A Non-local Topology-Preserving Segmentation-Guided Registration Model

In this paper, we address the issue of designing a theoretically well-motivated segmentation-guided registration method capable of handling large and smooth deformations. The shapes to be matched are viewed as hyperelastic materials and more precisely as Saint Venant–Kirchhoff ones and are implicitly modeled by level set functions. These are driven in order to minimize a functional containing both a nonlinear-elasticity-based regularizer prescribing the nature of the deformation, and a criterion that forces the evolving shape to match intermediate topology-preserving segmentation results. Theoretical results encompassing existence of minimizers, existence of a weak viscosity solution of the related evolution problem and asymptotic results are given. The study is then complemented by the derivation of the discrete counterparts of the asymptotic results provided in the continuous domain. Both a pure quadratic penalization method and an augmented Lagrangian technique (involving a related dual problem) are investigated with convergence results.     

DNA damage detection technique applying time-resolved fluorescence measurements

A novel DNA damage detection technique based on the characteristic fluorescence lifetimes exhibited by Pico-Green-single-stranded DNA and -double-stranded DNA complexes is employed to establish the damage produced on DNA isolated from sheep white blood cells following gamma radiation. This technique, which incorporates key concepts such as alkaline unwinding buffers and higher unwinding rates of damaged DNA compared to undamaged DNA, allows for the differentiation of DNA damage resulting from doses of gamma radiation in the 0-100-Gy range, with the potential of analyzing samples consisting of as little as 10(4) cells. Experiments were carried out using commercial DNA sources as well as DNA isolated from sheep white blood cells, suggesting its potential for use with isolated DNA from virtually any eukaryotic cell.     

LZgrep: a Boyer–Moore string matching tool for Ziv–Lempel compressed text

We present a Boyer–Moore (BM) approach to string matching over LZ78 and LZW compressed text. The idea is to search the text directly in compressed form instead of decompressing and then searching it. We modify the BM approach so as to skip text using the characters explicitly represented in the LZ78/LZW formats, modifying the basic technique where the algorithm can choose which characters to inspect. We present and compare several solutions for single and multipattern searches. We show that our algorithms obtain speedups of up to 50% compared to the simple decompress‐then‐search approach. Finally, we present a public tool, LZgrep, which uses our algorithms to offer grep‐like capabilities directly searching files compressed using Unix's Compress, a LZW compressor. LZgrep can also search files compressed with Unix gzip, using new decompress‐then‐search techniques we develop, which are faster than the current tools. This way, users can always keep their files in compressed form and still search them, uncompressing only when they want to see them. Copyright © 2005 John Wiley & Sons, Ltd.     

Switching class labels to generate classification ensembles

Ensembles that combine the decisions of classifiers generated by using perturbed versions of the training set where the classes of the training examples are randomly switched can produce a significant error reduction, provided that large numbers of units and high class switching rates are used. The classifiers generated by this procedure have statistically uncorrelated errors in the training set. Hence, the ensembles they form exhibit a similar dependence of the training error on ensemble size, independently of the classification problem. In particular, for binary classification problems, the classification performance of the ensemble on the training data can be analysed in terms of a Bernoulli process. Experiments on several UCI datasets demonstrate the improvements in classification accuracy that can be obtained using these class-switching ensembles.     

Searching in metric spaces by spatial approximation

We propose a new data structure to search in metric spaces. A metric space is formed by a collection of objects and a distance function defined among them which satisfies the triangle inequality. The goal is, given a set of objects and a query, retrieve those objects close enough to the query. The complexity measure is the number of distances computed to achieve this goal. Our data structure, called sa-tree (“spatial approximation tree”), is based on approaching the searched objects spatially, that is, getting closer and closer to them, rather than the classic divide-and-conquer approach of other data structures. We analyze our method and show that the number of distance evaluations to search among n objects is sublinear. We show experimentally that the sa-tree is the best existing technique when the metric space is hard to search or the query has low selectivity. These are the most important unsolved cases in real applications. As a practical advantage, our data structure is one of the few that does not need to tune parameters, which makes it appealing for use by non-experts. Edited by R. Sacks-Davis Received: 17 April 2001 / Accepted: 24 January 2002 / Published online: 14 May 2002     

Effective bandwidth estimation and testing for Markov sources

This work addresses the resource sharing problem in broadband communication networks that can guarantee some quality of service (QoS), and develops some results about data source and traffic modelling, especially in aspects of model testing and parameter estimation. The multiplexing of variable bit rate (VBR) sources poses a mathematical and statistical problem: the estimation of the resource requirements of a source or set of sources. The estimation method shall be simple enough to be practically implemented in the connection acceptance control (CAC) function.

In this paper, the VBR video sources are taken as a typical case of variable rate, with real-time constraints. This association of requirements makes the case especially interesting. A Markov model is assumed for the VBR sources. The validity of such models is under research; they seem to be appropriate at least in certain time scales. The model is tested against real video traces. In order to estimate the resource allocation or “channel occupation” of each source, the concept of equivalent bandwidth proposed by Kelly [Notes on effective bandwidth, in: F.P. Kelly, S. Zachary, I.B. Ziedins (Eds.), Stochastic Networks: Theory and Applications, Oxford University Press, Oxford, 1996, pp. 141] is used; it is based on a consistent mathematical theory, and has proven to be robust and useful for technical applications.

