bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulators Encoded in the
Escherichia coli
Type III Secretion System 2 Gene Cluster Influence Expression of Genes within the Locus for Enterocyte Effacement in Enterohemorrhagic
E. coli
O157:H7
Authors: Zhang Lihong , Chaudhuri Roy R. , Constantinidou Chrystala , Hobman Jon L. , Patel Mala D. , Jones Antony C. , Sarti Donatella , Roe Andrew J. , Vlisidou Isabella , Shaw Robert K. , Falciani Francesco , Stevens Mark P. , Gally David L. , Knutton Stuart , Frankel Gad , Penn Charles W. , Pallen Mark J. 
Published: November 2004

ABSTRACT

Enterohemorrhagic
Escherichia coli
(EHEC) O157:H7 subverts host cells through a type III secretion system encoded by the locus for enterocyte effacement (LEE). Genome sequencing of this pathotype revealed the existence of a gene cluster encoding components of a second cryptic type III secretion system,
E. coli
type III secretion system 2 (ETT2). Recently, we showed that the ETT2 gene cluster is present in whole or in part in the majority of
E. coli
strains but is unable to encode a functional secretion system in most strains, including EHEC O157:H7. However, here we show that mutational inhibition of two regulatory genes (ECs3720 or
etrA
and ECs3734 or
eivF
) from the ETT2 cluster in EHEC O157:H7 leads to greatly increased secretion of proteins encoded by the LEE and to increased adhesion to human intestinal cells. Studies in which transcriptional fusions and microarrays were used indicated that EtrA and EivF exert profound negative effects on gene transcription within the LEE. Consistent with these observations, expression of these regulators in an EHEC O26:H- strain led to suppression of protein secretion under LEE-inducing conditions. These findings provide fresh examples of the influence of mobile genetic elements on regulation of the LEE and of cross talk between type III secretion system gene clusters. In addition, they provide a cautionary tale because they show that the effects of regulatory genes can outlive widespread decay of other genes in a functionally coherent gene cluster, a phenomenon that we have named the “Cheshire cat effect.” It also seems likely that variations in the ETT2 regulator repertoire might account for strain-to-strain variation in secretion of LEE-encoded proteins.
In Vitro Model of
Bartonella henselae
-Induced Angiogenesis
Authors: Kirby James E. 
Published: November 2004

ABSTRACT

Bartonella henselae
is a gram-negative pathogen that causes angiogenesis. Here, I establish in vitro models to study
Bartonella
-induced blood vessel formation. I found that
B. henselae
induces long-term endothelial survival and tubular differentiation within type I collagen matrix.
Acellular Pertussis Vaccines and Complement Killing ofBordetella pertussis
Authors: Weiss Alison A. , Patton Angela K. , Millen Scott H. , Chang Swei-Ju , Ward Joel I. , Bernstein David I. 
Published: November 2004

ABSTRACTAntibody-dependent complement killing ofBordetella pertussisafter immunization with a three-component acellular pertussis vaccine was characterized. Postimmunization activity was unchanged for about half of the adult vaccine recipients. The responses of the other individuals were complex, with evidence of both beneficial and antagonistic responses occurring, sometimes in the same individual.
Effect of Inactivation of the HtrA-Like Serine Protease DegQ on the Virulence of
Salmonella enterica
Serovar Typhimurium in Mice
Authors: Farn Jacinta , Roberts Mark 
Published: November 2004

ABSTRACT

DegQ is a serine protease that is highly homologous to HtrA, an important virulence determinant of
Salmonella enterica
serovar Typhimurium. We examined if DegQ is involved in serovar Typhimurium pathogenesis. A serovar Typhimurium
degQ
mutant was as virulent as the wild-type strain in mice. However, a serovar Typhimurium
htrA degQ
mutant survived less well in murine organs, particularly in the liver, than a serovar Typhimurium
htrA
mutant. DegQ is not essential for serovar Typhimurium pathogenesis but may play a small role during salmonella growth at systemic sites.
AVERAGE MEASURE, DESCRIPTIVE COMPLEXITY AND APPROXIMATION OF MAXIMIZATION PROBLEMS
Authors: CRESCENZI PIERLUIGI , SILVESTRI RICCARDO 
Published: November 2004

