bluuebunny/crossref_metadata_2025 huggingface dataset:
Induction of Cationic Chicken Liver-Expressed Antimicrobial Peptide 2 in Response to
Salmonella enterica
Infection
Authors: Townes Claire L. , Michailidis Georgios , Nile Christopher J. , Hall Judith
Published: November 2004

Cationic antimicrobial peptides constitute part of the innate immune system and provide an essential role in the defense against infection. At present there is a paucity of information regarding the antimicrobial profile of the chicken (
Gallus gallus
). Using in silico studies, an expressed sequence tag (EST) clone was identified which encodes a novel cationic antimicrobial peptide, chicken liver-expressed antimicrobial peptide 2 (cLEAP-2). The predicted amino acid sequence composed a prepropeptide, and the active peptide contained four conserved cysteine amino acids. The gene was localized to chromosome 13, and analysis of the genome revealed three exons separated by two introns. The cLEAP-2 gene was expressed in a number of chicken epithelial tissues including the small intestine, liver, lung, and kidney. Northern analysis identified liver-specific cLEAP-2 splice variants, suggesting some degree of tissue-specific regulation. To investigate whether cLEAP-2 expression was constitutive or induced in response to microbial infection, 4-day-old birds were orally infected with
Salmonella
. Analyses of cLEAP-2 expression by semiquantitative reverse transcription-PCR indicated that cLEAP-2 mRNA was upregulated significantly in the small intestinal tissues and the liver, indicative of direct and systemic responses. The antimicrobial activity of cLEAP-2 against
Salmonella
was analyzed in vitro with a time-kill assay and recombinant cLEAP-2. Interestingly
Salmonella enterica
serovar Typhimurium SL1344 showed increased susceptibility to the active cationic peptide (amino acids 37 to 76) compared to
S. enterica
serovar Typhimurium C5 and
Salmonella enteritidis
. Taken together, these data suggest that cationic cLEAP-2 is part of the innate host defense mechanisms of the chicken.
Rhodococcus equi
-Infected Macrophages Are Recognized and Killed by CD8
+
T Lymphocytes in a Major Histocompatibility Complex Class I-Unrestricted Fashion
Authors: Patton Kristin M. , McGuire Travis C. , Fraser Darrilyn G. , Hines Stephen A.
Published: November 2004

The goal of this research was to examine the role of cytotoxic T lymphocytes (CTL) in the control of
Rhodococcus equi
and specifically to determine if
R. equi
-specific CD8
+
CTL occurred in the blood of immune horses. Equine peripheral blood mononuclear cells stimulated with antigen-presenting cells either infected with
R. equi
or exposed to soluble
R. equi
antigen lysed
R. equi
-infected target cells. Lysis was decreased to background by depletion of either CD2
+
or CD3
+
cells, indicating that the effector cell had a T-lymphocyte, but not NK cell, phenotype. Stimulation induced an increased percentage of CD8
+
T cells in the effector population, and depletion of CD8
+
T cells resulted in significantly decreased lysis of infected targets. Killing of
R. equi
-infected macrophages by effector cells was equally effective against autologous and equine leukocyte antigen A (classical major histocompatibility complex [MHC] class I) mismatched targets. To evaluate potential target antigens, target cells were infected with either virulent (80.6-kb plasmid-containing) or avirulent (plasmid-cured)
R. equi
. The degree of lysis was not altered by the presence of the plasmid, providing evidence that the virulence plasmid, which is required for survival within macrophages, was not necessary for recognition and killing of
R. equi
-infected cells. These data indicate that immunocompetent adult horses develop
R. equi-
specific CD8
+
CTL, which may play a role in immunity to
R. equi
. The apparent lack of restriction via classical MHC class I molecules suggests a novel or nonclassical method of antigen processing and presentation, such as presentation by CD1 or other nonclassical MHC molecules.
Adaptation of the Endogenous
Salmonella enterica
Serovar Typhi
clyA
-Encoded Hemolysin for Antigen Export Enhances the Immunogenicity of Anthrax Protective Antigen Domain 4 Expressed by the Attenuated Live-Vector Vaccine Strain CVD 908-
htrA
Authors: Galen James E. , Zhao Licheng , Chinchilla Magaly , Wang Jin Yuan , Pasetti Marcela F. , Green Jeffrey , Levine Myron M.
Published: November 2004

