RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

<p>Abstract</p> <p>Background</p> <p>With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression.</p> <p>Results</p> <p><it>RNACompress </it>employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that <it>RNACompress </it>achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as <it>Gencompress, winrar </it>and <it>gzip</it>. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective.</p> <p>Conclusion</p> <p>A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed <it>RNACompress</it>, as a useful tool for academic users. Extensive tests have shown that <it>RNACompress </it>is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. <it>RNACompress </it>also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules.</p

Learning and comparing functional connectomes across subjects

Functional connectomes capture brain interactions via synchronized fluctuations in the functional magnetic resonance imaging signal. If measured during rest, they map the intrinsic functional architecture of the brain. With task-driven experiments they represent integration mechanisms between specialized brain areas. Analyzing their variability across subjects and conditions can reveal markers of brain pathologies and mechanisms underlying cognition. Methods of estimating functional connectomes from the imaging signal have undergone rapid developments and the literature is full of diverse strategies for comparing them. This review aims to clarify links across functional-connectivity methods as well as to expose different steps to perform a group study of functional connectomes

Altered functional and structural brain network organization in autism.

Structural and functional underconnectivity have been reported for multiple brain regions, functional systems, and white matter tracts in individuals with autism spectrum disorders (ASD). Although recent developments in complex network analysis have established that the brain is a modular network exhibiting small-world properties, network level organization has not been carefully examined in ASD. Here we used resting-state functional MRI (n&nbsp;=&nbsp;42 ASD, n&nbsp;=&nbsp;37 typically developing; TD) to show that children and adolescents with ASD display reduced short and long-range connectivity within functional systems (i.e., reduced functional integration) and stronger connectivity between functional systems (i.e., reduced functional segregation), particularly in default and higher-order visual regions. Using graph theoretical methods, we show that pairwise group differences in functional connectivity are reflected in network level reductions in modularity and clustering (local efficiency), but shorter characteristic path lengths (higher global efficiency). Structural networks, generated from diffusion tensor MRI derived fiber tracts (n&nbsp;=&nbsp;51 ASD, n&nbsp;=&nbsp;43 TD), displayed lower levels of white matter integrity yet higher numbers of fibers. TD and ASD individuals exhibited similar levels of correlation between raw measures of structural and functional connectivity (n&nbsp;=&nbsp;35 ASD, n&nbsp;=&nbsp;35 TD). However, a principal component analysis combining structural and functional network properties revealed that the balance of local and global efficiency between structural and functional networks was reduced in ASD, positively correlated with age, and inversely correlated with ASD symptom severity. Overall, our findings suggest that modeling the brain as a complex network will be highly informative in unraveling the biological basis of ASD and other neuropsychiatric disorders

Modeling of the subgrid-scale term of the filtered magnetic field transport equation

Accurate subgrid-scale turbulence models are needed to perform realistic numerical magnetohydrodynamic (MHD) simulations of the subsurface flows of the Sun. To perform large-eddy simulations (LES) of turbulent MHD flows, three unknown terms have to be modeled. As a first step, this work proposes to use a priori tests to measure the accuracy of various models proposed to predict the SGS term appearing in the transport equation of the filtered magnetic field. It is proposed to evaluate the SGS model accuracy in term of "structural" and "functional" performance, i.e. the model capacity to locally approximate the unknown term and to reproduce its energetic action, respectively. From our tests, it appears that a mixed model based on the scale-similarity model has better performance.Comment: 10 pages, 5 figures; Center for Turbulence Research, Proceedings of the Summer Program 2010, Stanford Universit

The neurocognitive gains of diagnostic reasoning training using simulated interactive veterinary cases

The present longitudinal study ascertained training-associated transformations in the neural underpinnings of diagnostic reasoning, using a simulation game named “Equine Virtual Farm” (EVF). Twenty participants underwent structural, EVF/task-based and resting-state MRI and diffusion tensor imaging (DTI) before and after completing their training on diagnosing simulated veterinary cases. Comparing playing veterinarian versus seeing a colorful image across training sessions revealed the transition of brain activity from scientific creativity regions pre-training (left middle frontal and temporal gyrus) to insight problem-solving regions post-training (right cerebellum, middle cingulate and medial superior gyrus and left postcentral gyrus). Further, applying linear mixed-effects modelling on graph centrality metrics revealed the central roles of the creative semantic (inferior frontal, middle frontal and angular gyrus and parahippocampus) and reward systems (orbital gyrus, nucleus accumbens and putamen) in driving pre-training diagnostic reasoning; whereas, regions implicated in inductive reasoning (superior temporal and medial postcentral gyrus and parahippocampus) were the main post-training hubs. Lastly, resting-state and DTI analysis revealed post-training effects within the occipitotemporal semantic processing region. Altogether, these results suggest that simulation-based training transforms diagnostic reasoning in novices from regions implicated in creative semantic processing to regions implicated in improvised rule-based problem-solving

Combination antiretroviral therapy improves cognitive performance and functional connectivity in treatment-naïve HIV-infected individuals.

Our study aimed to investigate the short-term effect of combination antiretroviral therapy (cART) on cognitive performance and functional and structural connectivity and their relationship to plasma levels of antiretroviral (ARV) drugs. Seventeen ARV treatment-naïve HIV-infected individuals (baseline mean CD4 cell count, 479 ± 48 cells/mm3) were age matched with 17 HIV-uninfected individuals. All subjects underwent a detailed neurocognitive and functional assessment and magnetic resonance imaging. HIV-infected subjects were scanned before starting cART and 12 weeks after initiation of treatment. Uninfected subjects were assessed once at baseline. Functional connectivity (FC) was assessed within the default mode network while structural connectivity was assessed by voxel-wise analysis using tract-based spatial statistics (TBSS) and probabilistic tractography within the DMN. Tenofovir and emtricitabine blood concentration were measured at week 12 of cART. Prior to cART, HIV-infected individuals had significantly lower cognitive performance than control subjects as measured by the total Z-score from the neuropsychological tests assessing six cognitive domains (p = 0.020). After 12 weeks of cART treatment, there remained only a weak cognitive difference between HIV-infected and HIV-uninfected subjects (p = 0.057). Mean FC was lower in HIV-infected individuals compared with those uninfected (p = 0.008), but FC differences became non-significant after treatment (p = 0.197). There were no differences in DTI metrics between HIV-infected and HIV-uninfected individuals using the TBSS approach and limited evidence of decreased structural connectivity within the DMN in HIV-infected individuals. Tenofovir and emtricitabine plasma concentrations did not correlate with either cognitive performance or imaging metrics.ConclusionsTwelve weeks of cART improves cognitive performance and functional connectivity in ARV treatment-naïve HIV-infected individuals with relatively preserved immune function. Longer periods of observation are necessary to assess whether this effect is maintained