In this paper, we study a simple combinatorial property of maximization problems and we establish some interesting connections between such a property and the class [Formula: see text] defined by Papadimitriou and Yannakakis. In particular, we first prove that any maximization problem in [Formula: see text] has guaranteed average measure, that is, the average measure of the feasible solutions is no less than a constant fraction of the optimum measure (this intuitively justifies the fact that any problem in [Formula: see text] is approximable). Successively, we prove that there exist maximization problems that do not belong to [Formula: see text] but still have guaranteed average measure. Hence, such a property does not characterize the class [Formula: see text]. Finally, we show that there are several maximization problems which do not have guaranteed average measure and, hence, do not belong to [Formula: see text]. In this context, the notion of a problem with guaranteed average measure seems to be a powerful and very easy-to-use tool that allows us to prove that optimization problems are not in [Formula: see text].
RECENT ADVANCES ON TECHNIQUES OF STATIC FEEDFORWARD NETWORKS WITH SUPERVISED LEARNING
Authors: XU LEI , KLASA STAN , YUILLE ALAN 
Published: November 2004

The rediscovery and popularization of the backpropagation training technique for multilayer perceptrons as well as the invention of the Boltzmann machine learning algorithm has given a new boost to the study on supervised learning networks. In recent years, besides widely spread applications and various further improvements of the classical backpropagation technique, many new supervised learning models, techniques as well as theories, have also been proposed in a vast number of publications. This paper tries to give a rather systematic review on the recent advances on supervised learning techniques and models for static feedforward networks. We summarize a great number of developments into four aspects: (1) Various improvements and variants made on the classical backpropagation techniques for Multilayer(static) perceptron nets, for speeding up training, avoiding local minima, increasing the generalization ability as well as for many other interesting purposes. (2) A number of other learning methods for training multilayer (static) perceptron, such as derivative estimation by perturbation, direct weight update by perturbation, genetic algorithms, recursive least square estimate and extended Kalman filters, linear programming, the policy of fixing one layer while updating another, constructing networks by converting decision tree classifiers and others. (3) Various other feedforward models which are also able to implement function approximation, probability density estimation and classification, including various models of basis function expansion (e.g. radial basis functions, restricted coulomb energy, multivariate adaptive regression splines, trigonometric and polynomial bases, projection pursuit, basis function tree and many others) and several other supervised learning models. (4) Models with complex structures, e.g. modular architecture, hierarchy architecture and others. Altogether, we try to give a global picture of the present state of supervised learning techniques (not including all the theoretical developments) for training static feedforward networks.
CHARACTERIZATION OF ROAD-SIDE AEROSOLS BY PIXE AND SEM-EDX ANALYSIS
Authors: KASAHARA M. , SHINODA K. , TAKAHASHI K. , YOSHIDA K. 
Published: November 2004

The characteristics of the road-side particles were examined. The elemental concentrations of aerosol particle collected on the road-side were measured both by PIXE analysis as a bulk sample and SEM-EDX analysis as individual particle sample. For the data set of SEM-EDX, cluster analysis was applied. On an average, more than 80% of the aerosol particles are consisted of lighter elements such as C, O, N and H. Main metal components contained in the roadside particles were Si, Ca, Fe and Al that were mainly originated in soil.
AN MIN-BASED ARCHITECTURE FOR RECONFIGURABLE DE BRUIJN STRUCTURES
Authors: SRINIVAS S. , THULASIRAMAN K. , SWAMY M.N.S. 
Published: November 2004

This paper presents a novel parallel architecture based on a multistage interconnection network (MIN) for reconfigurable binary de Bruijn structures. The proposed architecture is able to assume distinct binary de Bruijn configurations (BDCs), where each configuration has the geometric pattern or structure as that of a binary de Bruijn graph. A system with N nodes or processing elements can generate N2/4 distinct BDCs. The novelty of the architecture is in the design of the switching network for interconnecting the nodes. The switching network adopted is an augmented shuffle-exchange MIN. The favorable features of the architecture include fast reconfiguration, simplified hardware in the MIN, absence of the need for reconfiguration hardware in the nodes, and simple routine control. The generation of BDCs is derived from an equation, called the Reconfiguration Equation, which is based on simple logical operations and defines the necessary interconnections among the nodes. It is shown that the architecture assumes interconnections according to this equation and consequently the proof of reconfiguration is given. The important properties of the reconfigurable de Bruijn structure are outlined. Finally, two features which are useful in enhancing the reconfigurability of the architecture are discussed. First, it is proved that the architecture can be augmented to generate partitioned de Bruijn configurations. Second, it is shown that the architecture can assume distinct binary tree configurations by a simple modification.
ALGORITHMS FOR MONTE CARLO SIMULATIONS OF THE ISING MODELS ON A SIMPLE CUBIC LATTICE
Authors: KAWASHIMA NAOKI , ITO NOBUYASU , KANADA YASUMASA 
Published: November 2004