Bacterial live-vector vaccines aim to deliver foreign antigens to the immune system and induce protective immune responses, and surface-expressed or secreted antigens are generally more immunogenic than cytoplasmic constructs. We hypothesize that an optimum expression system will use an endogenous export system to avoid the need for large amounts of heterologous DNA encoding additional proteins. Here we describe the cryptic chromosomally encoded 34-kDa cytolysin A hemolysin of
Salmonella enterica
serovar Typhi (ClyA) as a novel export system for the expression of heterologous antigens in the supernatant of attenuated
Salmonella
serovar Typhi live-vector vaccine strains. We constructed a genetic fusion of ClyA to the reporter green fluorescent protein and showed that in
Salmonella
serovar Typhi CVD 908-
htrA
, the fusion protein retains biological activity in both domains and is exported into the supernatant of an exponentially growing live vector in the absence of detectable bacterial lysis. The utility of ClyA for enhancing the immunogenicity of an otherwise problematic antigen was demonstrated by engineering ClyA fused to the domain 4 (D4) moiety of
Bacillus anthracis
protective antigen (PA). A total of 11 of 15 mice immunized intranasally with
Salmonella
serovar Typhi exporting the protein fusion manifested fourfold or greater rises in serum anti-PA immunoglobulin G, compared with only 1 of 16 mice immunized with the live vector expressing cytoplasmic D4 (
P
= 0.0002). In addition, the induction of PA-specific gamma interferon and interleukin 5 responses was observed in splenocytes. This technology offers exceptional versatility for enhancing the immunogenicity of bacterial live-vector vaccines.
Truncation of Fibronectin-Binding Proteins in
Staphylococcus aureus
Strain Newman Leads to Deficient Adherence and Host Cell Invasion Due to Loss of the Cell Wall Anchor Function
Authors: Grundmeier Matthias , Hussain Muzaffar , Becker Petra , Heilmann Christine , Peters Georg , Sinha Bhanu
Published: November 2004

Staphylococcus aureus
fibronectin-binding proteins (FnBPs) play a critical role in
S. aureus
pathogenesis. FnBPs mediate adhesion to fibronectin and invasion of mammalian cells, including epithelial, endothelial, and fibroblastic cells, by fibronectin bridging to the host cell fibronectin receptor integrin (α
5
)β
1
. Strain Newman is a laboratory strain frequently used for genetic, functional, and in vivo studies. However, despite pronounced production of FnBPs, strain Newman is only weakly adherent to immobilized Fn and weakly invasive. We examined whether these effects are due to a structural difference of FnBPs. Here, we show that both
fnbA
Newman
and
fnbB
Newman
contain a centrally located point mutation resulting in a stop codon. This leads to a truncation of both FnBPs at the end of the C domain at identical positions. Most likely, the stop codon occurred first in
fnbB
Newman
and was subsequently transferred to
fnbA
Newman
by replacement of the entire region encompassing the C, D, and W domains with the respective sequence of
fnbB
Newman
. Using heterologous expression in
Staphylococcus carnosus
, we found that truncated FnBPs were completely secreted into the culture medium and not anchored to the cell wall, since they lack the sortase motif (LPETG). Consequently, this led to a loss of FnBP-dependent functions, such as strong adhesion to immobilized fibronectin, binding of fibrinogen, and host cell invasion. This mutation may explain some of the earlier reported conflicting data with strain Newman. Thus, care should be taken when drawing negative conclusions about the role of FnBPs as a virulence factor in a given model.
Identification of a Novel Virulence Factor in
Burkholderia cenocepacia
H111 Required for Efficient Slow Killing of
Caenorhabditis elegans
Authors: Huber Birgit , Feldmann Friederike , Köthe Manuela , Vandamme Peter , Wopperer Julia , Riedel Kathrin , Eberl Leo
Published: November 2004

