bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic and Cell Biological Characterization of the Vaccinia Virus A30 and G7 Phosphoproteins
Authors: Mercer Jason , Traktman Paula
Published: May 2005

The vaccinia virus proteins A30 and G7 are known to play essential roles in early morphogenesis, acting prior to the formation of immature virions. Their repression or inactivation results in the accumulation of large virosomes, detached membrane crescents, and empty immature virions. We have undertaken further study of these proteins to place them within the context of the F10 kinase, the A14 membrane protein, and the H5 phosphoprotein, which have been the focus of previous studies within our laboratory. Here we confirm that both A30 and G7 undergo F10 kinase-dependent phosphorylation in vivo and recapitulate that modification of A30 in vitro. Although the detached crescents observed upon loss of A30 or G7 echo those seen upon repression of A14, no interaction between A30/G7 and A14 could be detected. We did, however, determine that the A30 and G7 proteins are unstable during nonpermissive
ts
H5 infections, suggesting that the loss of A30/G7 is the underlying cause for the formation of lacy or curdled virosomes. We also determined that the temperature-sensitive phenotype of the C
ts
11 virus is due to mutations in two codons of the G7L gene. Phenotypic analysis of nonpermissive C
ts
11 infections indicated that these amino acid substitutions compromise G7 function without impairing the stability of either G7 or A30. Utilizing C
ts
11 in conjunction with a rifampin release assay, we determined that G7 acts at multiple stages of virion morphogenesis that can be distinguished both by ultrastructural analysis and by monitoring the phosphorylation status of several viral proteins that undergo F10-mediated phosphorylation.
Inhibition of the Herpes Simplex Virus Type 1 DNA Polymerase Induces Hyperphosphorylation of Replication Protein A and Its Accumulation at S-Phase-Specific Sites of DNA Damage during Infection
Authors: Wilkinson Dianna E. , Weller Sandra K.
Published: May 2005

The treatment of mammalian cells with genotoxic substances can trigger DNA damage responses that include the hyperphosphorylation of replication protein A (RPA), a protein that plays key roles in the recognition, signaling, and repair of damaged DNA. We have previously reported that in the presence of a viral polymerase inhibitor, herpes simplex virus type 1 (HSV-1) infection induces the hyperphosphorylation of RPA (D. E. Wilkinson and S. K. Weller, J. Virol.
78:
4783-4796, 2004). We initiated the present study to further characterize this genotoxic response to HSV-1 infection. Here we report that infection in the presence of polymerase inhibitors triggers an S-phase-specific response to DNA damage, as demonstrated by induction of the hyperphosphorylation of RPA and its accumulation within viral foci specific to the S phase of the cell cycle. This DNA damage response occurred in the presence of viral polymerase inhibitors and required the HSV-1 polymerase holoenzyme as well as the viral single-stranded-DNA binding protein. Treatment with an inhibitor of the viral helicase-primase did not induce the hyperphosphorylation of RPA or its accumulation in infected cells. Taken together, these results suggest that the S-phase-specific DNA damage response to infection is dependent on the specific inhibition of the polymerase. Finally, RPA hyperphosphorylation was not induced during productive infection, indicating that active viral replication does not trigger this potentially detrimental stress response.
Mutational Analysis of Bovine Leukemia Virus Rex: Identification of a Dominant-Negative Inhibitor
Authors: Choi Eun-A , Hope Thomas J.
Published: May 2005

The Rex proteins of the delta-retroviruses act to facilitate the export of intron-containing viral RNAs. The Rex of bovine leukemia virus (BLV) is poorly characterized. To gain a better understanding of BLV Rex, we generated a reporter assay to measure BLV Rex function and used it to screen a series of point and deletion mutations. Using this approach, we were able to identify the nuclear export signal of BLV Rex. Further, we identified a dominant-negative form of BLV Rex. Protein localization analysis revealed that wild-type BLV Rex had a punctate nuclear localization and was associated with nuclear pores. In contrast, the dominant-negative BLV Rex mutation had a diffuse nuclear localization and no nuclear pore association. Overexpression of the dominant-negative BLV Rex altered the localization of the wild-type protein. This dominant-negative derivative of BLV Rex could be a useful tool to test the concept of intracellular immunization against viral infection in a large animal model.
Identification and Characterization of the Putative Fusion Peptide of the Severe Acute Respiratory Syndrome-Associated Coronavirus Spike Protein
Authors: Sainz Bruno , Rausch Joshua M. , Gallaher William R. , Garry Robert F. , Wimley William C.
Published: May 2005

Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is a newly identified member of the family
Coronaviridae
and poses a serious public health threat. Recent studies indicated that the SARS-CoV viral spike glycoprotein is a class I viral fusion protein. A fusion peptide present at the N-terminal region of class I viral fusion proteins is believed to initiate viral and cell membrane interactions and subsequent fusion. Although the SARS-CoV fusion protein heptad repeats have been well characterized, the fusion peptide has yet to be identified. Based on the conserved features of known viral fusion peptides and using Wimley and White interfacial hydrophobicity plots, we have identified two putative fusion peptides (SARS
WW-I
and SARS
WW-II
) at the N terminus of the SARS-CoV S2 subunit. Both peptides are hydrophobic and rich in alanine, glycine, and/or phenylalanine residues and contain a canonical fusion tripeptide along with a central proline residue. Only the SARS
WW-I
peptide strongly partitioned into the membranes of large unilamellar vesicles (LUV), adopting a β-sheet structure. Likewise, only SARS
WW-I
induced the fusion of LUV and caused membrane leakage of vesicle contents at peptide/lipid ratios of 1:50 and 1:100, respectively. The activity of this synthetic peptide appeared to be dependent on its amino acid (aa) sequence, as scrambling the peptide rendered it unable to partition into LUV, assume a defined secondary structure, or induce both fusion and leakage of LUV. Based on the activity of SARS
WW-I
, we propose that the hydrophobic stretch of 19 aa corresponding to residues 770 to 788 is a fusion peptide of the SARS-CoV S2 subunit.
Poliovirus Proteins Induce Membrane Association of GTPase ADP-Ribosylation Factor
Authors: Belov George A. , Fogg Mark H. , Ehrenfeld Ellie
Published: May 2005

