基于QRS波群的心律失常辅助诊断模型研究

基于对QRS波群的特征变量提取。利用减法聚类和自适应模糊神经网络构建心律失常辅助诊断模型,分析不同训练数据集对模型测试结果的影响。实验结果表明。该模型能准确识别不同类型的QRS波群,使用不同训练数据集对诊断结果存在影响,为进一步实现更复杂的心律失常辅助诊断模型提供方法。     

Increasing sequence correlation limits the efficiency of recombination in a multisite evolution model

The accumulation of preexisting beneficial alleles in a haploid population, under selection and infrequent recombination, and in the absence of new mutation events is studied numerically by means of detailed Monte Carlo simulations. On the one hand, we confirm our previous work, in that the accumulation rate follows modified single-site kinetics, with a timescale set by an effective selection coefficient s(eff) as shown in a previous work, and we confirm the qualitative features of the dependence of s(eff) on the population size and the recombination rate reported therein. In particular, we confirm the existence of a threshold population size below which evolution stops before the emergence of best-fit individuals. On the other hand, our simulations reveal that the population dynamics is essentially shaped by the steady accumulation of pairwise sequence correlation, causing sequence congruence in excess of what one would expect from a uniformly random distribution of alleles. By sequence congruence, we understand here the opposite of genetic distance, that is, the fraction of monomorphic sites of specified allele type in a pair of genomes (individual sequences). The effective selection coefficient changes more rapidly with the recombination rate and has a higher threshold in this parameter than found in the previous work, which neglected correlation effects. We examine this phenomenon by monitoring the time dependence of sequence correlation based on a set of sequence congruence measures and verify that it is not associated with the development of linkage disequilibrium. We also discuss applications to HIV evolution in infected individuals and potential implications for drug therapy.     

Pollen limitation and fruit abortion in a declining rare tree,the Eurasian yew (Taxus baccata L.): A reproductive cost of ecological marginality

Populations of rare tree species such as the dioecious and anemophilous yew (Taxus baccata) are especially prone to extinction if they occupy marginal habitats. This is the case of yew populations growing in Mediterranean mountains under dry climate and a severe anthropogenic disturbance regime, which show insufficient regeneration. We examined two of the likely mechanisms driving this population decline. The study was conducted in a central Spanish yew population in 2005 and 2006. On one hand, we tested for the effect of the amount of pollen received by female flowers by means of a pollen addition experiment. On the other hand, we tested for the effect of initial fruit set on abortion and mature fruit production. Finally, we evaluated the effect of the spatial arrangement of male and female yew trees on realized fecundity. The success of fertilization and fruiting in the experimental population was pollen-limited. Female trees aborted ca. 70% of the fruit set in both years and treatments. Fruit set was significantly influenced by the females' neighbourhood, with fecundity decreasing exponentially with distance to the nearest male in both years. Overall, our results indicate that factors associated with ecological marginality have a strong influence on yew performance.     

Meta-analysis of gene expression data: a predictor-based approach

MOTIVATION: With the increasing availability of cancer microarray data sets there is a growing need for integrative computational methods that evaluate multiple independent microarray data sets investigating a common theme or disorder. Meta-analysis techniques are designed to overcome the low sample size typical to microarray experiments and yield more valid and informative results than each experiment separately. RESULTS: We propose a new meta-analysis technique that aims at finding a set of classifying genes, whose expression level may be used to answering the classification question in hand. Specifically, we apply our method to two independent lung cancer microarray data sets and identify a joint core subset of genes which putatively play an important role in tumor genesis of the lung. The robustness of the identified joint core set is demonstrated on a third unseen lung cancer data set, where it leads to successful classification using very few top-ranked genes. Identifying such a set of genes is of significant importance when searching for biologically meaningful biomarkers. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Adaptive neuro-fuzzy inference technique for estimation of light penetration in reservoirs

An adaptive neuro-fuzzy inference technique has been adopted to estimate light levels in a reservoir. The data were collected randomly from Doğanci Dam Reservoir over a number of years. The input data set is a matrix with vectors of time, depth, sampling location, and incident solar radiation. The output data set is a vector representing light measured at various depths. Randomization and logarithmic transformations have been applied as preprocessing. One-half of the data have been utilized for training; testing and validation steps utilized one-fourth each. An adaptive neuro-fuzzy inference system (ANFIS) has been built as a prediction model for light penetration. Very high correlation values between predictions and real values on light measurements with relatively low root mean square error values have been obtained for training, test, and validation data sets. Elimination of the overtraining problem was ensured by satisfying close root mean square error values for all sets.     