Burkholderia cenocepacia
H111, which was isolated from a cystic fibrosis patient, employs a quorum-sensing (QS) system, encoded by
cep
, to control the expression of virulence factors as well as the formation of biofilms. The QS system is thought to ensure that pathogenic traits are expressed only when the bacterial population density is high enough to overwhelm the host before it is able to mount an efficient response. While the wild-type strain effectively kills the nematode
Caenorhabditis elegans
, the pathogenicity of mutants with defective quorum sensing is attenuated. To date, very little is known about the
cep
-regulated virulence factors required for nematode killing. Here we report the identification of a
cep
-regulated gene, whose predicted amino acid sequence is highly similar to the QS-regulated protein AidA of the plant pathogen
Ralstonia solanacearum
. By use of polyclonal antibodies directed against AidA, it is demonstrated that the protein is expressed in the late-exponential phase and accumulates during growth arrest. We show that
B. cenocepacia
H111 AidA is essential for slow killing of
C. elegans
but has little effect on fast killing, suggesting that the protein plays a role in the accumulation of the strain in the nematode gut. Thus, AidA appears to be required for establishing an infection-like process rather than acting as a toxin. Furthermore, evidence is provided that AidA is produced not only by
B. cenocepacia
but also by many other strains of the
Burkholderia cepacia
complex.
Characterization of Immunodominant and Potentially Protective Epitopes ofMannheimia haemolyticaSerotype 1 Outer Membrane Lipoprotein PlpE
Authors: Ayalew Sahlu , Confer Anthony W. , Blackwood Emily R.
Published: November 2004

Mannheimia haemolyticaserotype 1 (S1) is the most common bacterial isolate found in shipping fever pneumonia in beef cattle. Currently used vaccines againstM. haemolyticado not provide complete protection against the disease. Research withM. haemolyticaouter membrane proteins (OMPs) has shown that antibodies to one particular OMP from S1, PlpE, may be important in immunity. In a recently published work, members of our laboratory showed that recombinant PlpE (rPlpE) is highly immunogenic when injected subcutaneously into cattle and that the acquired immunity markedly enhanced resistance to experimental challenge (A. W. Confer, S. Ayalew, R. J. Panciera, M. Montelongo, L. C. Whitworth, and J. D. Hammer, Vaccine 21:2821-2829, 2003). The objective of this work was to identify epitopes of PlpE that are responsible for inducing the immune response. Western blot analysis of a series of rPlpE with nested deletions on both termini with bovine anti-PlpE hyperimmune sera showed that the immunodominant region is located close to the N terminus of PlpE. Fine epitope mapping, in which an array of overlapping 13-mer synthetic peptides attached to a derivatized cellulose membrane was probed with various affinity-purified anti-PlpE antibodies, identified eight highly reactive regions, of which region 2 (R2) was identified as the specific epitope. The R2 region is comprised of eight imperfect repeats of a hexapeptide (QAQNAP) and is located between residues 26 and 76. Complement-mediated bactericidal activity of affinity-purified anti-PlpE bovine antibodies confirmed that antibodies directed against the R2 region are effective in killingM. haemolytica.
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

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

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

Antibody-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

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.
Raffles, roles, and the outcome of sperm competition in sockeye salmon
Authors: Hoysak Drew J , Liley N Robin , Taylor Eric B
Published: November 2004

In species with male alternative reproductive phenotypes, one phenotype is usually disadvantaged in mating competition. In salmonid fishes, large late-maturing males pair with nesting females and maintain close contact before and during spawning. Small early-maturing males have little contact with nesting females and, during spawning, begin to release sperm after the paired male. The effects of male phenotype and timing of ejaculation on success in sperm competition are not known. In this study, we determined paternity of offspring resulting from in vitro competitive fertilizations to examine these two aspects of sperm competition in sockeye salmon, Oncorhynchus nerka (Walbaum, 1792). When we fertilized eggs with mixtures of equal numbers of sperm from each of two male age classes, we found that success in sperm competition did not depend on male age. However, success in these competitive fertilizations did not conform to the fair raffle model of sperm competition, since paternity in most of the clutches was biased in favour of one male. When we added milt from two males sequentially to a batch of eggs, we found that sperm from the second male fertilized fewer eggs than sperm from the first male, but the difference was less than expected. In addition, a male's success when his milt was added first was not correlated with his success when his milt was added second.
Does fresh vegetation protect avian nests from ectoparasites? An experiment with tree swallows
Authors: Dawson Russell D
Published: November 2004

