bluuebunny/crossref_metadata_2025 huggingface dataset:
Glycocalyx Restricts Adenoviral Vector Access to Apical Receptors Expressed on Respiratory Epithelium In Vitro and In Vivo: Role for Tethered Mucins as Barriers to Lumenal Infection
Authors: Stonebraker Jaclyn R. , Wagner Danielle , Lefensty Robert W. , Burns Kimberlie , Gendler Sandra J. , Bergelson Jeffrey M. , Boucher Richard C. , O'Neal Wanda K. , Pickles Raymond J.
Published: November 2004

Inefficient adenoviral vector (AdV)-mediated gene transfer to the ciliated respiratory epithelium has hindered gene transfer strategies for the treatment of cystic fibrosis lung disease. In part, the inefficiency is due to an absence of the coxsackie B and adenovirus type 2 and 5 receptor (CAR) from the apical membranes of polarized epithelia. In this study, using an in vitro model of human ciliated airway epithelium, we show that providing a glycosylphosphatidylinositol (GPI)-linked AdV receptor (GPI-CAR) at the apical surface did not significantly improve AdV gene transfer efficiency because the lumenal surface glycocalyx limited the access of AdV to apical GPI-CAR. The highly glycosylated tethered mucins were considered to be significant glycocalyx components that restricted AdV access because proteolytic digestion and inhibitors of O-linked glycosylation enhanced AdV gene transfer. To determine whether these in vitro observations are relevant to the in vivo situation, we generated transgenic mice expressing GPI-CAR at the surface of the airway epithelium, crossbred these mice with mice that were genetically devoid of tethered mucin type 1 (Muc1), and tested the efficiency of gene transfer to murine airways expressing apical GPI-human CAR (GPI-hCAR) in the presence and absence of Muc1. We determined that AdV gene transfer to the murine airway epithelium was inefficient even in GPI-hCAR transgenic mice but that the gene transfer efficiency improved in the absence of Muc1. However, the inability to achieve a high gene transfer efficiency, even in mice with a deletion of Muc1, suggested that other glycocalyx components, possibly other tethered mucin types, also provide a significant barrier to AdV interacting with the airway lumenal surface.
Hepatitis B Virus Nucleocapsids Formed by Carboxy-Terminally Mutated Core Proteins Contain Spliced Viral Genomes but Lack Full-Size DNA
Authors: Köck Josef , Nassal Michael , Deres Karl , Blum Hubert E. , von Weizsäcker Fritz
Published: November 2004

The carboxy-terminal sequence of the hepatitis B virus (HBV) core protein constitutes a nucleic acid binding domain that is rich in arginine residues and contains three serine phosphorylation sites. While dispensable for capsid assembly, this domain is involved in viral replication, as demonstrated by the effects of mutations on RNA packaging and/or reverse transcription; however, the underlying mechanisms are poorly understood. Here we tested a series of core protein mutants in which the three serine phosphorylation sites were replaced by glutamic acid, in parallel with a previously described deletion variant lacking the 19 C-terminal amino acid residues, for their ability to support viral replication in transfected hepatoma cells. Replacement of all serines and the deletion gave rise to nucleocapsids containing a smaller than wild-type DNA genome. Rather than a single-stranded DNA intermediate, as previously thought, this was a 2.0-kbp double-stranded DNA molecule derived from spliced pregenomic RNA (pgRNA). Interestingly, full-length pgRNA was associated with nucleocapsids but was found to be sensitive to nuclease digestion, while encapsidated spliced RNA and 3′ truncated RNA species were nuclease resistant. These findings suggest that HBV pgRNA encapsidation is directional and that a packaging limit is determined by the C-terminal portion of the core protein.
Efficacy of DNA and Fowlpox Virus Priming/Boosting Vaccines for Simian/Human Immunodeficiency Virus
Authors: Dale C. J. , De Rose R. , Stratov I. , Chea S. , Montefiori D. C. , Thomson S. , Ramshaw I. A. , Coupar B. E. H. , Boyle D. B. , Law M. , Kent S. J.
Published: November 2004

Further advances are required in understanding protection from AIDS by T-cell immunity. We analyzed a set of multigenic simian/human immunodeficiency virus (SHIV) DNA and fowlpox virus priming and boosting vaccines for immunogenicity and protective efficacy in outbred pigtail macaques. The number of vaccinations required, the effect of DNA vaccination alone, and the effect of cytokine (gamma interferon) coexpression by the fowlpox virus boost was also studied. A coordinated induction of high levels of broadly reactive CD4 and CD8 T-cell immune responses was induced by sequential DNA and fowlpox virus vaccination. The immunogenicity of regimens utilizing fowlpox virus coexpressing gamma interferon, a single DNA priming vaccination, or DNA vaccines alone was inferior. Significant control of a virulent SHIV challenge was observed despite a loss of SHIV-specific proliferating T cells. The outcome of challenge with virulent SHIV
mn229
correlated with vaccine immunogenicity except that DNA vaccination alone primed for protection almost as effectively as the DNA/fowlpox virus regimen despite negligible immunogenicity by standard assays. These studies suggest that priming of immunity with DNA and fowlpox virus vaccines could delay AIDS in humans.
Long-Term Excretion of Vaccine-Derived Poliovirus by a Healthy Child
Authors: Martín Javier , Odoom Kofi , Tuite Gráinne , Dunn Glynis , Hopewell Nicola , Cooper Gill , Fitzharris Catherine , Butler Karina , Hall William W. , Minor Philip D.
Published: November 2004

