Improved Combinatorial Group Testing Algorithms for Real-World Problem Sizes

We study practically efficient methods for performing combinatorial group testing. We present efficient non-adaptive and two-stage combinatorial group testing algorithms, which identify the at most d items out of a given set of n items that are defective, using fewer tests for all practical set sizes. For example, our two-stage algorithm matches the information theoretic lower bound for the number of tests in a combinatorial group testing regimen.Comment: 18 pages; an abbreviated version of this paper is to appear at the 9th Worksh. Algorithms and Data Structure

Improved Algorithms for Approximate String Matching (Extended Abstract)

The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants of the problem, including comparison of two strings, approximate pattern identification in a string or calculation of the longest common subsequence that two strings share. We designed an output sensitive algorithm solving the edit distance problem between two strings of lengths n and m respectively in time O((s-|n-m|)min(m,n,s)+m+n) and linear space, where s is the edit distance between the two strings. This worst-case time bound sets the quadratic factor of the algorithm independent of the longest string length and improves existing theoretical bounds for this problem. The implementation of our algorithm excels also in practice, especially in cases where the two strings compared differ significantly in length. Source code of our algorithm is available at http://www.cs.miami.edu/\~dimitris/edit_distanceComment: 10 page

Interaction of reed and acoustic resonator in clarinetlike systems

Sound emergence in clarinetlike instruments is investigated in terms of instability of the static regime. Various models of reed-bore coupling are considered, from the pioneering work of Wilson and Beavers ["Operating modes of the clarinet", J. Acoust. Soc. Am. 56, 653--658 (1974)] to more recent modeling including viscothermal bore losses and vena contracta at the reed inlet. The pressure threshold above which these models may oscillate as well as the frequency of oscillation at threshold are calculated. In addition to Wilson and Beavers' previous conclusions concerning the role of the reed damping in the selection of the register the instrument will play on, the influence of the reed motion induced flow is also emphasized, particularly its effect on playing frequencies, contributing to reduce discrepancies between Wilson and Beavers' experimental results and theory, despite discrepancies still remain concerning the pressure threshold. Finally, analytical approximations of the oscillating solution based on Fourier series expansion are obtained in the vicinity of the threshold of oscillation. This allows to emphasize the conditions which determine the nature of the bifurcation (direct or inverse) through which the note may emerge, with therefore important consequences on the musical playing performances

Comparative Methods for Gene Structure Prediction in Homologous Sequences

The increasing number of sequenced genomes motivates the use of evolutionary patterns to detect genes. We present a series of comparative methods for gene finding in homologous prokaryotic or eukaryotic sequences. Based on a model of legal genes and a similarity measure between genes, we find the pair of legal genes of maximum similarity. We develop methods based on genes models and alignment based similarity measures of increasing complexity, which take into account many details of real gene structures, e.g. the similarity of the proteins encoded by the exons. When using a similarity measure based on an exiting alignment, the methods run in linear time. When integrating the alignment and prediction process which allows for more fine grained similarity measures, the methods run in quadratic time. We evaluate the methods in a series of experiments on synthetic and real sequence data, which show that all methods are competitive but that taking the similarity of the encoded proteins into account really boost the performance

Iterated maps for clarinet-like systems

The dynamical equations of clarinet-like systems are known to be reducible to a non-linear iterated map within reasonable approximations. This leads to time oscillations that are represented by square signals, analogous to the Raman regime for string instruments. In this article, we study in more detail the properties of the corresponding non-linear iterations, with emphasis on the geometrical constructions that can be used to classify the various solutions (for instance with or without reed beating) as well as on the periodicity windows that occur within the chaotic region. In particular, we find a regime where period tripling occurs and examine the conditions for intermittency. We also show that, while the direct observation of the iteration function does not reveal much on the oscillation regime of the instrument, the graph of the high order iterates directly gives visible information on the oscillation regime (characterization of the number of period doubligs, chaotic behaviour, etc.)