Some species of birds incorporate fresh green vegetation into their nests. The adaptive significance of this behaviour, however, is unclear. The "nest protection hypothesis" suggests that volatile chemicals contained in green plants reduce populations of nest-dwelling ectoparasites. I tested this hypothesis with tree swallows, Tachycineta bicolor (Vieillot, 1808), a species that has large infestations of ectoparasites in its nests. I experimentally added green leaves of yarrow (Achillea millefolium L.) to nests and compared these nests to control nests. My results showed that nests with yarrow had significantly higher levels of infestation by fleas, and yarrow had no effect on the number of blow flies detected. There was no effect of yarrow on condition of parents, size of offspring, or the probability of nests fledging at least one young. I did, however, find that second-year (SY) females with yarrow added to their nests hatched significantly more eggs than control SY females. In addition, pairs with yarrow added to their nest were significantly less likely to suffer hatching failure and (or) brood reduction. These beneficial effects of yarrow cannot be explained by reductions in numbers of fleas or blow flies, and I suggest that these results may be due to reductions in numbers of other types of parasites not quantified in my study, such as flying insects or the diseases that they may vector. I discuss my findings for swallows in the context of results from previous studies of other species that habitually use green plant material such as yarrow in their nests.
Evidence for sexual partitioning of foraging mode in Western Sandpipers (Calidris mauri) during migration
Authors: Mathot Kimberley J , Elner Robert W
Published: November 2004

Migrating Western Sandpipers, Calidris mauri (Cabanis, 1857), observed feeding at an intertidal stopover site on the Fraser River delta, British Columbia, shifted their foraging mode from surface-pecking to probing over a 3-week period in April and May. We tested possible mechanisms to account for the field observations. Using control and shorebird exclusion plots over a 3-month period bracketing the migration, we determined that neither seasonal nor shorebird-induced changes in the relative availability of epifaunal compared with infaunal prey accounted for the decline in the prevalence of epifaunal feeding behaviour. However, strong peaks in both epi- and in-faunal prey densities coincided with the migration period, suggesting that migratory timing may be linked with the productivity schedule of major stopover sites. Males, which precede females in the migration and have relatively shorter bills, were observed to engage in epifaunal feeding more frequently than females. Thus, while foraging behaviour of the Western Sandpiper at a population level appears "plastic", the feeding repertoire of individuals is more specialized and results in sexual partitioning of prey resources. The implications of our findings for differential distribution patterns over the nonbreeding range and sex-related differences in contaminant profiles are discussed.
Satiation and compensation for short-term changes in food quality and availability in young Steller sea lions (Eumetopias jubatus)
Authors: Rosen David A.S , Trites Andrew W
Published: November 2004

Foraging theory predicts that animals should proportionately increase their food intake to compensate for reduced food energy content and (or) prey availability. However, the theoretical intake levels will, at some point, exceed the digestive capacity of the predator. We tested the ability of Steller sea lions, Eumetopias jubatus (Schreber, 1776), to compensate for short-term changes in prey energy density and availability, and quantified the maximum amount of food a young sea lion could consume. Five 1–2-year-old captive Steller sea lions were offered either herring (high energy) or capelin (low energy) each day or every second day. When prey were available on a daily basis, the sea lions compensated for differences in the energy content of herring and capelin by consuming sufficient quantities of each (8.3 vs. 14.0 kg·d–1, respectively) to maintain equivalent gross energy intakes. When herring was available only on alternate days, the sea lions increased their consumption by 52% to 11.5 kg·d–1, which was not sufficient to maintain an average gross intake equal to that maintained when herring was available every day. When capelin was available only on alternate days, some animals increased their intake for a few days, but average intake (15.2 kg·d–1) was far below levels observed during daily feeding. Generally, the sea lions appeared to reach their digestive limit at a level equivalent to 14%–16% of their body mass. Our findings suggest that Steller sea lions can alter their food intake in response to short-term changes in prey quality or availability, but that these variables can quickly combine to necessitate food intake levels that exceed the physiological digestive capacities of young animals.
Long-distance movements of harbour seals (Phoca vitulina) from a seasonally ice-covered area, the St. Lawrence River estuary, Canada
Authors: Lesage Véronique , Hammill Mike O , Kovacs Kit M
Published: November 2004