Poliovirus infection results in the disintegration of intracellular membrane structures and formation of specific vesicles that serve as sites for replication of viral RNA. The mechanism of membrane rearrangement has not been clearly defined. Replication of poliovirus is sensitive to brefeldin A (BFA), a fungal metabolite known to prevent normal function of the ADP-ribosylation factor (ARF) family of small GTPases. During normal membrane trafficking in uninfected cells, ARFs are involved in vesicle formation from different intracellular sites through interaction with numerous regulatory and coat proteins as well as in regulation of phospholipase D activity and cytoskeleton modifications. We demonstrate here that ARFs 3 and 5, but not ARF6, are translocated to membranes in HeLa cell extracts that are engaged in translation of poliovirus RNA. The accumulation of ARFs on membranes correlates with active replication of poliovirus RNA in vitro, whereas ARF translocation to membranes does not occur in the presence of BFA. ARF translocation can be induced independently by synthesis of poliovirus 3A or 3CD proteins, and we describe mutations that abolished this activity. In infected HeLa cells, an ARF1-enhanced green fluorescent protein fusion redistributes from Golgi stacks to the perinuclear region, where poliovirus RNA replication occurs. Taken together, the data suggest an involvement of ARF in poliovirus RNA replication.
Viral Class 1 RNase III Involved in Suppression of RNA Silencing
Authors: Kreuze Jan F. , Savenkov Eugene I. , Cuellar Wilmer , Li Xiangdong , Valkonen Jari P. T.
Published: May 2005

Double-stranded RNA (dsRNA)-specific endonucleases belonging to RNase III classes 3 and 2 process dsRNA precursors to small interfering RNA (siRNA) or microRNA, respectively, thereby initiating and amplifying RNA silencing-based antiviral defense and gene regulation in eukaryotic cells. However, we now provide evidence that a class 1 RNase III is involved in suppression of RNA silencing. The single-stranded RNA genome of sweet potato chlorotic stunt virus (SPCSV) encodes an RNase III (RNase3) homologous to putative class 1 RNase IIIs of unknown function in rice and
Arabidopsis
. We show that RNase3 has dsRNA-specific endonuclease activity that enhances the RNA-silencing suppression activity of another protein (p22) encoded by SPCSV. RNase3 and p22 coexpression reduced siRNA accumulation more efficiently than p22 alone in
Nicotiana benthamiana
leaves expressing a strong silencing inducer (i.e., dsRNA). RNase3 did not cause intracellular silencing suppression or reduce accumulation of siRNA in the absence of p22 or enhance silencing suppression activity of a protein encoded by a heterologous virus. No other known RNA virus encodes an RNase III or uses two independent proteins cooperatively for RNA silencing suppression.
Pseudorabies Virus Glycoprotein gD Contains a Functional Endocytosis Motif That Acts in Concert with an Endocytosis Motif in gB To Drive Internalization of Antibody-Antigen Complexes from the Surface of Infected Monocytes
Authors: Ficinska Jolanta , Van Minnebruggen Geert , Nauwynck Hans J. , Bienkowska-Szewczyk Krystyna , Favoreel Herman W.
Published: May 2005

Viral glycoproteins gB and gD of the swine alphaherpesvirus pseudorabies virus (PRV), which is closely related to human herpes simplex virus and varicella-zoster virus, are able to drive internalization of antibody-antigen complexes that may form at the cell surface of infected monocytes, thereby protecting these cells from efficient antibody-mediated lysis. We found earlier that gB relies on an endocytosis motif in its cytoplasmic domain for its function during this internalization process. Here, we report that the PRV gD protein also contains a functional endocytosis motif (YRLL) in its cytoplasmic domain that drives spontaneous endocytosis of gD from the cell surface early in infection and that acts in concert with the endocytosis motif in gB to contribute to efficient internalization of antibody-antigen complexes in PRV-infected monocytes.
Toll-Like Receptor Signaling Inhibits Hepatitis B Virus Replication In Vivo
Authors: Isogawa Masanori , Robek Michael D. , Furuichi Yoshihiro , Chisari Francis V.
Published: May 2005

Toll-like receptors (TLR) play a key role in innate immunity. To examine the ability of diverse TLRs to modulate hepatitis B virus (HBV) replication, HBV transgenic mice received a single intravenous injection of ligands specific for TLR2, TLR3, TLR4, TLR5, TLR7, and TLR9. All of the ligands except for TLR2 inhibited HBV replication in the liver noncytopathically within 24 h in a α/β interferon-dependent manner. The ability of these TLR ligands to induce antiviral cytokines at the site of HBV replication suggests that TLR activation could represent a powerful and novel therapeutic strategy for the treatment of chronic HBV infection.
Genome Replication and Progeny Virion Production of Herpes Simplex Virus Type 1 Mutants with Temperature-Sensitive Lesions in the Origin-Binding Protein
Authors: Schildgen Oliver , Gräper Sascha , Blümel Johannes , Matz Bertfried
Published: May 2005