A calculation of the equivalent bandwidth of a Markov source, given its parameters, can be found in the literature [IEEE ACM Trans. Networking 1 (4) (1993) 424]. But in fact, one can only estimate model and parameters. In this work, an estimation of the equivalent bandwidth is given, which can be obtained from real data. The convergence and the consistency of the estimation are studied, and practical bounds are found. Illustrative calculations are performed from real video traces that were obtained using a software MPEG coder, developed by the authors. The mathematical and statistical results are valid for whatever phenomenon that can be modelled as a Markov process.     

Hemodynamic changes in patients developing effective hypovolemia after total paracentesis

BACKGROUND/AIMS: In many centers paracentesis is considered the treatment of choice for tense ascites. However, the mechanism of effective hypovolemia after paracentesis, the main complication associated with this procedure, remains unknown. In the current study, systemic hemodynamics was sequentially studied before and after total paracentesis in 46 patients with cirrhosis and tense ascites. The aim of the study was to assess the mechanism of effective hypovolemia after paracentesis. METHODS: Plasma renin activity and aldosterone, mean arterial pressure, cardiac output (ECO-Doppler) and systemic vascular resistance were measured before, and 3 h, 6 h and 6 days after total paracentesis associated with plasma volume expansion. RESULTS: Effective hypovolemia after paracentesis (defined as 50% increase in plasma renin activity up to a level over 4 ng x m(-1) x h(-1) at the 6th day after paracentesis) occurred in 20 cases [plasma renin activity increased from 8+/-17 to 19+/-2.7 ng x m(-1) x h(-1)]. In the remaining 26 cases no changes in plasma renin activity [8.5+/-2.4 vs. 8.7+/-2.2 ng x m(-1) x h(-1)] were observed. The amounts of ascitic fluid volume removed were similar. Effective hypovolemia after paracentesis was associated with a significant decrease in mean arterial pressure (89+/-2 vs. 81+/-3 mmHg) and systemic vascular resistance [1263+/-67 vs. 1014+/-80 dyn x s(-1) x cm(-5)] 6 days after treatment. In contrast, no significant changes in these parameters were observed in patients not developing this complication. In the whole group of patients a significant inverse relation was observed between changes in plasma renin activity and in systemic vascular resistance (r=0.74;p< 0.001). CONCLUSIONS: These results indicate that effective hypovolemia after paracentesis in cirrhosis is predominantly due to an accentuation of the arteriolar vasodilation already present in these patients.     

Detection and Discrimination of Conspecific Scents by the Anguid Slow-Worm Anguis fragilis

We tested the ability of male slow-worms, Anguis fragilis, a limbless anguid lizard with secretive, semifossorial habits, to detect chemical associated with conspecifics by using a T-maze in the laboratory. Male slow-worms discriminated conspecific male and female scent deposits. Males selected the arm with female scent, suggesting that scent deposits may be used to locate potential mates. Also, male slow-worms did not avoid the chemicals of other males, suggesting that they are not territorial. However, males discriminated their own scent from those of other males, and spent more time exploring the arm with other male scent, which suggests that scent marks may bear information that could be used in future intrasexual social contexts. We conclude that discrimination of conspecifics based on scents may be more widespread than previously expected among lizards inhabiting visually restricted environments.     

Heavy metal bioaccumulation and macroinvertebrate community changes in a Mediterranean stream affected by acid mine drainage and an accidental spill (Guadiamar River, SW Spain)

In the 1998 Aznalcóllar mining accident, 5 million cubic meters of toxic waste were spilled into the Guadiamar River (SW Spain). This paper describes the likely effects of metal pollution on the macroinvertebrate community in the first 15 km of the river adjacent to the mine, 2 years after the spill. The contents of Zn, Cu, Pb, As, Cd, Tl, and Sb in water, sediment, and in the caddisfly Hydropsyche were analysed, together with some physico-chemical parameters. From the results of physico-chemical and community parameters, the studied area was divided into three sections: the first section contained upstream control stations, not affected by current mining activities, and with a diverse macroinvertebrate community structure (mean number of families = 19); the second section, close to the mine, was severely polluted, with more than 50 mg l(-1) of Zn or 1.6 mg l(-1) of Cu in water, a pH of nearly 4, and a very diminished macroinvertebrate community (three families); in the last section, 6-15 km downstream from the mine, the water quality improved, metal concentrations decreased, pH reached neutrality and the macroinvertebrate community comprised eight families. We also determined metal concentrations in the larvae of Hydropsyche and found increases of 3- to 35-fold (for Cu and Cd, respectively) compared to control sites. As far as we are aware, these values are the highest concentrations so far detected in this caddisfly anywhere in the world. Different patterns of metal and pH tolerance were identified in macroinvertebrates. Most of the species were intolerant to present pollution levels and were only present in control sites. Others were tolerant to metal pollution but not to low pH and were present in the main river downstream of the mine, while a very few species managed to live in the most polluted section, with very low pH and high metal concentrations.