Previous studies of harbour seal (Phoca vitulina L., 1758) movements indicate that this species is relatively sedentary throughout the year. However, few investigations have examined their movements and seasonal distribution patterns in ice-covered areas. This study used spatial analysis of ice data and movement data from harbour seals collected via satellite (n = 7) and VHF radiotelemetry (n = 15) to explore this species' spatial use patterns in a seasonally ice-covered region, the St. Lawrence River estuary, Canada. When solid ice formed within the bays of the estuary, four of the seven satellite-tagged animals (all adult males) left their summer haul-out areas, migrating 266 ± 202 km (range 65–520 km) to over-wintering sites. The seals exhibited preference for areas of light to intermediate ice conditions during the winter months; at least six of the seven seals occupied areas with lighter ice conditions than those that prevailed generally in the study area. Evidence of high abundance of potential prey for harbour seals in the estuary during winter suggests that reduced availability of adequate food resources is not the primary factor which influences the movement and distribution patterns of harbour seals. Movement patterns observed during the ice-free period concur with previously reported harbour seal behaviour; the seals remained near the coast (<6.1–11.0 km from shore) in shallow water areas (<50 m deep in 100% VHF and 90% SLTDRs (satellite-linked time-depth recorders)) and travelled only short distances (15–45 km) from capture sites. None of the VHF- or satellite-tagged seals crossed the 350 m deep Laurentian channel, which suggests that this deep body of water might represent a physical barrier to this coastal population.
Correlation of depth and heart rate in harbour seal pups
Authors: Hicks J L , O'Hara Hines R J , Schreer J F , Hammill M O
Published: November 2004

Harbour seal (Phoca vitulina L., 1758) pups are aquatically active from birth and have been shown to develop increased cardiac control throughout the nursing period. In an attempt to quantify and compare these developmental changes, data previously collected on pups in the St. Lawrence River estuary, Quebec, Canada, were analyzed. Time–depth recorders and heart-rate recorders were employed on eight pups to obtain depth and heart-rate measurements simultaneously. Analyses involved partitioning the data into intervals of surface–dive–surface. These intervals were then allocated into nine consecutive segments: presurface, predive surface, descent, prebottom, bottom, postbottom, ascent, postdive surface, and postsurface. Mean heart rate for each segment was then correlated with the mean depth per segment and overall dive duration. With increasing dive depth, a decrease in heart-rate variability with age was observed. There was no apparent relationship between mean heart rate during the dive and overall dive duration. The proportion of time spent in the lower heart-rate mode was observed to increase with age during most phases of a dive. Relative changes in mean heart rate between consecutive dive segments indicated an initial decrease in mean heart rate prior to submersion and an increasing trend before surfacing. These findings indicate that harbour seal pups develop increased cardiac control prior to weaning and that anticipatory cardiac responses to diving and surfacing (bradycardia and tachycardia, respectively) may be evident.
Demographic responses of Virginia opossums to limitation at their northern boundary
Authors: Kanda L Leann , Fuller Todd K
Published: November 2004

The precise response of a population at its distributional edge to the limiting extrinsic factor should be mediated by the demography of the species. We applied this principle to understanding the northern distributional potential of the Virginia opossum (Didelphis virginiana Kerr, 1792). We reviewed the literature for demographic data that we then used to build model populations. Juvenile over-winter survival was adjusted to determine the survival necessary for a stable population. To put the results in the context of life-history strategy and ecological niche, we built models for two other medium-sized mammals with similar distributions, the raccoon (Procyon lotor (L., 1758)) and the muskrat (Ondatra zibethicus (L., 1766)). Northern raccoon populations may sustain juvenile winter survival rates of <0.50 because adult females live to reproduce in multiple years. Muskrat juveniles may need a winter survival rate of only 0.40 in average years because reproduction is very high. In contrast, young northern opossums need a survival rate of 0.81 over winter to compensate for low prewinter survival. Raccoons and muskrats, through different life-history strategies, should be able to expand their northern distribution to the winter-induced physiological limit. However, opossum populations should fail before the average individual physiological limit is reached.
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].
Scheduling of incompatible jobs on unrelated machines
Authors: Jansen Klaus
Published: November 2004

We study a general scheduling problem where each job j∈J has an execution time e(j, Mi)∈ℝ+ on a machine of type Mi∈M and where we have an incompatibility relation between the jobs. Given a price p(Mi)∈ℝ+ for each machine of type Mi and a deadline d∈IR+, we consider the problem to select a minimum cost set of machines for which there exists a schedule with make-span at most d. We propose an approximation method where the solution is at most [Formula: see text] away from the optimum. The method is based on a graph theoretical problem which we have studied for several graph classes.
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.
PATTERN STORAGE AND HOPFIELD NEURAL ASSOCIATIVE MEMORY WITH HIDDEN STRUCTURE
Authors: TAN SHAOHUA , HAO JIANBIN , VANDEWALLE JOOS
Published: November 2004

