The impact of measurement errors in the identification of regulatory networks

Background: There are several studies in the literature depicting measurement error in gene expression data and also, several others about regulatory network models. However, only a little fraction describes a combination of measurement error in mathematical regulatory networks and shows how to identify these networks under different rates of noise. Results: This article investigates the effects of measurement error on the estimation of the parameters in regulatory networks. Simulation studies indicate that, in both time series (dependent) and non-time series (independent) data, the measurement error strongly affects the estimated parameters of the regulatory network models, biasing them as predicted by the theory. Moreover, when testing the parameters of the regulatory network models, p-values computed by ignoring the measurement error are not reliable, since the rate of false positives are not controlled under the null hypothesis. In order to overcome these problems, we present an improved version of the Ordinary Least Square estimator in independent (regression models) and dependent (autoregressive models) data when the variables are subject to noises. Moreover, measurement error estimation procedures for microarrays are also described. Simulation results also show that both corrected methods perform better than the standard ones (i.e., ignoring measurement error). The proposed methodologies are illustrated using microarray data from lung cancer patients and mouse liver time series data. Conclusions: Measurement error dangerously affects the identification of regulatory network models, thus, they must be reduced or taken into account in order to avoid erroneous conclusions. This could be one of the reasons for high biological false positive rates identified in actual regulatory network models.

Offline Detection, Identification, and Correction of Branch Parameter Errors Based on Several Measurement Snapshots

This paper proposes a three-stage offline approach to detect, identify, and correct series and shunt branch parameter errors. In Stage 1 the branches suspected of having parameter errors are identified through an Identification Index (II). The II of a branch is the ratio between the number of measurements adjacent to that branch, whose normalized residuals are higher than a specified threshold value, and the total number of measurements adjacent to that branch. Using several measurement snapshots, in Stage 2 the suspicious parameters are estimated, in a simultaneous multiple-state-and-parameter estimation, via an augmented state and parameter estimator which increases the V - theta state vector for the inclusion of suspicious parameters. Stage 3 enables the validation of the estimation obtained in Stage 2, and is performed via a conventional weighted least squares estimator. Several simulation results (with IEEE bus systems) have demonstrated the reliability of the proposed approach to deal with single and multiple parameter errors in adjacent and non-adjacent branches, as well as in parallel transmission lines with series compensation. Finally the proposed approach is confirmed on tests performed on the Hydro-Quebec TransEnergie network.

Operant measurement of auditory threshold in prelingually deaf users of cochlear implants: II

Two experiments evaluated an operant procedure for establishing stimulus control using auditory and electrical stimuli as a baseline for measuring the electrical current threshold of electrodes implanted in the cochlea. Twenty-one prelingually deaf children, users of cochlear implants, learned a Go/No Go auditory discrimination task (i.e., pressing a button in the presence of the stimulus but not in its absence). When the simple discrimination baseline became stable, the electrical current was manipulated in descending and ascending series according to an adapted staircase method. Thresholds were determined for three electrodes, one in each location in the cochlea (basal, medial, and apical). Stimulus control was maintained within a certain range of decreasing electrical current but was eventually disrupted. Increasing the current recovered stimulus control, thus allowing the determination of a range of electrical currents that could be defined as the threshold. The present study demonstrated the feasibility of the operant procedure combined with a psychophysical method for threshold assessment, thus contributing to the routine fitting and maintenance of cochlear implants within the limitations of a hospital setting.

Study of C- and O-glycosylflavones in sugarcane extracts using liquid chromatography: exact mass measurement mass spectrometry

The flavonoids present in sugarcane (Saccharum officinarum) extracts were analyzed by liquid chromatography - mass spectrometry (LC-MS), and a study of the fragmentation patterns of selected flavonoids was conducted using orthogonal acceleration time-of-flight electrospray ionization mass spectrometry (ESI-oa-ToF MS). Seven C- and O-glycosylflavones were identified in the extracts, namely, schaftoside, isoschaftoside, luteolin-8-C-(rhamnosylglucoside), vitexin, orientin, tricin-7-O-neohesperidoside and tricin-7-O-glucoside. Of these, five were identified in the absence of direct comparison with their respective standards. The described method also permitted the differentiation of the 6-C and 8-C isomeric flavones, schaftoside and isoschaftoside. The combination of fragmentation data and exact mass measurement showed to be complimentary to the HPLC-UV-MS techniques previously utilized for isomers discrimination in sugarcane studies.

Mobility and social network effects on extremist opinions

Understanding the emergence of extreme opinions and in what kind of environment they might become less extreme is a central theme in our modern globalized society. A model combining continuous opinions and observed discrete actions (CODA) capable of addressing the important issue of measuring how extreme opinions might be has been recently proposed. In this paper I show extreme opinions to arise in a ubiquitous manner in the CODA model for a multitude of social network structures. Depending on network details reducing extremism seems to be possible. However, a large number of agents with extreme opinions is always observed. A significant decrease in the number of extremists can be observed by allowing agents to change their positions in the network.

Direct measurement of intrinsic atomic scale magnetostriction

Using differential x-ray absorption spectroscopy (DiffXAS) we have measured and quantified the intrinsic, atomic-scale magnetostriction of Fe(81)Ga(19). By exploiting the chemical selectivity of DiffXAS, the Fe and Ga local environments have been assessed individually. The enhanced magnetostriction induced by the addition of Ga to Fe was found to originate from the Ga environment, where lambda(gamma,2)(approximate to (3/2)lambda(100)) is 390 +/- 40 ppm. In this environment, < 001 > Ga-Ga pair defects were found to exist, which mediate the magnetostriction by inducing large strains in the surrounding Ga-Fe bonds. For the first time, intrinsic, chemically selective magnetostrictive strain has been measured and quantified at the atomic level, allowing true comparison with theory.