Genome replication of herpes simplex viruses (HSV) in cultured cells is thought to be started by the action of the virus-encoded origin-binding protein (OBP). In experiments using two HSV-1 mutants with temperature-sensitive lesions in the helicase domain of OBP, we demonstrated that this function is essential during the first 6 hours of the lytic cycle. Once DNA synthesis has started, this function is no longer required, suggesting that origin-driven initiation of viral DNA replication is a single event rather than a continuous process.
LARMOR PRECESSION TIME, WIGNER DELAY TIME AND THE LOCAL DENSITY OF STATES IN A QUANTUM WIRE
Authors: SINGHA DEO P.
Published: May 2005

Buttiker–Thomas–Pretre (BTP) [Z. Phys.B94, 133 (1994)] proposed that the concepts behind the Larmor precession time tell us that it is possible to define exactly the local density of states (LDOS) in terms of the scattering matrix. However, we take into account evanescent modes and show that for an impurity in a quantum wire, this is in principle not exactly true. We also prove that the Wigner delay time gives correct superluminal times at the Fano resonances, in spite of the fact that the stationary phase approximation is not valid there.
THERMODYNAMICS OF FEW-PARTICLE SYSTEMS
Authors: TARASOV VASILY E.
Published: May 2005

We consider the wide class of few-particle systems that have some analog of the thermodynamic laws. These systems are characterized by the distributions that are determined by the Hamiltonian and satisfy the Liouville equation. Few-particle systems of this class are described by a non-holonomic constraint: the power of non-potential forces is directly proportional to the velocity of the elementary phase volume change. The coefficient of this proportionality is determined by the Hamiltonian. In the general case, the examples of the few-particle systems of this class are the constant temperature systems, canonical-dissipative systems, and Fermi–Bose classical systems.
A NOVEL OF SURFACE WAVE MICROWAVE PLASMA CVD METHOD ON THE PREPARATION OF NITROGENATED AMORPHOUS CARBON FILMS
Authors: RUSOP M. , ADHIKARY S. , OMER A. M. M. , ADHIKARI S. , UCHIDA H. , SOGA T. , JIMBO T. , UMENO M.
Published: May 2005

We have studied the influence of the methane gas ( CH4) pressure on the surface morphology, composition, structural and electrical properties of nitrogenated amorphous carbon ( a-C:N ) films grown by surface wave microwave plasma chemical vapor deposition (SWMP-CVD) using Scanning electron microscopy (SEM), Atomic force microscopy (AFM), Auger electron spectroscopy (AES), X-rays photoelectron spectroscopy (XPS), UV-visible spectroscopy and 4-point probe resistance measurement. We have succeeded in growing a-C:N films using a novel method of SWMP-CVD at room temperature and found that the surface morphology, bonding, optical and electrical properties of a-C:N films are strongly dependent on the CH4gas sources and the a-C:N films grown at higher CH4gas pressure have relatively high electrical conductivity.
TWO GENERATOR 4-ENGEL GROUPS
Authors: TRAUSTASON GUNNAR
Published: May 2005

Using known results on 4-Engel groups one can see that a 4-Engel group is locally nilpotent if and only if all its 3-generator subgroups are nilpotent. As a step towards settling the question whether all 4-Engel groups are locally nilpotent we show that all 2-generator 4-Engel groups are nilpotent.
CHARACTERISTIC RELATIONS FOR A FINITE-BY-NILPOTENT GROUP
Authors: ENDIMIONI GÉRARD
Published: May 2005

We improve previous results by showing that a finitely generated soluble group G is finite-by-nilpotent if and only if for all a, b ∈ G, there exists a positive integer n such that [a, nb] belongs to γn+2().<a>′.
COMPLETE REWRITING SYSTEMS FOR CODIFIED SUBMONOIDS
Authors: MALHEIRO ANTÓNIO
Published: May 2005

Given a complete rewriting system R on X and a subset X0of X+satisfying certain conditions, we present a complete rewriting system for the submonoid of M(X;R) generated by X0. The obtained result will be applied to the group of units of a monoid satisfying H1= D1. On the other hand we prove that all maximal subgroups of a monoid defined by a special rewriting system are isomorphic.
THE CONJUGACY PROBLEM AND RELATED PROBLEMS IN LATTICE-ORDERED GROUPS
Authors: HOLLAND W. CHARLES , TSABAN BOAZ
Published: May 2005

We study, from a constructive computational point of view, the techniques used to solve the conjugacy problem in the "generic" lattice-ordered group Aut(ℝ). We use these techniques in order to show that for all f, g ∈ Aut (ℝ), the equation xfx = g is effectively solvable in Aut(ℝ).
PROPER ACTIONS OF AUTOMORPHISM GROUPS OF FREE PRODUCTS OF FINITE GROUPS
Authors: CHEN YUQING , GLOVER HENRY H. , JENSEN CRAIG A.
Published: May 2005

If G is a free product of finite groups, let Σ Aut 1(G) denote all (necessarily symmetric) automorphisms of G that do not permute factors in the free product. We show that a McCullough–Miller and Gutiérrez–Krstić derived (also see Bogley–Krstić) space of pointed trees is an [Formula: see text]-space for these groups.
THE PERKINS SEMIGROUP HAS CO-NP-COMPLETE TERM-EQUIVALENCE PROBLEM
Authors: SEIF STEVE
Published: May 2005