The illusion of owning a third arm

Could it be possible that, in the not-so-distant future, we will be able to reshape the human body so as to have extra limbs? A third arm helping us out with the weekly shopping in the local grocery store, or an extra artificial limb assisting a paralysed person? Here we report a perceptual illusion in which a rubber right hand, placed beside the real hand in full view of the participant, is perceived as a supernumerary limb belonging to the participant''s own body. This effect was supported by questionnaire data in conjunction with physiological evidence obtained from skin conductance responses when physically threatening either the rubber hand or the real one. In four well-controlled experiments, we demonstrate the minimal required conditions for the elicitation of this “supernumerary hand illusion”. In the fifth, and final experiment, we show that the illusion reported here is qualitatively different from the traditional rubber hand illusion as it is characterised by less disownership of the real hand and a stronger feeling of having two right hands. These results suggest that the artificial hand ‘borrows’ some of the multisensory processes that represent the real hand, leading to duplication of touch and ownership of two right arms. This work represents a major advance because it challenges the traditional view of the gross morphology of the human body as a fundamental constraint on what we can come to experience as our physical self, by showing that the body representation can easily be updated to incorporate an additional limb.     

Efficient biased estimation of evolutionary distances when substitution rates vary across sites

This paper deals with phylogenetic inference when the variability of substitution rates across sites (VRAS) is modeled by a gamma distribution. We show that underestimating VRAS, which results in underestimates for the evolutionary distances between sequences, usually improves the topological accuracy of phylogenetic tree inference by distance-based methods, especially when the molecular clock holds. We propose a method to estimate the gamma shape parameter value which is most suited for tree topology inference, given the sequences at hand. This method is based on the pairwise evolutionary distances between sequences and allows one to reconstruct the phylogeny of a high number of taxa (>1,000). Simulation results show that the topological accuracy is highly improved when using the gamma shape parameter value given by our method, compared with the true (unknown) value which was used to generate the data. Furthermore, when VRAS is high, the topological accuracy of our distance-based method is better than that of a maximum likelihood approach. Finally, a data set of Maoricicada species sequences is analyzed, which confirms the advantage of our method.     

Protein Information and Knowledge Extractor: Discovering biological information from proteomics data

One of the main goals in proteomics is to solve biological and molecular questions regarding a set of identified proteins. In order to achieve this goal, one has to extract and collect the existing biological data from public repositories for every protein and afterward, analyze and organize the collected data. Due to the complexity of this task and the huge amount of data available, it is not possible to gather this information by hand, making it necessary to find automatic methods of data collection. Within a proteomic context, we have developed Protein Information and Knowledge Extractor (PIKE) which solves this problem by automatically accessing several public information systems and databases across the Internet. PIKE bioinformatics tool starts with a set of identified proteins, listed as the most common protein databases accession codes, and retrieves all relevant and updated information from the most relevant databases. Once the search is complete, PIKE summarizes the information for every single protein using several file formats that share and exchange the information with other software tools. It is our opinion that PIKE represents a great step forward for information procurement and drastically reduces manual database validation for large proteomic studies. It is available at http://proteo.cnb.csic.es/pike .     

Electro weak enantioselection and the origin of life

All biomolecules are of one hand — but what determines which hand? Why is life based on L-amino acids and D-sugars rather than D-amino acids and L-sugars? We believe the symmetry-breaker could be the weak force, which causes enantiomers to differ very slightly in energy. In this paper we present our calculations of this parity-violating energy difference (PVED) for a range of important biomolecules, and in nearly all cases it is indeed the ‘natural’ enantiomer which is the more stable.     

A musculoskeletal model of the hand and wrist: model definition and evaluation

Abstract

To improve our understanding on the neuromechanics of finger movements, a comprehensive musculoskeletal model is needed. The aim of this study was to build a musculoskeletal model of the hand and wrist, based on one consistent data set of the relevant anatomical parameters. We built and tested a model including the hand and wrist segments, as well as the muscles of the forearm and hand in OpenSim. In total, the model comprises 19 segments (with the carpal bones modeled as one segment) with 23 degrees of freedom and 43 muscles. All required anatomical input data, including bone masses and inertias, joint axis positions and orientations as well as muscle morphological parameters (i.e. PCSA, mass, optimal fiber length and tendon length) were obtained from one cadaver of which the data set was recently published. Model validity was investigated by first comparing computed muscle moment arms at the index finger metacarpophalangeal (MCP) joint and wrist joint to published reference values. Secondly, the muscle forces during pinching were computed using static optimization and compared to previously measured intraoperative reference values. Computed and measured moment arms of muscles at both index MCP and wrist showed high correlation coefficients (r?=?0.88 averaged across all muscles) and modest root mean square deviation (RMSD?=?23% averaged across all muscles). Computed extrinsic flexor forces of the index finger during index pinch task were within one standard deviation of previously measured in-vivo tendon forces. These results provide an indication of model validity for use in estimating muscle forces during static tasks.     

