurons and their firing under synaptic inputs in a differential manner.

Distributed classifier based on genetically engineered bacterial cell cultures.

We describe a conceptual design of a distributed classifier formed by a population of genetically engineered microbial cells. The central idea is to create a complex classifier from a population of weak or simple classifiers. We create a master population of cells with randomized synthetic biosensor circuits that have a broad range of sensitivities toward chemical signals of interest that form the input vectors subject to classification. The randomized sensitivities are achieved by constructing a library of synthetic gene circuits with randomized control sequences (e.g., ribosome-binding sites) in the front element. The training procedure consists in reshaping of the master population in such a way that it collectively responds to the "positive" patterns of input signals by producing above-threshold output (e.g., fluorescent signal), and below-threshold output in case of the "negative" patterns. The population reshaping is achieved by presenting sequential examples and pruning the population using either graded selection/counterselection or by fluorescence-activated cell sorting (FACS). We demonstrate the feasibility of experimental implementation of such system computationally using a realistic model of the synthetic sensing gene circuits.

Chemical discrimination in turbulent gas mixtures with MOX sensors validated by gas chromatography-mass spectrometry.

Chemical detection systems based on chemo-resistive sensors usually include a gas chamber to control the sample air flow and to minimize turbulence. However, such a kind of experimental setup does not reproduce the gas concentration fluctuations observed in natural environments and destroys the spatio-temporal information contained in gas plumes. Aiming at reproducing more realistic environments, we utilize a wind tunnel with two independent gas sources that get naturally mixed along a turbulent flow. For the first time, chemo-resistive gas sensors are exposed to dynamic gas mixtures generated with several concentration levels at the sources. Moreover, the ground truth of gas concentrations at the sensor location was estimated by means of gas chromatography-mass spectrometry. We used a support vector machine as a tool to show that chemo-resistive transduction can be utilized to reliably identify chemical components in dynamic turbulent mixtures, as long as sufficient gas concentration coverage is used. We show that in open sampling systems, training the classifiers only on high concentrations of gases produces less effective classification and that it is important to calibrate the classification method with data at low gas concentrations to achieve optimal performance.

Hypocretin (orexin) regulation of sleep-to-wake transitions.

The hypocretin (Hcrt), also known as orexin, peptides are essential for arousal stability. Here we discuss background information about the interaction of Hcrt with other neuromodulators, including norepinephrine and acetylcholine probed with optogenetics. We conclude that Hcrt neurons integrate metabolic, circadian and limbic inputs and convey this information to a network of neuromodulators, each of which has a different role on the dynamic of sleep-to-wake transitions. This model may prove useful to predict the effects of orexin receptor antagonists in sleep disorders and other conditions.

Estimation of the limit of detection using information theory measures.

Definitions of the limit of detection (LOD) based on the probability of false positive and/or false negative errors have been proposed over the past years. Although such definitions are straightforward and valid for any kind of analytical system, proposed methodologies to estimate the LOD are usually simplified to signals with Gaussian noise. Additionally, there is a general misconception that two systems with the same LOD provide the same amount of information on the source regardless of the prior probability of presenting a blank/analyte sample. Based upon an analogy between an analytical system and a binary communication channel, in this paper we show that the amount of information that can be extracted from an analytical system depends on the probability of presenting the two different possible states. We propose a new definition of LOD utilizing information theory tools that deals with noise of any kind and allows the introduction of prior knowledge easily. Unlike most traditional LOD estimation approaches, the proposed definition is based on the amount of information that the chemical instrumentation system provides on the chemical information source. Our findings indicate that the benchmark of analytical systems based on the ability to provide information about the presence/absence of the analyte (our proposed approach) is a more general and proper framework, while converging to the usual values when dealing with Gaussian noise.

Computational models to understand decision making and pattern recognition in the insect brain.

Odor stimuli reaching olfactory systems of mammals and insects are characterized by remarkable non-stationary and noisy time series. Their brains have evolved to discriminate subtle changes in odor mixtures and find meaningful variations in complex spatio-temporal patterns. Insects with small brains can effectively solve two computational tasks: identify the presence of an odor type and estimate the concentration levels of the odor. Understanding the learning and decision making processes in the insect brain can not only help us to uncover general principles of information processing in the brain, but it can also provide key insights to artificial chemical sensing. Both olfactory learning and memory are dominantly organized in the Antennal Lobe (AL) and the Mushroom Bodies (MBs). Current computational models yet fail to deliver an integrated picture of the joint computational roles of the AL and MBs. This review intends to provide an integrative overview of the computational literature analyzed in the context of the problem of classification (odor discrimination) and regression (odor concentration estimation), particularly identifying key computational ingredients necessary to solve pattern recognition.

Control of sleep-to-wake transitions via fast aminoacid and slow neuropeptide transmission.