The vectorized Monte Carlo algorithm by multi-spin coding is extended to the ±J Ising spin glass model on a simple cubic lattice in a magnetic field. Explicit logical expression is given for this algorithm. In addition, shorter logical expressions are found in some special cases. They are given for the heat-bath method under the general condition and for the Metropolis method under the condition, H = 0.
DIMENSIONAL REGULARIZATION IN THE 1/N EXPANSION
Authors: CAMPOSTRINI MASSIMO , ROSSI PAOLO 
Published: November 2004

Two classes of renormalizable 1/N expandable two-dimensional models are analyzed to O(1/N) and the asymptotic behavior of the renormalized two-point functions is nonperturbatively evaluated. These results are taken as a benchmark to study the applicability of dimensional regularization and perturbative minimal subtraction renormalization to the context of the 1/N expansion. Perturbation theory is applied to O(1/N) diagrams to all orders in the weak coupling constant and, after resummation, the same finite renormalization group invariant asymptotic amplitudes are obtained. As a byproduct, the O(1/N) contributions to renormalization group Z functions in the minimal subtraction scheme are extracted and the critical index η is evaluated and compared to previous nonperturbative results, finding complete agreement. The appendix is devoted to the extension of these results to a supersymmetric version of the models.
HEADS, EYES AND HEAD-EYE SYSTEMS
Authors: PAHLAVAN KOUROSH , EKLUNDH JAN-OLOF 
Published: November 2004

Active vision systems can be considered as systems that integrate visual sensing and action. Sensing includes detection of actions/events and results also in specific actions/manipulations. This paper mainly addresses the basic issues in the design of a head-eye system for the study of active-purposive vision. The design complexity of such a head is defined by the activeness of the visual system. Although we have not had the motivation to exactly reproduce the biological solutions in a robot, we claim that the designer should carefully consider the solutions offered by evolution. The flexibility of the behavioral pattern of the system is constrained by the mechanical structure and the computational architecture used in the control system of the head. The purpose of the paper is to describe the mechanical structure as well as the computational architecture of the KTH-head from this perspective.
MULTI-MODULAR NEURAL NETWORK ARCHITECTURES: APPLICATIONS IN OPTICAL CHARACTER AND HUMAN FACE RECOGNITION
Authors: SOULIE FRANÇOISE FOGELMAN , VIENNET EMMANUEL , LAMY BERTRAND 
Published: November 2004

In practical applications, recognition accuracy is sometimes not the only criterion; capability to reject erroneous patterns might also be needed. We show that there is a trade-off between these two properties. An efficient solution to this trade-off is brought about by the use of different algorithms implemented in various modules, i.e. multi-modular architectures. We present a general mechanism for designing and training multi-modular architectures, integrating various neural networks into a unique pattern recognition system, which is globally trained. It is possible to realize, within the system, feature extraction and recognition in successive modules which are cooperatively trained. We discuss various rejection criteria for neural networks and multi-modular architectures. We then give two examples of such systems, study their rejection capabilities and show how to use them for segmentation. In handwritten optical character recognition, our system achieves performances at state-of-the-art level, but is eight times faster. In human face recognition, our system is intended to work in the real world.
APPLICATION OF GLOBAL METHODS FOR ANALYZING DYNAMICAL SYSTEMS TO SHIP ROLLING MOTION AND CAPSIZING
Authors: FALZARANO JEFFREY M. , SHAW STEVEN W. , TROESCH ARMIN W. 
Published: November 2004