This paper is concerned with the formulation of neural associative memories. Centered around the fundamental issue of the memory storage, we examine the deficiencies associated with the standard Hopfield net. To overcome the problems, we pursue a data-driven design approach by modifying the configuration of the Hopfield net to allow hidden structures. As important results, we show how the well-known sum-of-outer product rule can be utilized to explore the freedom provided by the hidden structures leading to the desired memory performance.
THE USE OF OPTICAL FLOW FOR THE AUTONOMOUS NAVIGATION
Authors: Malisia Antonio , Baghino Andrea , Campani Marco , Straforini Marco , Torre Vincent
Published: November 2004

Insects and a lot of other animals use the optical flow to control the direction of their motion and to avoid obstacles. This paper describes experiments suggesting the possible use of the optical flow for the navigation of a robot moving in indoor and outdoor environments. In indoor scenes, such as corridors, offices and laboratories, the optical flow is used to detect and localize obstacles. These routines are based on the computation of a reduced optical flow. Almost real time performance was obtained with standard workstations, such as SUN 3 or SUN Sparcstation 1. The mobile vehicle is usually able to avoid large obstacles such as a chair or a human, but it is not able to avoid thin obstacles such as a rod or a bar. The avoidance performances of the proposed algorithm critically depend on the feedback loop between the vision module and the motor system. In outdoor scenes the optical flow can be used to understand the egomotion, that is to obtain information on the absolute velocity of the moving vehicle. The optical flow is corrected for shocks and vibration present during image acquisition. Regions of the image are extracted, where the optical flow is reliable, and the information on egomotion is recovered from the optical flow here obtained. These results suggest that the optical flow can be successfully used by biological and artificial systems for controlling their motion and for avoiding obstacles.
CLASSIFICATION OF THE DECAYS OF THE Z0 INTO b AND c QUARK PAIRS USING A NEURAL NETWORK
Authors: Eerola P. , Kalkkinen J. , De Angelis A. , Cosmo G. , De Groot N. , Los M. , Lyons L. , Torassa E. , Vallazza E.
Published: November 2004

A classifier based on a Feed-Forward Neural Network has been used for separating a sample of about 123,500 selected hadronic decays of the Z0, collected by DELPHI during 1991, into three classes according to the flavour of the original quark pair: [Formula: see text] (unresolved), [Formula: see text] and [Formula: see text] The classification has been used to compute the partial widths of the Z0 into b and C quark pairs.
QUANTITATIVE ANALYSIS ON THE EFFECTS OF COMPONENTS OF MS MEDIUM USING PIXE TECHNIQUE
Authors: LI YAO , LI HUA , SHEN DALENG , YAO HUIYING , ZENG XIANZHOU , XU WEIDONG , YANG FUJIA
Published: November 2004

The PIXE system with a detective sensitivity of 10–11 g for elements was used to study the quantitative effects of the components of Murashige and Skoog (M&S) salts. Concentrations of 14 elements in Polygonum tenuicaule cultured in M&S medium with different modifications were analysed. The physiological function of M&S salts and such integral components as KH 2 PO 4, FeSO 4, KNO 3 and CaCl 2 were disclosed. Some features of M&S medium and plant absorption mechanism are reported for the first time.
SIMULTANEOUS PIXE ANALYSIS OF SOME ADJACENT ELEMENTS
Authors: PEISACH M. , MATETA N.A. , PILLAY A.E.
Published: November 2004

There is often a need to determine simultaneously both elements of an adjacent elemental pair whose K α and K β X-rays cannot be adequately resolved by the detector. The extent to which specific adjacent elements (viz. K-Ca and V-Cr) mutually interfered with each other was studied by PIXE on thick and thin targets specially prepared from synthetic mixtures. To monitor the lowest relative concentration for which significant results can be obtained, the concentration of each element in each of the pairs studied was systematically changed.
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.
PARABOLIC VECTOR BUNDLES AND HERMITIAN-YANG-MILLS CONNECTIONS OVER A RIEMANN SURFACE
Authors: PORITZ JONATHAN A.
Published: November 2004