Anticipation of pain enhances the nociceptive transmission and functional connectivity within pain network in rats

Background: Expectation is a very potent pain modulator in both humans and animals. There is evidence that pain transmission neurons are modulated by expectation preceding painful stimuli. Nonetheless, few studies have examined the influence of pain expectation on the pain-related neuronal activity and the functional connectivity within the central nociceptive network. Results: This study used a tone-laser conditioning paradigm to establish the pain expectation in rats, and simultaneously recorded the anterior cingulate cortex (ACC), the medial dorsal thalamus (MD), and the primary somatosensory cortex (SI) to investigate the effect of pain expectation on laser-induced neuronal responses. Cross-correlation and partial directed coherence analysis were used to determine the functional interactions within and between the recorded areas during nociceptive transmission. The results showed that under anticipation condition, the neuronal activity to the auditory cue was significantly increased in the ACC area, whereas those to actual noxious stimuli were enhanced in all the recorded areas. Furthermore, neuronal correlations within and between these areas were significantly increased under conditions of expectation compared to those under non-expectation conditions, indicating an enhanced synchronization of neural activity within the pain network. In addition, information flow from the medial (ACC and MD) to the lateral (SI cortex) pain pathway increased, suggesting that the emotion-related neural circuits may modulate the neuronal activity in the somatosensory pathway during nociceptive transmission. Conclusion: These results demonstrate that the nociceptive processing in both medial and lateral pain systems is modulated by the expectation of pain.

Border figure detection using a phase oscillator network with dynamical coupling

Oscillator networks have been developed in order to perform specific tasks related to image processing. Here we analytically investigate the existence of synchronism in a pair of phase oscillators that are short-range dynamically coupled. Then, we use these analytical results to design a network able of detecting border of black-and-white figures. Each unit composing this network is a pair of such phase oscillators and is assigned to a pixel in the image. The couplings among the units forming the network are also dynamical. Border detection emerges from the network activity.

AtPIN: Arabidopsis thaliana Protein Interaction Network

Background: Protein-protein interactions (PPIs) constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. Description: All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C(3)) which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW) calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS) (AT5G26710) we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630), a disease resistance protein (AT3G50950) and a zinc finger protein (AT5G24930), which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening. Conclusions: AtPIN is a friendly and easy-to-use tool that aggregates information on Arabidopsis thaliana PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at http://bioinfo.esalq.usp.br/atpin.

Measurement of ethylene production during banana ripening

Introduction. This protocol aims at measuring fruit ethylene production during ripening. It can be used to compare ethylene production between different banana varieties or to compare ethylene production between fruit produced in different pedo-climatic conditions. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. This part describes the required laboratory materials and the three steps necessary for calculating the amount of ethylene produced during banana postharvest ripening. Possible troubleshooting is considered.

Biochemical characterization of pulp of banana fruit: measurement of soluble sugars, organic acids, free ACC and in vitro ACC oxidase

Introduction. We present some protocols aiming at partially characterizing banana fruit quality through measurement of some key biochemical parameters. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. This part describes the required laboratory materials and the steps necessary for achieving four protocols making it possible to measure sugar, organic acids and free ACC contents, and in vitro ACC oxidase activity. Results. Standard results obtained by using the protocols described are presented in the figures.

Measurement of banana green life

Introduction. This protocol aims at measuring the storage life potential of banana fruit, and at determining the physiological age of fruit. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. This part describes the required laboratory materials and the five steps necessary for calculating the banana green life duration, which corresponds to the number of days between the fruit harvest and climacteric crisis. Results. The measurement of O-2 and CO2 concentrations allows one to detect the climacteric peak which marks the end of the banana green life.

Measurement of fungicide efficacy on post-harvest diseases: wound anthracnose, quiescent anthracnose, crown rot

Introduction. This protocol aims at evaluating (a) the efficacy of new fungicides for the control of post-harvest diseases, (b) the efficacy of various application methods for the chemical control of post-harvest diseases, and (c) the quality of the fungicide solution during the same packing day where this solution is recycled. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. Materials required and details of the eighteen steps of the protocol (fruit sampling and inoculum preparation, wound anthracnose study, quiescent anthracnose study, and crown-rot study) are described. Results. Comparison between untreated control bananas and bananas treated with fungicide allows the calculation of the fungicide treatment efficacy.

Particle competition for complex network community detection

In many real situations, randomness is considered to be uncertainty or even confusion which impedes human beings from making a correct decision. Here we study the combined role of randomness and determinism in particle dynamics for complex network community detection. In the proposed model, particles walk in the network and compete with each other in such a way that each of them tries to possess as many nodes as possible. Moreover, we introduce a rule to adjust the level of randomness of particle walking in the network, and we have found that a portion of randomness can largely improve the community detection rate. Computer simulations show that the model has good community detection performance and at the same time presents low computational complexity. (C) 2008 American Institute of Physics.

Generalized connectivity between any two nodes in a complex network

This article focuses on the identification of the number of paths with different lengths between pairs of nodes in complex networks and how these paths can be used for characterization of topological properties of theoretical and real-world complex networks. This analysis revealed that the number of paths can provide a better discrimination of network models than traditional network measurements. In addition, the analysis of real-world networks suggests that the long-range connectivity tends to be limited in these networks and may be strongly related to network growth and organization.