Ship capsizing is a highly nonlinear dynamic phenomenon where global system behavior is dominant. However the industry standards for analysis are limited to linear dynamics or nonlinear statics. Until recently, most nonlinear dynamic analysis relied upon perturbation methods which are severely restricted both with respect to the relative size of the nonlinearity and the region of consideration in the phase space (i.e., they are usually restricted to a small local region about a single equilibrium), or on numerical studies of idealized system models. In this work, recently developed global analysis techniques (e.g., those found in Guckenheimer and Holmes [1986], and Wiggins [1988, 1990]) are used to study transient rolling motions of a small ship which is subjected to a periodic wave excitation. This analysis is based on determining criteria which can predict the qualitative nature of the invariant manifolds which represent the boundary between safe and unsafe initial conditions, and how these depend on system parameters for a specific ship model. Of particular interest is the transition which this boundary makes from regular to fractal, implying a loss in predictability of the ship’s eventual state. In this paper, actual ship data is used in the development of the model and the effects of various ship and wave parameters on this transition are investigated. Finally, lobe dynamics are used to demonstrate how unpredictable capsizing can occur.
SIMULTANEOUS CONTAINMENT OF SEVERAL POLYGONS: ANALYSIS OF THE CONTACT CONFIGURATIONS
Authors: DEVILLERS OLIVIER 
Published: November 2004

The main concern of this paper is the detection of double contact configurations for some polygons moving in translation in a polygonal environment. We first establish some general properties about such configurations and give conditions of existence of double contacts for two or three objects. For three convex polygons moving in a polygonal environment or three simple polygons moving in a rectangle there always exists a double contact. Two examples without possibility of double contacts are given, one with three polygons (not convex) moving in a polygonal environment, and one with four convex polygons moving in a rectangle. We deduce an algorithm detecting a double contact position in time O(n2) (resp. O(n3)) for two (resp. three) convex polygons of constant sizes moving in a non-convex polygon of size n.
FACTORED ARC CONSISTENCY FOR RETE MATCH
Authors: PERLIN MARK W. 
Published: November 2004

RETE match for production systems and Arc Consistency (AC) filtering are two efficient AI algorithms that are designed for particular constraint satisfaction problems (CSP). Interestingly, it is possible to integrate the two within a common framework, and provide RETE with the lookahead advantages of AC. Unfortunately, the resulting quadratic dependence of AC on working memory (WM) size precludes the application of AC to RETE, since RETE responds to incremental changes in WM. Recent results in AC graph factorization, however, reduce the quadratic dependence to just linear for certain classes of problems, including RETE. In this paper, we present RETE and AC within the unified framework of Call-Graph Caching (CGC) evaluation. We describe factored arc consistency (FAC) and its use in an integrated FAC/RETE algorithm that provides RETE match with AC lookahead. We discuss our implementations, promising initial empirical results, and explore FAC/RETE’s applicability conditions and extensions. We conclude that incorporating factored AC into RETE match is an interesting and potentially useful application of arc consistency methods to the RETE CSP.
THE MACHINE LEARNING TOOLBOX CONSULTANT
Authors: GRANER NICOLAS , SHARMA SUNIL , SLEEMAN D. , RISSAKIS MICHALIS , CRAW SUSAN , MOORE CHRIS 
Published: November 2004

The Machine Learning Toolbox contains a set of ten Machine Learning algorithms, integrated with a common interface and common knowledge representation language. An essential component of the Toolbox is the Consultant, a knowledge-based system that advises novice users about which algorithm they could use for a particular application. We show how the Consultant’s architecture evolved, through its successive implementations, from a rigid rule-based expert system to a flexible information browsing system supporting user experimentation. In particular, we show how a task description can be elicited from the user in three different modes and exploited by several functions to provide advice and explanations at various levels of detail. The system’s output also increased in sophistication: initially limited to the recommendation of a suitable algorithm, it now includes detailed information about the algorithm and its usage, and will be extended to help the user interpret and improve the results of learning.
A LOGICAL FRAMEWORK FOR CONCEPT LEARNING WITH BACKGROUND KNOWLEDGE
Authors: KOUNALIS EMMANUEL , RUSINOWITCH MICHAEL 
Published: November 2004