When Right Feels Left: Referral of Touch and Ownership between the Hands

Feeling touch on a body part is paradigmatically considered to require stimulation of tactile afferents from the body part in question, at least in healthy non-synaesthetic individuals. In contrast to this view, we report a perceptual illusion where people experience “phantom touches” on a right rubber hand when they see it brushed simultaneously with brushes applied to their left hand. Such illusory duplication and transfer of touch from the left to the right hand was only elicited when a homologous (i.e., left and right) pair of hands was brushed in synchrony for an extended period of time. This stimulation caused the majority of our participants to perceive the right rubber hand as their own and to sense two distinct touches – one located on the right rubber hand and the other on their left (stimulated) hand. This effect was supported by quantitative subjective reports in the form of questionnaires, behavioral data from a task in which participants pointed to the felt location of their right hand, and physiological evidence obtained by skin conductance responses when threatening the model hand. Our findings suggest that visual information augments subthreshold somatosensory responses in the ipsilateral hemisphere, thus producing a tactile experience from the non-stimulated body part. This finding is important because it reveals a new bilateral multisensory mechanism for tactile perception and limb ownership.     

Dynamics of the central bottleneck: dual-task and task uncertainty

Why is the human brain fundamentally limited when attempting to execute two tasks at the same time or in close succession? Two classical paradigms, psychological refractory period (PRP) and task switching, have independently approached this issue, making significant advances in our understanding of the architecture of cognition. Yet, there is an apparent contradiction between the conclusions derived from these two paradigms. The PRP paradigm, on the one hand, suggests that the simultaneous execution of two tasks is limited solely by a passive structural bottleneck in which the tasks are executed on a first-come, first-served basis. The task-switching paradigm, on the other hand, argues that switching back and forth between task configurations must be actively controlled by a central executive system (the system controlling voluntary, planned, and flexible action). Here we have explicitly designed an experiment mixing the essential ingredients of both paradigms: task uncertainty and task simultaneity. In addition to a central bottleneck, we obtain evidence for active processes of task setting (planning of the appropriate sequence of actions) and task disengaging (suppression of the plan set for the first task in order to proceed with the next one). Our results clarify the chronometric relations between these central components of dual-task processing, and in particular whether they operate serially or in parallel. On this basis, we propose a hierarchical model of cognitive architecture that provides a synthesis of task-switching and PRP paradigms.     

Contig selection in physical mapping.

In physical mapping, one orders a set of genetic landmarks or a library of cloned fragments of DNA according to their position in the genome. Our approach to physical mapping divides the problem into smaller and easier subproblems by partitioning the probe set into independent parts (probe contigs). For this purpose we introduce a new distance function between probes, the averaged rank distance (ARD) derived from bootstrap resampling of the raw data. The ARD measures the pairwise distances of probes within a contig and smoothes the distances of probes across different contigs. It shows distinct jumps at contig borders. This makes it appropriate for contig selection by clustering. We have designed a physical mapping algorithm that makes use of these observations and seems to be particularly well suited to the delineation of reliable contigs. We evaluated our method on data sets from two physical mapping projects. On data from the recently sequenced bacterium Xylella fastidiosa, the probe contig set produced by the new method was evaluated using the probe order derived from the sequence information. Our approach yielded a basically correct contig set. On this data we also compared our method to an approach which uses the number of supporting clones to determine contigs. Our map is much more accurate. In comparison to a physical map of Pasteurella haemolytica that was computed using simulated annealing, the newly computed map is considerably cleaner. The results of our method have already proven helpful for the design of experiments aimed at further improving the quality of a map.     

Efficient TPA-based auditing scheme for secure cloud storage

In recent years, how to design efficient auditing protocol to verify the integrity of users’ data, which is stored in cloud services provider (CSP), becomes a research focus. Homomorphic message authentication code (MAC) and homomorphic signature are two popular techniques to respectively design private and public auditing protocols. On the one hand, it is not suitable for the homomorphic-MAC-based auditing protocols to be outsourced to third-party auditor (TPA), who has more professional knowledge and computational abilities, although they have high efficiencies. On the other hand, the homomorphic-signature-based ones are very suitable for employing TPA without compromising user’s signing key but have very low efficiency (compared to the former case). In this paper, we propose a new auditing protocol, which perfectly combines the advantages of above two cases. In particular, it is almost as efficient as a homomorphic-MAC-based protocol proposed by Zhang et al. recently. Moreover, it is also suitable for outsourcing to TPA because it does not compromise the privacy of users’ signing key, which can be seen from our security analysis. Finally, numerical analysis and experimental results demonstrate the high-efficiency of our protocol.