A semigroup term is a finite word in the alphabet x1, x2,…. The length of a term p, denoted by |p|, is the number of variables in p, including multiplicities. The term-equivalence problem for a finite semigroup S has as an instance a pair of terms {p,q} with size |p| + |q| and asks whether p ≈ q is an identity over S. It is proved here that [Formula: see text], the six-element Perkins semigroup, has co-NP-complete term-equivalence problem, a result which leads to the completion of the classification of he term-equivalence problems for monoid extensions of aperiodic Rees matrix semigroups. From the main result it follows that there exist finite semigroups with tractable term-equivalence problems but having subsemigroups and homomorphic images with co-NP-complete term-equivalence problems.
CONSTRUCTIVE RECOGNITION OF NORMALIZERS OF SMALL EXTRA-SPECIAL MATRIX GROUPS
Authors: NIEMEYER ALICE C.
Published: May 2005

The members of the class C6in Aschbacher's structure theorem for subgroups of the general linear group GL (d,q) are the normalizers of certain absolutely irreducible, symplectic-type r-groups, where r is a prime, d a power of r and q ≡ 1 ( mod r). For a prime r > 2 and d = r, we present a constructive one-sided Monte Carlo algorithm to recognize whether or not a given subgroup G of GL (r,q) contains a normal extra-special r-group of order r3and exponent r. In the former case the algorithm returns a homomorphism from G into SL (2,r) with kernel being the extra-special r-group times the center.
TAMENESS OF THE PSEUDOVARIETY OF ABELIAN GROUPS
Authors: ALMEIDA JORGE , DELGADO MANUEL
Published: May 2005

In this paper we prove that the pseudovariety of Abelian groups is hyperdecidable and moreover that it is completely tame. This is a consequence of the fact that a system of group equations on a free Abelian group with certain rational constraints is solvable if and only if it is solvable in every finite quotient.
HOW FINITE IS A THREE-ELEMENT UNARY ALGEBRA?
Authors: HYNDMAN J. , PITKETHLY J. G.
Published: May 2005

We show that, within the class of three-element unary algebras, there is a tight connection between a finitely based quasi-equational theory, finite rank, enough algebraic operations (from natural duality theory) and a special injectivity condition.
MINIMAL CUBINGS
Authors: NIBLO GRAHAM , SAGEEV MICHAH , SCOTT PETER , SWARUP GADDE A.
Published: May 2005

We combine ideas of Scott and Swarup on good position for almost invariant subsets of a group with ideas of Sageev on constructing cubings from such sets. We construct cubings which are more canonical than in Sageev's original construction. We also show that almost invariant sets can be chosen to be in very good position.
DETERMINING THE DIMENSIONS OF VARIABLES IN PHYSICS ALGEBRAIC EQUATIONS
Authors: LIEW C. W. , SHAPIRO JOEL A. , SMITH D. E.
Published: May 2005

This paper describes work on methods that evaluate algebraic solutions to word problems in physics. Many current tutoring systems rely on substantial scaffolding and consequently require students to completely describe every variable used in the solution. A heuristic, based on constraint propagation, capable of inferring the description of variables (i.e., the possible dimensions and physics concepts) is shown to be highly reliable on three real world data sets, one covering a few problems with a small number of student answers and two others covering a large class of problems (~100) with a large number of student answers (~11,000). The heuristic uniquely determines the dimensions of all the variables in 91–92% of the equation sets. By asking the student for dimension information about one variable, an additional 3% of the sets can be determined. An ITS tutoring system can use this heuristic to reason about a student's answers even when the scaffolding and context are removed.
CLASSIFICATION IN CATEGORY CONJUNCTION: THE LOGIC OF OVEREXTENSION
Authors: COSTELLO FINTAN J.
Published: May 2005

Traditional approaches to semantics give a set-theoretic account of category conjunction, in which an item will be a member of a conjunction A&B only if it is a member of the single category A and a member of the single category B. However, a number of studies have found that people do not follow this set-theoretic account when classifying items in certain natural-language conjunctions. For example, Hampton1 found that while people tend to classify 'toucans' as non-members of the single category 'pet', they classify 'toucans' as members of the conjunction 'pet bird'. This paper describes a general approach to category conjunction that gives a logically consistent explanation for the occurrence of overextension in these conjunctions. The paper also describes a computational model implementing this approach, and an experiment using conjunctions of controlled, laboratory-learned categories to test this model. This computational model gave a good fit to both classification and overextension results in the experiment. The approach to conjunction implemented in this model may provide a useful tool for AI models of classification, allowing them to reason about category conjunction in a way that reflects human reasoning.
A GRAPH MATCHING ALGORITHM AND ITS APPLICATION TO CONCEPTUAL SYSTEM TRANSLATION
Authors: FENG YING , GOLDSTONE ROBERT L. , MENKOV VLADIMIR
Published: May 2005

ABSURDIST II, an extension to ABSURDIST, is an algorithm using attributed graph matching to find translations between conceptual systems. It uses information about the internal structure of systems by itself, or in combination with external information about concept similarities across systems. It supports systems with multiple types of weighted or unweighted, directed or undirected relations between concepts. The algorithm exploits graph sparsity to improve computational efficiency. We present the results of experiments with a number of conceptual systems, including artificially constructed random graphs with introduced distortions.
APPLICATIVE AND COMBINATORY CATEGORIAL GRAMMAR AND SUBORDINATE CONSTRUCTIONS IN FRENCH
Authors: BISKRI ISMAÏL
Published: May 2005