A central process in many kinds of learning is the process of generalization or concept learning from a set of training instances (a set of examples and counterexamples) in the presence of some Background Knowledge. Given a set of examples and counterexamples of a concept, the learner induces a general concept that describes all of the positive examples and none of the counterexamples, and is consistent with the Background Knowledge. We present here a logical framework to induce concept descriptions from a given set of examples and counterexamples in the presence of Background Knowledge described by a set of Horn clauses. In particular, we provide: 1) a definition of what is meant by “a learnable concept” from examples and counterexamples in the presence of Background Knowledge described by a set H of Horn clauses”. Broadly speaking, in our framework, a learnable concept C is an atom which is true (valid) in the least Herbrand model of H but false in some other models of H and, 2) a methodology to induce general concept descriptions from concept examples and counterexamples in Horn theories. We give an automatic method, based on a well-founded ordering on the elements of H, which is the basis for checking validity in the least Herbrand model of H. This work generalizes, unifies, and provides a logical framework of previous studies on the concept-learning-from-examples paradigm.
THEORETICAL STUDY BY MEANS OF COMPUTER SIMULATION OF CONDITIONS IN WHICH EXTRASYSTOLES CAN TRIGGER VENTRICULAR FIBRILLATION. VALIDATION BY EPICARDIAL MAPPINGS
Authors: BARDOU ALAIN L. , AUGER PIERRE M. , CARDINAL RENÉ , DUMÉE PHILIPPE , BIRKUI PIERRE J. , EUW DOMINIQUE VON , GOVAERE MARIE-CLAUDE 
Published: November 2004

A cellular automata model of ventricular activation wave propagation has been developed in order to study the mechanisms of ventricular fibrillation induction. A 256X256 matrix is used to simulate a muscle layer in the ventricular wall. Huyghens’ construction method is used in order to compute the wave front position instant by instant. In this work, this model is specifically applied to the study of relationships between extrasystoles and sudden cardiac death. This theoretical study shows that if a ventricular extrasystole is initiated in contiguity of transitory block zone, it immediately initiates a rotating wave invading the entire myocardium, this rotating wave being self-sustained and not spontaneously reversible. Experimental validation derived from cardiac mapping experiments performed in canine preparations of myocardial infarction showed that an extrasystole induced by electrical stimulation in the neighbourhood of zone of temporary block induced by lidocaine is able to trigger a reentry phenomenon similar to that obtained with the computer model. These results provide evidence that transient fluctuations in refractoriness is a major risk factor when combined with ventricular extrasystole. Furthermore, it appears that this risk factor may be amplified under ischemic conditions and pharmacologic interventions aimed at suppressing ventricular extrasystoles (e.g., lidocaine).
Book Reviews
Authors: Mooney James 
Published: November 2004

Book reviewed in this article:Bibliothek auserwählten serbischer Meisterwerke, mit literarhistorischen Einleitungen. Herausgegeben von Dr Friedrich S. Krauss.Band V —Die Blume von Cannosa.— Mater Dolorosa: Zwei Novellen von Vid Vuletiĉ Vukasoviĉ, Band VI —Liebe und Leben im Her‐zogland—Zwölf Erzählungen von SvetozarĈoroviĉ.
BOOK REVIEWS
Authors: Kroeber A. L. 
Published: November 2004

Book reviewed in this article:SOUTH AMERICA: Los Principios de la Civilizacion en la Sierra Peruana. Max Uhle.SOUTH AMERICA: Origines Centroamericanos. Max Uhle. (IbidSOUTH AMERICA: Influencias Mayas en el Alto Ecuador. Max Uhle. (IbidSOUTH AMERICA: Los Principios de las Antiguas Civilizaciones Peruanas. Max Uhle.SOUTH AMERICA: Fundamentos Etnicos y Arqueología de Arica y Tacna. Max Uhle.Civilizaciones Mayoides de la Costa Pacifica de Sudamérica. Max Uhle. (Ibid.
Book Reviews
Authors: Tozzer Alfred M. 
Published: November 2004

Book reviewed in this article:MEXICO, CENTRAL AND SOUTH AMERICA: Excavations at Zacatenco. George C. Vaillant.MEXICO, CENTRAL AND SOUTH AMERICA: Excavations at Ticoman. George C. Vaillant. (Same series, Vol. 32, Part 2, 1931.)MEXICO, CENTRAL AND SOUTH AMERICA: Excavations at Gualupita. Suzannah B. and George C. Vaillant. (Same series, Vol. 35, Part 1, 1934.)MEXICO, CENTRAL AND SOUTH AMERICA: Excavations at El Arbolillo. George C. Vaillant. (Same series, Vol. 35, Part 2, 1935.)MEXICO, CENTRAL AND SOUTH AMERICA: Early Cultures in the Valley of Mexico: Results of the Stratigraphical Project of the American Museum of Natural History in the Valley of Mexico, 1928–1933. George C. Vaillant. (Same series, Vol. 35, Part 3, 1935.)