The description of spatial pattern using two-dimensional spectral analysis

Two-dimensional spectral analysis is a general interrogative technique for describing spatial patterns. Not only is it able to detect all possible scales of pattern which can be present in the data but it is also sensitive to directional components. Four functions are described: the autocorrelation function; the periodogram; and, the R- and Θ-spectra which respectively summarize the periodogram in terms of scale and directional components of pattern. The use of these functions is illustrated by their application to a simple wave pattern, a wave pattern with added noise, and patterns simulating competition and invasion processes.     

Effect of ill-fitting dentures on the swallowing duration in patients using polygraphy

doi: 10.1111/j.1741‐2358.2011.00536.x Effect of ill‐fitting dentures on the swallowing duration in patients using polygraphy Background: Surface electromyography (SEMG) has been widely used in the recent years to study swallowing physiology, offering a valid and reliable tool for identifying normal swallowing. The goal of our study was to assess the contribution of denture fitness in the age‐related increase of swallowing duration. Methods: Twenty denture wearers and 20 dentate individuals were analysed using SEMG and a computerised kinesiography of mandibular movement. Three spontaneous saliva swallowings were recorded for each patient with both their old and new prostheses. Three spontaneous saliva swallowings were recorded for each dentate person in two different recording sessions. Results: Old prosthesis mean swallowing time was 1.84 (SD ± 0.85) seconds while the new well‐fitting prostheses needed a 1.28 (SD ± 0.55) (p = 0.0009) swallowing time. The difference in swallowing time was significant (p = 0.01) between dentate subjects and individuals wearing an old prosthesis. No significant difference was found between dentate subjects and the same prosthesis wearers when a new well‐fitting prosthesis was worn. Conclusion: Data presented in this work suggest that part of the increased duration of swallowing showed by elderly and healthy people is because of incorrect an dental prosthesis. Prolongation of swallowing duration in the elderly population could be reconsidered in the light of the quality of dental device worn by the aged population.     

Disconnection of a basal ganglia circuit in juvenile songbirds attenuates the spectral differentiation of song syllables

Similar to language acquisition by human infants, juvenile male zebra finches (Taeniopygia guttata) imitate an adult (tutor) song by transitioning from repetitive production of one or two undifferentiated protosyllables to the sequential production of a larger and spectrally heterogeneous set of syllables. The primary motor region that controls learned song is driven by a confluence of input from two premotor pathways: a posterior pathway that encodes the adult song syllables and an anterior pathway that includes a basal ganglia (BG)‐thalamo‐cortical circuit. Similar to mammalian motor‐learning systems, the songbird BG circuit is thought to be necessary for shaping juvenile vocal behaviour (undifferentiated protosyllables) toward specific targets (the tutor's song syllables). Here, we tested the hypothesis that anterior pathway activity contributes to the process of protosyllable differentiation. Bilateral ablation of lateral magnocellular nucleus of the anterior nidopallium (LMAN) was used to disconnect BG circuitry at ages before protosyllable production and differentiation. Comparison to surgical controls revealed that protosyllables fail to differentiate in birds that received juvenile LMAN ablation—the adult songs of birds with >80% bilateral LMAN ablation consisted of only one or two syllables produced with the repetitive form and spectral structure that characterizes undifferentiated protosyllables in normal juveniles. Our findings support a role for BG circuitry in shaping juvenile vocal behaviour toward the acoustic structure of the tutor song and suggest that posterior pathway function remains in an immature “default” state when developmental interaction with the anterior pathway is reduced or eliminated. © 2013 Wiley Periodicals, Inc. Develop Neurobiol 74: 574–590, 2014     

Quantitative analysis of SILAC data sets using spectral counting

We report a new quantitative proteomics approach that combines the best aspects of stable isotope labeling of amino acids in cell culture (SILAC) labeling and spectral counting. The SILAC peptide count ratio analysis (SPeCtRA, http://proteomics.mcw.edu/visualize ) method relies on MS² spectra rather than ion chromatograms for quantitation and therefore does not require the use of high mass accuracy mass spectrometers. The inclusion of a stable isotope label allows the samples to be combined before sample preparation and analysis, thus avoiding many of the sources of variability that can plague spectral counting. To validate the SPeCtRA method, we have analyzed samples constructed with known ratios of protein abundance. Finally, we used SPeCtRA to compare endothelial cell protein abundances between high (20 mM) and low (11 mM) glucose culture conditions. Our results demonstrate that SPeCtRA is a protein quantification technique that is accurate and sensitive as well as easy to automate and apply to high‐throughput analysis of complex biological samples.     