In this article we will present a classification and an analysis, by means of Applicative and Combinatory Categorial Grammar (ACCG), of relative, completive and indirect interrogative propositions in French introduced by "que" and "qui". Applicative and Combinatory Categorial Grammar is a generalization of standard Categorial Grammar. It is represented by a canonical association between Steedman's Combinatory Categorial rules and Curry's combinators. This model is included in the general framework of Applicative and Cognitive Grammar with three levels of representation: (i) phenotype (concatened expressions); (ii) genotype (applicative expressions); (iii) the cognitive representations (meaning of linguistic predicates). We are interested only in phenotype and genotype levels.
SEDATION OF SIMULATED ICU PATIENTS USING REINFORCEMENT LEARNING BASED CONTROL
Authors: SINZINGER ERIC D. , MOORE BRETT
Published: May 2005

The Intensive Care Unit (ICU) is a challenging environment to both patient and caregiver. Continued shortages in staffing increase risk to patients. To evaluate the use of intelligent systems in the improvement of patient care, an intelligent agent was developed to regulate ICU patient sedation. A temporal differencing form of reinforcement learning was used to train the agent in the administration of intravenous propofol in simulated ICU patients. The agent utilized a well-studied pharmacokinetic model to calculate the distribution of drug within the patient. Pharmacodynamics were then estimated for the drug effect. A derivative of the electroencephalograms, the bispectral index, served as the system control variable. The agent demonstrated satisfactory control of the simulated patient's consciousness level in static and dynamic setpoint conditions. The agent demonstrated superior stability and responsiveness when compared to a well-tuned PID controller, the control method of choice in closed-loop sedation control literature.
UNDERSTANDING CASE BASED RECOMMENDATION: A SIMILARITY KNOWLEDGE PERSPECTIVE
Authors: O' SULLIVAN DERRY , SMYTH BARRY , WILSON DAVID
Published: May 2005

Recommender systems bring together ideas from information retrieval and filtering, user profiling, and machine learning in an attempt to provide users with more proactive and personalized information systems. Forwarded as a response to the information overload problem, recommender systems have enjoyed considerable theoretical and practical successes, with a range of core techniques and a compelling array of evaluation studies to demonstrate success in many real-world domains. That said, there is much yet to understand about the strengths and weaknesses of recommender systems technologies and in this article, we make a fine-grained analysis of a successful case-based recommendation approach. We describe a detailed, fine-grained ablation study of similarity knowledge and similarity metric contributions to improved system performance. In particular, we extend our earlier analyses to examine how measures of interestingness can be used to identify and analyse relative contributions of segments of similarity knowledge. We gauge the strengths and weaknesses of knowledge components and discuss future work as well as implications for research in the area.
MODELING SELECTIVE PERCEPTION OF COMPLEX, NATURAL SCENES
Authors: CANOSA ROXANNE
Published: May 2005

Computational modeling of the human visual system is of current interest to developers of artificial vision systems, primarily because a biologically-inspired model can offer solutions to otherwise intractable image understanding problems. The purpose of this study is to present a biologically-inspired model of selective perception that augments a stimulus-driven approach with a high-level algorithm that takes into account particularly informative regions in the scene. The representation is compact and given in the form of a topographic map of relative perceptual conspicuity values. Other recent attempts at compact scene representation consider only low-level information that codes salient features such as color, edge, and luminance values. The previous attempts do not correlate well with subjects' fixation locations during viewing of complex images or natural scenes. This study uses high-level information in the form of figure/ground segmentation, potential object detection, and task-specific location bias. The results correlate well with the fixation densities of human viewers of natural scenes, and can be used as a preprocessing module for image understanding or intelligent surveillance applications.
PROTOTYPE CLASSIFIER DESIGN WITH PRUNING
Authors: LI JIANG , MANRY MICHAEL T. , YU CHANGHUA , WILSON D. RANDALL
Published: May 2005

Algorithms reducing the storage requirement of the nearest neighbor classifier (NNC) can be divided into three main categories: Fast searching algorithms, Instance-based learning algorithms and Prototype based algorithms. We propose an algorithm, LVQPRU, for pruning NNC prototype vectors and a compact classifier with good performance is obtained. The basic condensing algorithm is applied to the initial prototypes to speed up the learning process. The learning vector quantization (LVQ) algorithm is utilized to fine tune the remaining prototypes during each pruning iteration. We evaluate LVQPRU on several data sets along with 12 other algorithms using ten-fold cross-validation. Simulation results show that the proposed algorithm has high generalization accuracy and good storage reduction ratios.
LEARNING TASK-SPECIFIC SENSING, CONTROL AND MEMORY POLICIES
Authors: RAJENDRAN SRIVIDHYA , HUBER MANFRED
Published: May 2005

AI agents and robots that can adapt and handle multiple tasks in real time promise to be a powerful tool. To address the control challenges involved in such systems, the underlying control approach has to take into account the important sensory information. Modern sensors, however, can generate huge amounts of data, rendering the processing and representation of all sensor data in real time computationally intractable. This issue can be addressed by developing task-specific focus of attention strategies that limit the sensory data that is processed at any point in time to the data relevant for the given task. Alone, however, this mechanism is not adequate for solving complex tasks since the robot also has to maintain selected pieces of past information. This necessitates AI agents and robots to have the capability to remember significant past events that are required for task completion. This paper presents an approach that considers focus of attention as a problem of selecting controller and feature pairs to be processed at any given point in time to optimize system performance. This approach is further extended by incorporating short term memory and a learned memory management policy. The result is a system that learns control, sensing, and memory policies that are task-specific and adaptable to real world situations using feedback from the world in a reinforcement learning framework. The approach is illustrated using table cleaning, sorting, stacking, and copying tasks in the blocks world domain.
RECURRENT NEURAL NETWORKS FOR MUSICAL PITCH MEMORY AND CLASSIFICATION
Authors: FRANKLIN JUDY A. , LOCKE KRYSTAL K.
Published: May 2005