We study a certain moduli space of irreducible Hermitian-Yang-Mills connections on a unitary vector bundle over a punctured Riemann surface. The connections used have non-trivial holonomy around the punctures lying in fixed conjugacy classes of U (n) and differ from each other by elements of a weighted Sobolev space; these connections give rise to parabolic bundles in the sense of Mehta and Seshadri. We show in fact that the moduli space of stable parabolic bundles can be identified with our moduli space of HYM connections, by proving that every stable bundle admits a unique unitary gauge orbit of Hermitian-Yang-Mills connections.
SEPARATION PROPERTIES AND OPERATING FUNCTIONS ON A SPACE OF CONTINUOUS FUNCTIONS
Authors: HATORI OSAMU
Published: November 2004

Characterizations of the space CR (X) of all real-valued continuous functions on a compact Hausdorff space X among its subspaces are investigated under the circumstances of operating functions. One of the main purpose in this paper is to disprove the following conjecture: if a non-affine function operates on an ultraseparating real Banach function space E on X, then E = CR (X). A positive answer is given in the case that E satisfies a stronger separation axiom than ultraseparation one, which the real part of an ultraseparating Banach function algebra satisfies. For the original conjecture a counterexample is given; there is an ultraseparating real Banach function space on a compact metric space Y on which the function |·| operates, but it does not coincide with CR (Y). A characterization is given for non-affine functions which operate only on CR (X) among ultraseparating real Banach function spaces on X. By using these results the symbolic calculus on real Banach function spaces is investigated without extra hypothesis of ultraseparation. Several non-local-Lipschitz functions are shown not to operate on a real Banach function space E on X unless E = CR (X). In particular, the function tp defined on [0,1) for a p with 0 < p < 1 or the standard Cantor function on [0, 1] never operates on a real Banach function space E on X unless E = CR (X). Functions which operate on the real part of a real function algebra are also investigated. A positive answer is given for the conjecture that only affine functions operate on the real part of a non-trivial real function algebra.
APPLICATION OF MONOMER-DIMER ALGORITHMS IN STRONG COUPLING QCD
Authors: Fingberg J.
Published: November 2004

We study the finite temperature chiral phase transition of SU(3) lattice QCD in the strong coupling limit using the monomer dimer polymer MDP representation of the partition function. By Monte Carlo simulation we measured the chiral condensate and the susceptibility as a function of temperature for various values of the quark mass. The effect of a global symmetry of the lattice action is discussed in terms of critical exponents.
ON THE CALCULATION OF THE HEAT CAPACITY IN PATH INTEGRAL MONTE CARLO SIMULATIONS
Authors: MARX D. , NIELABA P. , BINDER K.
Published: November 2004

In Path Integral Monte Carlo simulations the systems partition function is mapped to an equivalent classical one at the expense of a temperature-dependent Hamiltonian with an additional imaginary time dimension. As a consequence the standard relation linking the heat capacity Cv to the energy fluctuations, −2, which is useful in standard classical problems with temperature-independent Hamiltonian, becomes invalid. Instead, it gets replaced by the general relation [Formula: see text] for the intensive heat capacity estimator; β being the inverse temperature and the subscript P indicates the P-fold discretization in the imaginary time direction. This heatcapacity estimator has the advantage of being based directly on the energy estimatorand thus requires no extra computational effort and is suited for extensive phase diagramstudies. As an example, numerical results are presented for a two-dimensional fluid withinternal magnetic quantum degrees of freedom. We discuss in detail origin and consequences of the excess term. Due to the subtraction of two relatively large contributions ofsimilar absolute magnitude a large statistical effort would be necessary for very accurateheat capacity estimates.
GISMO: AN OBJECT-ORIENTED PROGRAM FOR HIGH- ENERGY PHYSICS EVENT SIMULATION AND RECONSTRUCTION
Authors: ATWOOD W.B. , BURNETT T. , CAILLIAU R. , MYERS D.R. , STORR K.M.
Published: November 2004

Gismo is a highly interactive program, with an iconic human interface and a 3D graphics display, which was developed in order to investigate the feasibility of using object-oriented programming within high-energy physics. It allows the user to design a detector and save it to disk, to track Monte Carlo events through such a detector, to simulate the detector response, and to reconstruct an event from this response. Gismo was developed using Objective-C and the Interface Builder on a NeXT computer, and the speed with which it was possible to build an application of this complexity indicates that the techniques used warrant further investigation.
A DISCRETE MODEL FOR LATE STAGE COARSENING
Authors: KOLB M.
Published: November 2004

