Identifying statistical dependence in genomic sequences via mutual information estimates

Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (DNA or RNA) that are statistically correlated. We develop a precise and reliable methodology, based on the notion of mutual information, for finding and extracting statistical as well as structural dependencies. A simple threshold function is defined, and its use in quantifying the level of significance of dependencies between biological segments is explored. These tools are used in two specific applications. First, for the identification of correlations between different parts of the maize zmSRp32 gene. There, we find significant dependencies between the 5' untranslated region in zmSRp32 and its alternatively spliced exons. This observation may indicate the presence of as-yet unknown alternative splicing mechanisms or structural scaffolds. Second, using data from the FBI's Combined DNA Index System (CODIS), we demonstrate that our approach is particularly well suited for the problem of discovering short tandem repeats, an application of importance in genetic profiling.Comment: Preliminary version. Final version in EURASIP Journal on Bioinformatics and Systems Biology. See http://www.hindawi.com/journals/bsb

A nanoindentation investigation of local strain rate sensitivity in dual-phase Ti alloys

Using nanoindentation we have investigated the local strain rate sensitivity in dual-phase Ti alloys, Ti-6Al-2Sn-4Zr-xMo (x=2 and 6), as strain rate sensitivity could be a potential factor causing cold dwell fatigue. Electron backscatter diffraction (EBSD) was used to select hard and soft grain orientations within each of the alloys. Nanoindentation based tests using the continuous stiffness measurement (CSM) method were performed with variable strain rates, on the order of 10−1 to 10−3s−1. Local strain rate sensitivity is determined using a power law linking equivalent flow stress and equivalent plastic strain rate. Analysis of residual impressions using both a scanning electron microscope (SEM) and a focused ion beam (FIB) reveals local deformation around the indents and shows that nanoindentation tested structures containing both α and β phases within individual colonies. This indicates that the indentation results are derived from averaged α/β properties. The results show that a trend of local rate sensitivity in Ti6242 and Ti6246 is strikingly different; as similar rate sensitivities are found in Ti6246 regardless of grain orientation, whilst a grain orientation dependence is observed in Ti6242. These findings are important for understanding dwell fatigue deformation modes, and the methodology demonstrated can be used for screening new alloy designs and microstructures

The dimensions of personality in humans and other animals: A comparative and evolutionary perspective

This paper considers the structure and proximate mechanisms of personality in humans and other animals. Significant similarities were found between personality structures and mechanisms across species in at least two broad traits: Extraversion and Neuroticism. The factor space tapped by these personality dimensions is viewed as a general integrative framework for comparative and evolutionary studies of personality in humans and other animals. Most probably, the cross-species similarities between the most broad personality dimensions like Extraversion and Neuroticism as well as other Big Five factors reflect conservative evolution: constrains on evolution imposed by physiological, genetic and cognitive mechanisms. Lower-order factors, which are more species- and situation-specific, would be adaptive, reflecting correlated selection on and trade-offs between many traits

Erosion-corrosion behaviour of Zirconia WC-6Co, WC-6Ni and SS316

The current study investigates a ceramic, two cermets and a metal under solid-liquid impingement with 3.5% NaCl and 150mg/l hydraulic fracturing sand at two extreme angles of impact, 90° and 20°. The materials tested were Zirconia, sintered WC-6Co, sintered WC-6Ni and SS316. Each material was exposed to a testing regime using re-circulating impinging jet apparatus with a velocity of 19m/s and one hour duration. The electrochemical properties of the materials were investigated in-situ through anodic and cathodic polarisation and application of cathodic protection. Post experimental analysis of the degraded surface was completed using Scanning Electron Microscopy (SEM) and Optical 3D Imaging. Zirconia exhibited a brittle response to erosion-corrosion testing with the mass loss at 90° being fifty times greater than the negligible mass loss at 20°. WC-6Co and WC-6Ni both outperformed SS316 under all solid-liquid impingement erosion-corrosion testing regimes. WC-6Ni exhibited slightly better erosion-corrosion resistance over WC-6Co at both 90° and 20°. SS316 had the best corrosion resistance and showed passivation during anodic polarisations in solid-liquid impingement conditions. The nickel binder increased the corrosion resistance of WC-6Ni over WC-6Co. Cathodic protection was successfully applied on sintered WC-6Co and SS316 isolating the key components of erosion-corrosion

Differential Behavioral Responses to\ud Cocaethylene of Long-Evans and\ud Sprague-Dawley Rats: Role of Serotonin