We present results from experiments in using several pitch representations for jazz-oriented musical tasks performed by a recurrent neural network. We have run experiments with several kinds of recurrent networks for this purpose, and have found that Long Short-term Memory networks provide the best results. We show that a new pitch representation called Circles of Thirds works as well as two other published representations for these tasks, yet it is more succinct and enables faster learning. We then discuss limited results using other types of networks on the same tasks.
A GENERATE-AND-SENSE APPROACH TO AUTOMATED MUSIC COMPOSITION
Authors: KIM SUNJUNG , ANDRÉ ELISABETH
Published: May 2005

Nobody would deny that music may evoke deep and profound emotions. In this paper, we present a perceptual music composition system that aims at the controlled manipulation of a user's emotional state. In contrast to traditional composing techniques, the single components of a composition, such as melody, harmony, rhythm and instrumentation, are selected and combined in a user-specific manner without requiring the user to continuously provide comments on the music employing input devices, such as keyboard or mouse.
ON FERMION ENTANGLEMENT
Authors: KAPLAN T. A.
Published: May 2005

Under the historical definition of entanglement, namely that encountered in Einstein–Podolski–Rosen (EPR)–type experiments, it is shown that a particular Slater determinant is entangled. Thus a definition which holds that any Slater determinant is unentangled, found in the literature, is inconsistent with the historical definition. A generalization of the historical definition that embodies its meaning as quantum correlation of observables, in the spirit of the work of many others, but is much simpler and more physically transparent, is presented.
Effects of the JNK inhibitor anthra[1,9-cd]pyrazol-6(2H)-one (SP-600125) on soluble guanylyl cyclase α1 gene regulation and cGMP synthesis
Authors: Krumenacker Joshua S. , Kots Alexander , Murad Ferid
Published: May 2005

The decreased expression of the nitric oxide (NO) receptor, soluble guanylyl cyclase (sGC), occurs in response to multiple stimuli in vivo and in cell culture and correlates with various disease states such as hypertension, inflammation, and neurodegenerative disorders. The ability to understand and modulate sGC expression and cGMP levels in any of these conditions could be a valuable therapeutic tool. We demonstrate herein that the c-Jun NH2-terminal kinase JNK II inhibitor anthra[1,9- cd]pyrazol-6(2 H)-one (SP-600125) completely blocked the decreased expression of sGCα1-subunit mRNA by nerve growth factor (NGF) in PC12 cells. Inhibitors of the ERK and p38 MAPK pathways, PD-98059 and SB-203580, had no effect. SP-600125 also inhibited the NGF-mediated decrease in the expression of sGCα1 protein as well as sGC activity in PC12 cells. Other experiments revealed that decreased sGCα1 mRNA expression through a cAMP-mediated pathway, using forskolin, was not blocked by SP-600125. We also demonstrate that TNF-α/IL-1β stimulation of rat fetal lung (RFL-6) fibroblast cells resulted in sGCα1 mRNA inhibition, which was blocked by SP-600125. Expression of a constitutively active JNKK2-JNK1 fusion protein in RFL-6 cells caused endogenous sGCα1 mRNA levels to decrease, while a constitutively active ERK2 protein had no effect. Collectively, these data demonstrate that SP-600125 may influence the intracellular levels of the sGCα1-subunit in certain cell types and may implicate a role for c-Jun kinase in the regulation of sGCα1 expression.
Wnt/β-catenin signaling activates growth-control genes during overload-induced skeletal muscle hypertrophy
Authors: Armstrong Dustin D. , Esser Karyn A.
Published: May 2005

β-Catenin is a transcriptional activator shown to regulate the embryonic, postnatal, and oncogenic growth of many tissues. In most research to date, β-catenin activation has been the unique downstream function of the Wnt signaling pathway. However, in the heart, a Wnt-independent mechanism involving Akt-mediated phosphorylation of glycogen synthase kinase (GSK)-3β was recently shown to activate β-catenin and regulate cardiomyocyte growth. In this study, results have identified the activation of the Wnt/β-catenin pathway during hypertrophy of mechanically overloaded skeletal muscle. Significant increases in β-catenin were determined during skeletal muscle hypertrophy. In addition, the Wnt receptor, mFrizzled (mFzd)-1, the signaling mediator disheveled-1, and the transcriptional co-activator, lymphocyte enhancement factor (Lef)-1, are all increased during hypertrophy of the overloaded mouse plantaris muscle. Experiments also determined an increased association between GSK-3β and the inhibitory frequently rearranged in advanced T cell-1 protein with no increase in GSK-3β phosphorylation (Ser9). Finally, skeletal muscle overload resulted in increased nuclear β-catenin/Lef-1 expression and induction of the transcriptional targets c-Myc, cyclin D1, and paired-like homeodomain transcription factor 2. Thus this study provides the first evidence that the Wnt signaling pathway induces β-catenin/Lef-1 activation of growth-control genes during overload induced skeletal muscle hypertrophy.
Activation of NHE3 by dexamethasone requires phosphorylation of NHE3 at Ser663 by SGK1
Authors: Wang Dongsheng , Sun Hong , Lang Florian , Yun C. Chris
Published: May 2005