     

Best linear unbiased allele-frequency estimation in complex pedigrees

Many types of genetic analyses depend on estimates of allele frequencies. We consider the problem of allele-frequency estimation based on data from related individuals. The motivation for this work is data collected on the Hutterites, an isolated founder population, so we focus particularly on the case in which the relationships among the sampled individuals are specified by a large, complex pedigree for which maximum likelihood estimation is impractical. For this case, we propose to use the best linear unbiased estimator (BLUE) of allele frequency. We derive this estimator, which is equivalent to the quasi-likelihood estimator for this problem, and we describe an efficient algorithm for computing the estimate and its variance. We show that our estimator has certain desirable small-sample properties in common with the maximum likelihood estimator (MLE) for this problem. We treat both the case when parental origin of each allele is known and when it is unknown. The results are extended to prediction of allele frequency in some set of individuals S based on genotype data collected on a set of individuals R. We compare the mean-squared error of the BLUE, the commonly used naive estimator (sample frequency) and the MLE when the latter is feasible to calculate. The results indicate that although the MLE performs the best of the three, the BLUE is close in performance to the MLE and is substantially easier to calculate, making it particularly useful for large complex pedigrees in which MLE calculation is impractical or infeasible. We apply our method to allele-frequency estimation in a Hutterite data set.     

A Norway spruce FLOWERING LOCUS T homolog is implicated in control of growth rhythm in conifers

Growth in perennial plants possesses an annual cycle of active growth and dormancy that is controlled by environmental factors, mainly photoperiod and temperature. In conifers and other nonangiosperm species, the molecular mechanisms behind these responses are currently unknown. In Norway spruce (Picea abies L. Karst.) seedlings, growth cessation and bud set are induced by short days and plants from southern latitudes require at least 7 to 10 h of darkness, whereas plants from northern latitudes need only 2 to 3 h of darkness. Bud burst, on the other hand, is almost exclusively controlled by temperature. To test the possible role of Norway spruce FLOWERING LOCUS T (FT)-like genes in growth rhythm, we have studied expression patterns of four Norway spruce FT family genes in two populations with a divergent bud set response under various photoperiodic conditions. Our data show a significant and tight correlation between growth rhythm (both bud set and bud burst), and expression pattern of one of the four Norway spruce phosphatidylethanolamine-binding protein gene family members (PaFT4) over a variety of experimental conditions. This study strongly suggests that one Norway spruce homolog to the FT gene, which controls flowering in angiosperms, is also a key integrator of photoperiodic and thermal signals in the control of growth rhythms in gymnosperms. The data also indicate that the divergent adaptive bud set responses of northern and southern Norway spruce populations, both to photoperiod and light quality, are mediated through PaFT4. These results provide a major advance in our understanding of the molecular control of a major adaptive trait in conifers and a tool for further molecular studies of adaptive variation in plants.     

Evaluating Virtual Cells and Multistage Flow Shops: An Analytical Approach

The implementation of cellular manufacturing can be carried out through the creation of manufacturing cells (i.e., groups of dissimilar machines dedicated to a set of part types that are placed in close proximity to one another) or virtual cells (i.e., the dedication of specific machines within the current departments to a prespecified set of part types). Typically, the former involves the reorganization of the shop floor and provides the operational benefit of reduced materials handling. On the other hand, the latter configuration is simpler to implement and easier to reconfigure in light of product demand changes, but it may not offer the same operational benefits. In this paper, we propose and validate analytical approximations for comparing the performance of virtual cells and multistage flow shops. Using these approximations and hypothetical data, we identify some key factors that influence the implementation of virtual cells in a multistage flow shop environment. We conclude with an application of our approximations to industrial data.     

Hay fever symptoms compared to atmospheric pollen counts and floral phenology within Paris suburban area in 1987 and 1988

Summary Owing to the great pollen sensitivity of some allergic patients and without effective pollen forecasting, it is often difficult to set a preventive therapy of pollinosis. In 1987 and 1988 we compared the symptoms of 45 patients sensitive to grass pollen, daily pollen counts data recorded by a gravimetric and a volumetric sampler as well as meteorological data and observations of floral phenology. Symptoms appeared to be strictly correlated with peak periods of pollen dispersion, but we observed allergic symptoms in our patients long before atmospheric pollen was detected by the pollen traps. On the other hand, these early occurring symptoms seemed to be connected with the first Gramineae flowering.