Automated region of interest retrieval and classification using spectral analysis

Efficient use of whole slide imaging in pathology needs automated region of interest (ROI) retrieval and classification, through the use of image analysis and data sorting tools. One possible method for data sorting uses Spectral Analysis for Dimensionality Reduction. We present some interesting results in the field of histopathology and cytohematology. In histopathology, we developed a Computer-Aided Diagnosis system applied to low-resolution images representing the totality of histological breast tumour sections. The images can be digitized directly at low resolution or be obtained from sub-sampled high-resolution virtual slides. Spectral Analysis is used (1) for image segmentation (stroma, tumour epithelium), by determining a "distance" between all the images of the database, (2) for choosing representative images and characteristic patterns of each histological type in order to index them, and (3) for visualizing images or features similar to a sample provided by the pathologist. In cytohematology, we studied a blood smear virtual slide acquired through high resolution oil scanning and Spectral Analysis is used to sort selected nucleated blood cell classes so that the pathologist may easily focus on specific classes whose morphology could then be studied more carefully or which can be analyzed through complementary instruments, like Multispectral Imaging or Raman MicroSpectroscopy.     

The analysis of circular dichroism spectra of natural DNAs using spectral components from synthetic DNAs

We have tested 21 different basis sets of synthetic DNA circular dichroism spectra and have slected one for use in spectral analyses of natural DNAs. This “standard” set consists of spectra of eight polymers: poly[d(A-A-T)·d(A-T-T)], poly[d(A-G-G)·d(C-C-T)], poly[d(A-T)·d(A-T)], poly[d(G-C)·d(G-C)], poly[d(A-G)·d(C-T)], poly[d(A-C)·d(G-T)], poly[d(A-T-C)·d(G-A-T)], and poly[d(A-G-C)·d(G-C-T)]. This basis set, applied according to the first-neighbor polymer procedure of Gray and Tinoco, allows a more uniformly accurate spectral analysis of six natural complex DNAs and eight (A+T)-rich satellite DNAs for base composition and first-neighbor frequencies than was previously possible. We find that spectra of poly[d(A)·d(T)] and/or poly[d(A-C-T-)·d(A-G-T)] are not generally required for good analysis results but we show in this and the following paper that these spectra are needed for the most accurate analyses of some satellite DNAs.     

The interpretation of process from pattern using two-dimensional spectral analysis: modelling single species patterns in vegetation

Two-dimensional spectral analyses of spatial patterns are made using (i) the autocorrelation function, (ii) the periodogram, and its polar summary (iii) the R-spectrum and (iv) the -spectrum. Together these give a sensitive analysis of both the complete range of scales of pattern and directional components which exist in data sets and we illustrate how the significance of observed spectral features can be assessed.We investigate the spatial pattern of Calluna vulgaris in a regenerating woodland and of Epilobium angustifolium spreading in a woodland following the thinning of trees. Evidence in the spectra is found for directional, clumping and inhibition patterns, and is discussed in relation to spectra obtained from simulations of known pattern generating processes. Hypotheses about the important biological, environmental and management influences on the structure of the communities are examined.We gratefully acknowledge the Swedish Coniferous Biome Project and Dr P. J. Diggle for access to the heather data.     

Affective state and acceptance of dentures in elderly patients

Objective : To examine the relationship between the affective state and acceptance of dentures by elderly patients. Setting : Dental Outpatient clinics and a residential home for the elderly. Bialystok, Poland. Design : Cross sectional survey of denture wearers. Subjects : One hundred and forty one patients between the ages of 60–94. Intervention : A semi-structured interview, which focused on the patient's self-evaluation of their affective state, and a clinical examination. Results : There was a trend for the negative affects (irritability, boredom, anger, loneliness, helplessness) to relate to denture intolerance and for the positive affects (joy, peace, usefulness) to relate to denture acceptance. Conclusions : Anger related significantly t o intolerance of upper and lower dentures. The relationship of age and gender to the acceptance of dentures in the present sample was not significant.     