Glucocorticoids stimulate Na+ absorption by activation of the epithelial Na+/H+ exchanger NHE3 in the kidney and intestine. It has been thought that glucocorticoid-induced activation of NHE3 is solely dependent on transcriptional induction of the NHE3 gene. While the transcriptional regulation remains an essential part of the chronic effect of glucocorticoids, a previous study by us identified the serum- and glucocorticoid-inducible kinase 1 (SGK1) as an important component of the activation of NHE3 by glucocorticoids. In this work, we have demonstrated phosphorylation of NHE3 by SGK1 as the key mechanism for the stimulation of the transport activity by glucocorticoids. By using in vitro SGK1 kinase assay and site-directed mutagenesis, we have identified Ser663 of NHE3 to be the major site of phosphorylation by SGK1. Ser663 is invariantly conserved in all NHE3 proteins from several species, and the mutation of Ser663 to Ala blocks the effect of dexamethasone, demonstrating the importance of phosphorylation at Ser663. We also show that phosphorylation of NHE3 precedes the changes in NHE3 activity, and the increased activity is associated with an increased amount of NHE3 proteins in the surface membrane. These data reveal that dexamethasone activates NHE3 activity by phosphorylating the NHE3 protein, which initiates trafficking of the protein into the plasma membrane.
Transient upregulation of GRP and its receptor critically regulate colon cancer cell motility during remodeling
Authors: Glover Sarah , Nathaniel Rajkumar , Shakir Lubna , Perrault Cecile , Anderson Rebecca K. , Tran-Son-Tay Roger , Benya Richard V.
Published: May 2005

Gastrin-releasing peptide (GRP) is typically viewed as a growth factor in cancer. However, we have suggested that in colon cancer, GRP acts primarily as a morphogen when it and its receptor (GRP-R) are aberrantly upregulated. As such, GRP/GRP-R act(s) primarily to modulate processes contributing to the assumption or maintenance of tumor differentiation. One of the most important such processes is the ability of tumor cells to achieve directed motility in the context of tissue remodeling. Yet the cellular conditions affecting GRP/GRP-R expression, and the biochemical pathways involved in mediating its morphogenic properties, remain to be established. To study this, we evaluated the human colon cancer cell lines Caco-2 and HT-29 cells. We found that confluent cells do not express GRP/GRP-R. In contrast, disaggreation and plating at subconfluent densities results in rapid GRP/GRP-R upregulation followed by their progressive decrease as confluence is achieved. GRP/GRP-R coexpression correlated with that of focal adhesion kinase (FAK) phosphorylation of Tyr397, Tyr407, Tyr861, and Tyr925 but not Tyr576 or Tyr577. To more specifically evaluate the kinetics of GRP/GRP-R upregulation, we wounded confluent cell monolayers. At t = 0 h GRP/GRP-R were not expressed, yet cells immediately began migrating into the gap created by the wound. GRP/GRP-R were first detected at ∼2 h, and maximal levels were observed at ∼6 h postwounding. The GRP-specific antagonist [d-Phe6]-labeled bombesin methyl ester had no effect on cell motility before GRP-R expression. In contrast, this agent increasingly attenuated cell motility with increasing GRP-R expression such that from t = 6 h onward no further cell migration into the gap was observed. Overall, these findings indicate the existence of GRP-independent and -dependent phases of tumor cell remodeling with the latter mediating colon cancer cell motility during remodeling via FAK.
Binding of acellular, native and cross-linked human hemoglobins to haptoglobin: enhanced distribution and clearance in the rat
Authors: Ship Noam J. , Toprak Ayça , Lai Roseanna P. , Tseng Eric , Kluger Ronald , Pang K. Sandy
Published: May 2005

It is well established that hemoglobin resulting from red cell lysis binds to haptoglobin in plasma to form a complex. The increased molecular size precludes its filtration by the kidneys, redirecting it toward hepatocellular entry. Chemically cross-linked hemoglobins are designed to be resistant to renal excretion, even in the absence of haptoglobin. The manner in which binding to haptoglobin influences the pharmacokinetics of acellular cross-linked and native hemoglobins was investigated after intravenous injection of radiolabeled native human hemoglobin and trimesyl-(Lys82)β-(Lys82)β cross-linked human hemoglobin, at trace doses, into rats. Under these conditions, there is sufficient plasma haptoglobin for binding with hemoglobin. In vitro binding assayed by size-exclusion chromatography for bound and free hemoglobin revealed that, at <8 μM hemoglobin, native human hemoglobin was completely bound to rat haptoglobin, whereas only ∼30% of trimesyl-(Lys82)β-(Lys82)β cross-linked hemoglobin was bound. Plasma disappearance of low doses (0.31 μmol/kg) of native and cross-linked hemoglobins was monoexponential (half-life = 23 and 33 min, respectively). The volume of distribution (40 vs. 19 ml/kg) and plasma clearance (1.22 vs. 0.4 ml·min−1·kg−1) were higher for native than for cross-linked hemoglobin. Native and cross-linked human hemoglobins were found primarily in the liver, and not in the kidney, heart, lung, or spleen, mostly as degradation products. These pharmacokinetic findings suggest that the binding of hemoglobin to haptoglobin enhances its hepatocellular entry, clearance, and distribution.
Events at the Host-Microbial Interface of the Gastrointestinal Tract III. Cell-to-cell signaling among microbial flora, host, and pathogens: there is a whole lot of talking going on
Authors: Clarke Marcie B. , Sperandio Vanessa
Published: May 2005