A discrete model for the late stages of order parameter conserving coarsening is studied in one and in two dimensions. Starting from stationary, unstable solutions, the growth dynamics is related to the evolution of relevant perturbations near these solutions.
NUMERICAL STUDY OF FINITE SIZE SCALING FOR FIRST ORDER PHASE TRANSITIONS
Authors: BILLOIRE ALAIN
Published: November 2004

I present reaults of simulations of the q=10 and q=20 2-d Potts models in the transition region. The asymptotic finite size behavior sets in only for extremely large lattices. We learn from this simulation that finite size scaling cannot be used to decide that a transition is first order.
WEIGHT RATIO FIXING AT FIRST ORDER PHASE TRANSITIONS
Authors: LIPPERT THOMAS , SCHILLING KLAUS , UEBERHOLZ PEER , BHANOT GYAN
Published: November 2004

The presence of strong metastabilities in computer simulations of models showing a first order phase transition hinders a reliable determination of the weight ratio between the two phases. We discuss a new phenomenological method which allows an accurate fixing of the weight ratio using the standard multihistogram procedure.
CELLULAR AUTOMATA AS A COMPUTATIONAL MODEL FOR LOW-LEVEL VISION
Authors: BROGGI ALBERTO , D'ANDREA VINCENZO , DESTRI GIULIO
Published: November 2004

In this paper we discuss the use of the Cellular Automata (CA) computational model in computer vision applications on massively parallel architectures. Motivations and guidelines of this approach to low-level vision in the frame of the PROMETHEUS project are discussed. The hard real-time requirement of actual application can be only satisfied using an ad hoc VLSI massively parallel architecture (PAPRICA). The hardware solutions and the specific algorithms can be efficiently verified and tested only using, as a simulator, a general purpose machine with a parent architecture (CM-2). An example of application related to feature extraction is discussed.
BIOLOGICALLY REALISTIC AND ARTIFICIAL NEURAL NETWORK SIMULATORS ON THE CONNECTION MACHINE
Authors: HAMMARLUND PER , LEVIN BJÖRN , LANSNER ANDERS
Published: November 2004

We describe two neural network (NN) simulators implemented on the Connection Machine (CM). The first program is aimed at biologically realistic simulations and the second at recurrent artificial NNs. Both programs are currently used as simulation engines in research within the SANS group as well as in other groups. The program for biologically realistic NN simulations on the CM is called BIOSIM. The aim is to simulate NNs in which the neurons are modeled with a high degree of biological realism. The cell model used is a compartmentalized abstraction of the neuron. It includes sodium, potassium, calcium, and calcium dependent potassium channels. Synaptic interaction includes conventional chemical synapses as well as voltage gated NMDA synapses. On a CM with 8K processors the program is typically capable of handling some tens of thousands of compartments and more than ten times as many synapses. The artificial NN simulator implements the SANS model, a recurrent NN model closely related to the Hopfield model. The aim has been to effectively support large network simulations, in the order of 8–16K units, on an 8K CM. To make the simulator optimal for different applications, it supports both fully and sparsely connected networks. The implementation for sparsely connected NNs uses a compacted weight matrix. Both implementations are optimized for sparse activity.
POMPC: A C LANGUAGE FOR DATA PARALLELISM
Authors: PARIS NICOLAS
Published: November 2004

POMPC is a parallel language dedicated to the programming of Massively Parallel Computers according to a synchronous Data Parallel model. It is an extension of the ANSI C language and follows its philosophy. Parallelism is explicitly handled by the definition of collections of parallel variables and the definition of communication primitives. A methodology is presented in order to easily port the language on different target architectures. Virtualization is introduced to handle simultaneously several collections of different sizes and shapes. Virtualization management is a key point of the compilation process. Programmer, architecture, compilation and system points of view lead to a special implementation of the virtualization mixing physical and virtual parallel objects. The implementation of the virtualization is adapted for the development of communication libraries and also adapted to enlarge the asynchronous sections of code for SPMD architecture. The portability of the POMPC language is validated by several implementations for mono/multi-process simulation on UNIX machines, for the Connection Machine CM-2, for the MasPar MP-1 and a compiler is in preparation for the iPSC-860.