OMWSA: detection of DNA repeats using moving window spectral analysis

Repetitive DNA sequences play paramount biological roles, such as gene variation and regulatory functions on gene expressions. Until now, detection of various kinds of DNA repeats accurately is still an open problem. In this article, we propose a new method and a visualization tool for detecting DNA repeats in a 2D plane of location and frequency by using optimized moving window spectral analysis. The spectrogram can display the general distribution of repetitive sequences while showing the repeat period, length and location without any prior knowledge. Experimental results demonstrate that our method is accurate and robust even under the condition of excessive mutating and interleaving. AVAILABILITY: Available on http://www.hy8.com/~tec/sw01/omwsa01.zip. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Short-window spectral analysis using AMVAR and multitaper methods: a comparison

We compare two popular methods for estimating the power spectrum from short data windows, namely the adaptive multivariate autoregressive (AMVAR) method and the multitaper method. By analyzing a simulated signal (embedded in a background Ornstein–Uhlenbeck noise process) we demonstrate that the AMVAR method performs better at detecting short bursts of oscillations compared to the multitaper method. However, both methods are immune to jitter in the temporal location of the signal. We also show that coherence can still be detected in noisy bivariate time series data by the AMVAR method even if the individual power spectra fail to show any peaks. Finally, using data from two monkeys performing a visuomotor pattern discrimination task, we demonstrate that the AMVAR method is better able to determine the termination of the beta oscillations when compared to the multitaper method.     

Testing the phylogeny of swordtail fishes using split decomposition and spectral analysis

We examine ways of testing for the reliability of inference from biological sequence data using sequences from Xiphophorus fishes and newly implemented methodology for sequence analysis. The approach we take provides one means to examine the fit between model and data for different sequences and hence to evaluate heterogeneity between data sets. In the case of the present study we show D-loop sequences to be a better molecule for studying the phylogeny of Xiphophorus fishes than cytochrome b sequences. The results of the split decomposition and spectral analysis confirm an earlier phylogenetic hypothesis which had been based on maximum parsimony, neighbor-joining, maximum likelihood analyses. Correspondence to: A. Meyer     

Automatic analysis of sleep using two parameters based on principal component analysis of electroencephalography spectral data

A computer program for the analysis of a sleep electroencephalogram (EEG) is presented. The method relies on two steps. First, a spectral analysis is performed for signals recorded from one or more electrode locations. Then, two EEG parameters are obtained by storing the spectral activity in a multidimensional space, whose dimension is reduced using principal component analysis (PCA) techniques. The main advantage of these parameters is in describing the process of sleep on a continuous scale as a function of time. Validation of the method was performed with the data collected from 16 subjects (8 young volunteers and 8 elderly insomniacs). Results snowed that the parameters correlate highly with the hypnograms established by conventional visual scoring. This signal parametrisation, however, offers more information regarding the time course of sleep, since small variations within individual sleep stages as well as smooth transitions between stages are assessed. Finally, the concurrent use of both parameters provides an original way of considering sleep as a dynamic process evolving cyclically in a single plane.     

Two-dimensional finite element analysis of stresses developed in the supporting tissues under complete dentures using teeth with different cusp angulations

Statement of problem: The selection of appropriate teeth for complete denture occlusion is very important for long‐term success, and adequate maintenance of the residual alveolar ridge. Purpose: The purpose of this study was to determine the stress generated underneath the complete denture by altering the cuspal angulations of the denture teeth. Material and methods: A two‐dimensional finite element model of a coronal section of maxillary and mandibular complete dentures, mucosa and alveolar bone in the first molar region was designed. The occlusal aspect of the denture teeth was altered to make 33°, 20°, 0° cuspal angulation. All the nodes at the bases of maxillary and mandibular alveolar bone of finite element analysis models were restrained in all directions. A functional occlusal load of 50 N was applied through the mandibular model base. To design these models and to analyse them, EMRC’s NISA II finite element analysis computer software was used. In these models, the elements were selected (a, b, c, d, e, f) in the region where it was necessary to determine the stresses generated in both the maxillary and mandibular portions. Results: The results were interpreted as Von Mises stresses and were observed in pre‐defined areas. The stress patterns observed within model with each type of posterior occlusion, showed unique variations as well as some similarities. Conclusion: Stresses of greater magnitude were observed in cuspal teeth, 33° and 20° respectively, where as 0° teeth showed a slightly less magnitude of stress generated.