Vortex nozzle interaction in solid rocket motors: A scaling law for upstream acoustic response

In solid rocket motors, vortex nozzle interactions can be a source of large-amplitude pressure pulsations. Using a two-dimensional frictionless flow model, a scaling law is deduced, which describes the magnitude of a pressure pulsation as being proportional to the product of the dynamic pressure of the upstream main flow and of vortex circu- lation. The scaling law was found to be valid for both an integrated noz- zle with surrounding cavity and a nozzle geometry without surrounding cavity that forms a right angle with the combustion chamber side wall. Deviations from the scaling law only occur when unrealistically strong circulations are considered

The Physicist's Guide to the Orchestra

An experimental study of strings, woodwinds (organ pipe, flute, clarinet, saxophone and recorder), and the voice was undertaken to illustrate the basic principles of sound production in music instruments. The setup used is simple and consists of common laboratory equipment. Although the canonical examples (standing wave on a string, in an open and closed pipe) are easily reproduced, they fail to explain the majority of the measurements. The reasons for these deviations are outlined and discussed.Comment: 11 pages, 10 figures (jpg files). Submitted to European Journal of Physic

Women with polycystic ovary syndrome present with altered endometrial expression of stanniocalcin-1

Stanniocalcin-1 (STC-1) is a pro-survival factor that protects tissues against stressors, such as hypoxia and inflammation. STC-1 is co-expressed with the endometrial receptivity markers, and recently endometrial STC-1 was reported to be dysregulated in endometriosis, a condition linked with endometrial progesterone resistance and inflammation. These features are also common in the endometrium in women with polycystic ovary syndrome (PCOS), the most common endocrine disorder in women. Given that women with PCOS present with subfertility, pregnancy complications, and increased risk for endometrial cancer, we investigated endometrial STC-1 expression in affected women. Endometrial biopsy samples were obtained from women with PCOS and controls, including samples from overweight/obese women with PCOS before and after a 3-month lifestyle intervention. A total of 98 PCOS and 85 control samples were used in immunohistochemistry, reverse-transcription polymerase chain reaction, or in vitro cell culture. STC-1 expression was analyzed at different cycle phases and in endometrial stromal cells (eSCs) after steroid hormone exposure. The eSCs were also challenged with 8-bromo-cAMP and hypoxia for STC-1 expression. The findings indicate that STC-1 expression is not steroid hormone mediated although secretory-phase STC-1 expression was blunted in PCOS. Lower expression seems to be related to attenuated STC-1 response to stressors in PCOS eSCs, shown as downregulation of protein kinase A activity. The 3-month lifestyle intervention did not restore STC-1 expression in PCOS endometrium. More studies are warranted to further elucidate the mechanisms behind the altered endometrial STC-1 expression and rescue mechanism in the PCOS endometrium. Summary sentence Endometrial expression of STC-1 in the secretory phase is blunted in women with PCOS, suggesting impaired protection against stress.Peer reviewe

Speaker-independent emotion recognition exploiting a psychologically-inspired binary cascade classification schema

In this paper, a psychologically-inspired binary cascade classification schema is proposed for speech emotion recognition. Performance is enhanced because commonly confused pairs of emotions are distinguishable from one another. Extracted features are related to statistics of pitch, formants, and energy contours, as well as spectrum, cepstrum, perceptual and temporal features, autocorrelation, MPEG-7 descriptors, Fujisakis model parameters, voice quality, jitter, and shimmer. Selected features are fed as input to K nearest neighborhood classifier and to support vector machines. Two kernels are tested for the latter: Linear and Gaussian radial basis function. The recently proposed speaker-independent experimental protocol is tested on the Berlin emotional speech database for each gender separately. The best emotion recognition accuracy, achieved by support vector machines with linear kernel, equals 87.7%, outperforming state-of-the-art approaches. Statistical analysis is first carried out with respect to the classifiers error rates and then to evaluate the information expressed by the classifiers confusion matrices. © Springer Science+Business Media, LLC 2011