Humans have an important association with their intestinal microbial flora. The microbial flora helps to shape the mammalian innate immune system, absorbs nutrients, and plays an intricate role on intestinal development. Microbes and mammals communicate with each other through an array of hormone and hormonelike chemical compounds. These “signals,” however, are hijacked by bacterial pathogens, such as enterohemorrhagic Eschrichia coli (EHEC), to activate its virulence genes, colonize the host, and start the disease process. This review explores the cell-to-cell signaling events in the gastrointestinal tract that lead EHEC to regulate its virulence genes in a coordinate manner.
Heart rate variability responses to hypoxic and hypercapnic exposures in different mouse strains
Authors: Campen Matthew J. , Tagaito Yugo , Jenkins Todd P. , Balbir Alex , O’Donnell Christopher P.
Published: May 2005

Heart rate variability (HRV) is a well-characterized, noninvasive means of assessing cardiac autonomic nervous system activity. This study examines the basic cardiac responses to hypoxic and hypercapnic challenges in seven strains of commonly used inbred mice (A/J, BALB/cJ, C3H/HeJ, C57BL/6J, CBA/J, DBA/2J, and FVB/J). Adult male mice, 8–12 wk of age, were chronically instrumented to a femoral artery catheter for the continuous measurement of systemic arterial blood pressure and heart rate. Mice were exposed to multiple 4-min periods of hypoxia (10% O2), hypercapnia (5% CO2), and combined hypoxia/hypercapnia (10% O2 + 5% CO2). HRV was derived from pulse intervals of the blood pressure tracings. Hypoxia induced increases in high-frequency HRV power and decreased low-frequency (LF) HRV power in most strains. Hypercapnia led to decreased high-frequency HRV power and increased LF HRV power in most strains. Strain differences were most notable in regard to the concomitant exposures of hypoxia and hypercapnia, with FVB/J mice mirroring their own response to hypercapnia alone, whereas CBA/J mice mirrored their own responses to hypoxia. As blood pressure is most likely the driving factor for heart rate changes via the baroreflex pathway, it is interesting that LF, considered to reflect cardiac sympathetic activity, was negatively correlated with heart rate, suggesting that LF changes are driven by baroreflex oscillation and not necessarily by absolute sympathetic or parasympathetic activity to the heart. These findings suggest that genetic background can influence the centrally mediated cardiovascular responses to basic hypoxic and hypercapnic challenges.
Positive end-expiratory pressure differentially alters pulmonary hemodynamics and oxygenation in ventilated, very premature lambs
Authors: Polglase Graeme R. , Morley Colin J. , Crossley Kelly J. , Dargaville Peter , Harding Richard , Morgan David L. , Hooper Stuart B.
Published: May 2005

In mature lungs, elevated positive end-expiratory pressure (PEEP) reduces pulmonary blood flow (PBF) and increases pulmonary vascular resistance (PVR). However, the effect of PEEP on PBF in preterm infants with immature lungs and a patent ductus arteriosus is unknown. Fetal sheep were catheterized at 124 days of gestation (term ∼147 days), and a flow probe was placed around the left pulmonary artery to measure PBF. At 127 days, lambs were delivered and ventilated from birth with a tidal volume of 5 ml/kg and 4-cmH2O PEEP; PEEP was changed to 0, 8, and 12 cmH2O in random order, returning to 4 cmH2O between each change. Increasing PEEP from 4 to 8 cmH2O and from 4 to 12 cmH2O decreased PBF by 20.5 and 41.0%, respectively, and caused corresponding changes in PVR; reducing PEEP from 4 to 0 cmH2O did not affect PBF. Despite decreasing PBF, increasing PEEP from 4 to 8 cmH2O and 12 cmH2O improved oxygenation of lambs. Increasing and decreasing PEEP from 4 cmH2O significantly changed the contour of the PBF waveform; at a PEEP of 12 cmH2O, end-diastolic flow was reduced by 82.8% and retrograde flow was reestablished. Although increasing PEEP improves oxygenation, it adversely affects PBF and PVR shortly after birth, alters the PBF waveform, and reestablishes retrograde flow during diastole.
Elevated temperature decreases sensitivity of P2X purinergic receptors in skeletal muscle arteries
Authors: Kluess Heidi A. , Buckwalter John B. , Hamann Jason J. , Clifford Philip S.
Published: May 2005

We hypothesized that elevated temperatures would attenuate but that reduced temperatures would potentiate the tension mediated by vascular P2X purinergic receptors. The femoral arteries of 24 rats were dissected out and placed in modified Krebs-Henseleit buffer. Arteries were cut into 2-mm sections and mounted in organ tissue baths. Maximal tension (g) was measured during a KCl and norepinephrine challenge. Tension was measured during doses of α,β-methylene ATP (10−7 to 10−3 M), phenylephrine (10−7 to 10−4 M), and acetylcholine (10−9 to 10−5 M), with tissue bath temperature adjusted to 35, 37, and 41°C. Dose-response curves were fit using nonlinear regression analysis to calculate the EC50 and slope. The peak tension was lower with α,β-methylene ATP during 41°C (1.49 ± 0.14 g) compared with 35°C (2.08 ± 0.09 g) and 37°C (1.94 ± 0.09 g; P < 0.05). Slope and EC50 were not affected by temperature. Tension produced by phenylephrine and relaxation to acetylcholine were not affected by temperature. These data indicate that the vasoconstrictor response to α,β-methylene ATP is sensitive to temperature. Moderate cooling does not potentiate P2X-mediated vasoconstriction, but elevated temperature attenuates the vasoconstrictor response to P2X purinergic receptors.