Cocaethylene is a neuroactive metabolite derived from the concurrent consumption of cocaine and ethanol. The effects of cocaethylene on locomotor activity, stereotypy, and rearing in Long-Evans and Sprague-Dawley rats were compared.A single cocaine injection (molar equivalent of 60 μmol/kg cocaethylene, intraperitoneal) elicited a robust series of motor output behaviors, including locomotion, stereotypy, and rearing over a 30-minute testing period in Long-Evans rats. In contrast, cocaethylene administration,\ud under comparable testing conditions, produced no significant changes in locomotor and investigatory behaviors. Because cocaethylene has relatively little impact on serotonin (5-HT) reuptake as opposed to reuptake of dopamine, we pretreated Long-Evans rats with fluoxetine (10 mg/kg; IP), a selective 5-HT reuptake inhibitor. Fluoxetine profoundly augmented cocaethylene-stimulated behaviors in this rat phenotype. To examine whether other rat strains exhibit a similar response to cocaethylene, Sprague-Dawley rats were injected (IP) with cocaethylene and their behavior patterns monitored over a 30-minute testing period. Cocaethylene produced marked locomotor and exploratory behaviors in this strain, suggesting therefore that Long-Evans and Sprague-\ud Dawley rats differ in their response to cocaethylene. To relate these behavioral differences to possible structural differences in the neuronal density of dopaminergic or\ud serotonergic neurons, Long-Evans and Sprague-Dawley brains were evaluated for tyrosine hydroxylase and 5-HT immunocytochemistry. No gross morphological differences\ud in neuronal architecture or density were found in the ventral tegmental area or dorsal raphe nucleus of the two rat phenotypes. These results indicate that two commonly used rat strains show a differential response to cocaethylene and the neurochemical basis for this behavioral difference may be related to synaptic 5-HT bioavailability

The comparative value of feline virology research: can findings from the feline lentiviral vaccine be translated to humans?

Feline immunodeficiency virus (FIV) is a lentivirus of domestic cats that shares several similarities with its human counterpart, human immunodeficiency virus (HIV). Their analogies include genomic organization, lymphocyte tropism, viral persistence and induction of immunodeficiency. FIV is the only lentivirus for which a commercial vaccine is registered for prevention in either human or veterinary medicine. This provides a unique opportunity to investigate the mechanisms of protection induced by lentivirus vaccines at the population level and might contribute to the development of efficacious HIV vaccines. As well as having comparative value for vaccine studies, FIV research has shed some light on the relationship between lentiviral tropism and pathogenesis. Recent studies in our laboratory demonstrated that the interaction between FIV and its primary receptor changes as disease progresses, reminiscent of the receptor switch observed as disease progresses in HIV infected individuals. Here we summarise findings illustrating that, in addition to its veterinary significance, FIV has comparative value, providing a useful model to explore lentivirus–host interactions and to examine potential immune correlates of protection against HIV infection

Wavelet-based filtration procedure for denoising the predicted CO2 waveforms in smart home within the Internet of Things

The operating cost minimization of smart homes can be achieved with the optimization of the management of the building's technical functions by determination of the current occupancy status of the individual monitored spaces of a smart home. To respect the privacy of the smart home residents, indirect methods (without using cameras and microphones) are possible for occupancy recognition of space in smart homes. This article describes a newly proposed indirect method to increase the accuracy of the occupancy recognition of monitored spaces of smart homes. The proposed procedure uses the prediction of the course of CO2 concentration from operationally measured quantities (temperature indoor and relative humidity indoor) using artificial neural networks with a multilayer perceptron algorithm. The mathematical wavelet transformation method is used for additive noise canceling from the predicted course of the CO2 concentration signal with an objective increase accuracy of the prediction. The calculated accuracy of CO2 concentration waveform prediction in the additive noise-canceling application was higher than 98% in selected experiments.Web of Science203art. no. 62

Effect of crowding on the electron transfer process from plastocyanin and cytochrome c6 to photosystem I: a comparative study from cyanobacteria to green algae

Plastocyanin and cytochrome c 6, the alternate donor proteins to photosystem I, can be acidic, neutral or basic; the role of electrostatics in their interaction with photosystem I vary accordingly for cyanobacteria, algae and plants. The effect of different crowding agents on the kinetics of the reaction between plastocyanin or cytochrome c 6 and photosystem I from three different cyanobacteria, Synechocystis PCC 6803, Nostoc PCC 7119 and Arthrospira maxima, and a green alga, Monoraphidium braunii, has been investigated by laser flash photolysis, in order to elucidate how molecular crowding affects the interaction between the two donor proteins and photosystem I. The negative effect of viscosity on the interaction of the two donors with photosystem I for the three cyanobacterial systems is very similar, as studied by increasing sucrose concentration. Bovine serum albumin seems to alter the different systems in a specific way, probably by means of electrostatic interactions with the donor proteins. Ficoll and dextran behave in a parallel manner, favouring the interaction by an average factor of 2, although this effect is somewhat less pronounced in Nostoc. With regards to the eukaryotic system, a strong negative effect of viscosity is able to overcome the favourable effect of any crowding agent, maybe due to stronger donor/photosystem I electrostatic interactions or the structural nature of the eukaryotic photosystem I-enriched membrane particles.Spanish Ministry of Innovation and Science BFU2006-01361Andalusian Government PAI BIO-02