The Locus Coeruleus (LC) modulates cortical, subcortical, cerebellar, brainstem and spinal cord circuits and it expresses receptors for neuromodulators that operate in a time scale of several seconds. Evidences from anatomical, electrophysiological and optogenetic experiments have shown that LC neurons receive input from a group of neurons called Hypocretins (HCRTs) that release a neuropeptide called hypocretin. It is less known how these two groups of neurons can be coregulated using GABAergic neurons. Since the time scales of GABA A inhibition is several orders of magnitude faster than the hypocretin neuropeptide effect, we investigate the limits of circuit activity regulation using a realistic model of neurons. Our investigation shows that GABA A inhibition is insufficient to control the activity levels of the LCs. Despite slower forms of GABA A can in principle work, there is not much plausibility due to the low probability of the presence of slow GABA A and lack of robust stability at the maximum firing frequencies. The best possible control mechanism predicted by our modeling analysis is the presence of inhibitory neuropeptides that exert effects in a similar time scale as the hypocretin/orexin. Although the nature of these inhibitory neuropeptides has not been identified yet, it provides the most efficient mechanism in the modeling analysis. Finally, we present a reduced mean-field model that perfectly captures the dynamics and the phenomena generated by this circuit. This investigation shows that brain communication involving multiple time scales can be better controlled by employing orthogonal mechanisms of neural transmission to decrease interference between cognitive processes and hypothalamic functions.

Apis mellifera octopamine receptor 1 (AmOA1) expression in antennal lobe networks of the honey bee (Apis mellifera) and fruit fly (Drosophila melanogaster).

Octopamine (OA) underlies reinforcement during appetitive conditioning in the honey bee and fruit fly, acting via different subtypes of receptors. Recently, antibodies raised against a peptide sequence of one honey bee OA receptor, AmOA1, were used to study the distribution of these receptors in the honey bee brain (Sinakevitch et al., 2011). These antibodies also recognize an isoform of the AmOA1 ortholog in the fruit fly (OAMB, mushroom body OA receptor). Here we describe in detail the distribution of AmOA1 receptors in different types of neurons in the honey bee and fruit fly antennal lobes. We integrate this information into a detailed anatomical analysis of olfactory receptor neurons (ORNs), uni- and multi-glomerular projection neurons (uPNs, and mPNs) and local interneurons (LNs) in glomeruli of the antennal lobe. These neurons were revealed by dye injection into the antennal nerve, antennal lobe, medial and lateral antenno-protocerbral tracts (m-APT and l-APT), and lateral protocerebral lobe (LPL) by use of labeled cell lines in the fruit fly or by staining with anti-GABA. We found that ORN receptor terminals and uPNs largely do not show immunostaining for AmOA1. About seventeen GABAergic mPNs leave the antennal lobe through the ml-APT and branch into the LPL. Many, but not all, mPNs show staining for AmOA1. AmOA1 receptors are also in glomeruli on GABAergic processes associated with LNs. The data suggest that in both species one important action of OA in the antennal lobe involves modulation of different types of inhibitory neurons via AmOA1 receptors. We integrated this new information into a model of circuitry within glomeruli of the antennal lobes of these species.

Gain control network conditions in early sensory coding.

Gain control is essential for the proper function of any sensory system. However, the precise mechanisms for achieving effective gain control in the brain are unknown. Based on our understanding of the existence and strength of connections in the insect olfactory system, we analyze the conditions that lead to controlled gain in a randomly connected network of excitatory and inhibitory neurons. We consider two scenarios for the variation of input into the system. In the first case, the intensity of the sensory input controls the input currents to a fixed proportion of neurons of the excitatory and inhibitory populations. In the second case, increasing intensity of the sensory stimulus will both, recruit an increasing number of neurons that receive input and change the input current that they receive. Using a mean field approximation for the network activity we derive relationships between the parameters of the network that ensure that the overall level of activity of the excitatory population remains unchanged for increasing intensity of the external stimulation. We find that, first, the main parameters that regulate network gain are the probabilities of connections from the inhibitory population to the excitatory population and of the connections within the inhibitory population. Second, we show that strict gain control is not achievable in a random network in the second case, when the input recruits an increasing number of neurons. Finally, we confirm that the gain control conditions derived from the mean field approximation are valid in simulations of firing rate models and Hodgkin-Huxley conductance based models.

Two-dimensional wavelet transform feature extraction for porous silicon chemical sensors.

Designing reliable, fast responding, highly sensitive, and low-power consuming chemo-sensory systems has long been a major goal in chemo-sensing. This goal, however, presents a difficult challenge because having a set of chemo-sensory detectors exhibiting all these aforementioned ideal conditions are still largely un-realizable to-date. This paper presents a unique perspective on capturing more in-depth insights into the physicochemical interactions of two distinct, selectively chemically modified porous silicon (pSi) film-based optical gas sensors by implementing an innovative, based on signal processing methodology, namely the two-dimensional discrete wavelet transform. Specifically, the method consists of using the two-dimensional discrete wavelet transform as a feature extraction method to capture the non-stationary behavior from the bi-dimensional pSi rugate sensor response. Utilizing a comprehensive set of measurements collected from each of the aforementioned optically based chemical sensors, we evaluate the significance of our approach on a complex, six-dimensional chemical analyte discrimination/quantification task problem. Due to the bi-dimensional aspects naturally governing the optical sensor response to chemical analytes, our findings provide evidence that the proposed feature extractor strategy may be a valuable tool to deepen our understanding of the performance of optically based chemical sensors as well as an important step toward attaining their implementation in more realistic chemo-sensing applications.