A child was found to be excreting type 1 vaccine-derived poliovirus (VDPV) with a 1.1% sequence drift from Sabin type 1 vaccine strain in the VP1 coding region 6 months after he was immunized with oral live polio vaccine. Seventeen type 1 poliovirus isolates were recovered from stools taken from this child during the following 4 months. Contrary to expectation, the child was not deficient in humoral immunity and showed high levels of serum neutralization against poliovirus. Selected virus isolates were characterized in terms of their antigenic properties, virulence in transgenic mice, sensitivity for growth at high temperatures, and differences in nucleotide sequence from the Sabin type 1 strain. The VDPV isolates showed mutations at key nucleotide positions that correlated with the observed reversion to biological properties typical of wild polioviruses. A number of capsid mutations mapped at known antigenic sites leading to changes in the viral antigenic structure. Estimates of sequence evolution based on the accumulation of nucleotide changes in the VP1 coding region detected a “defective” molecular clock running at an apparent faster speed of 2.05% nucleotide changes per year versus 1% shown in previous studies. Remarkably, when compared to several type 1 VDPV strains of different origins, isolates from this child showed a much higher proportion of nonsynonymous versus synonymous nucleotide changes in the capsid coding region. This anomaly could explain the high VP1 sequence drift found and the ability of these virus strains to replicate in the gut for a longer period than expected.
Prototype Foamy Virus Envelope Glycoprotein Leader Peptide Processing Is Mediated by a Furin-Like Cellular Protease, but Cleavage Is Not Essential for Viral Infectivity
Authors: Duda Anja , Stange Annett , Lüftenegger Daniel , Stanke Nicole , Westphal Dana , Pietschmann Thomas , Eastman Scott W. , Linial Maxine L. , Rethwilm Axel , Lindemann Dirk
Published: November 2004

Analogous to cellular glycoproteins, viral envelope proteins contain N-terminal signal sequences responsible for targeting them to the secretory pathway. The prototype foamy virus (PFV) envelope (Env) shows a highly unusual biosynthesis. Its precursor protein has a type III membrane topology with both the N and C terminus located in the cytoplasm. Coexpression of FV glycoprotein and interaction of its leader peptide (LP) with the viral capsid is essential for viral particle budding and egress. Processing of PFV Env into the particle-associated LP, surface (SU), and transmembrane (TM) subunits occur posttranslationally during transport to the cell surface by yet-unidentified cellular proteases. Here we provide strong evidence that furin itself or a furin-like protease and not the signal peptidase complex is responsible for both processing events. N-terminal protein sequencing of the SU and TM subunits of purified PFV Env-immunoglobulin G immunoadhesin identified furin consensus sequences upstream of both cleavage sites. Mutagenesis analysis of two overlapping furin consensus sequences at the PFV LP/SU cleavage site in the wild-type protein confirmed the sequencing data and demonstrated utilization of only the first site. Fully processed SU was almost completely absent in viral particles of mutants having conserved arginine residues replaced by alanines in the first furin consensus sequence, but normal processing was observed upon mutation of the second motif. Although these mutants displayed a significant loss in infectivity as a result of reduced particle release, no correlation to processing inhibition was observed, since another mutant having normal LP/SU processing had a similar defect.
Cooperation between Different Forms of the Human Papillomavirus Type 1 E4 Protein To Block Cell Cycle Progression and Cellular DNA Synthesis
Authors: Knight Gillian L. , Grainger John R. , Gallimore Phillip H. , Roberts Sally
Published: November 2004

Posttranslational modification—oligomerization, phosphorylation, and proteolytic cleavage—of the human papillomavirus (HPV) E4 protein occurs as the infected keratinocytes migrate up through the suprabasal wart layers. It has been postulated that these events modify E4 function during the virus life cycle. In HPV type 1 (HPV1)-induced warts, N-terminal sequences are progressively cleaved from the full-length E4 protein (E1
∧
E4) of 17 kDa to produce a series of polypeptides of 16, 11 and 10 kDa. Here, we have shown that in human keratinocytes, a truncated protein (E4-16K), equivalent to the 16-kDa species, mediated a G
2
arrest in the cell cycle that was dependent on a threonine amino acid in a proline-rich domain of the protein. Reconstitution of cyclin B1 expression in E4-16K cells reversed the G
2
arrest. Expression of E4-16K also induced chromosomal rereplication, and this was associated with aberrant nuclear morphology. Perturbation of the mitotic cell cycle was a biological activity specific to the truncated protein. However, coexpression of the full-length E1
∧
E4 protein and the truncated E4-16K protein inhibited normal cellular proliferation and cellular DNA rereplication but did not prevent cells from arresting in G
2
. Our findings provide the first evidence to support the hypothesis that proteolytic cleavage of the E1
∧
E4 protein modifies its function. Also, different forms of the HPV1 E4 protein cooperate to negatively influence keratinocyte proliferation. We predict that these distinct biological activities of E4 act to support efficient amplification of the viral genome in suprabasal keratinocytes.
A Dominant Role for CD8+-T-Lymphocyte Selection in Simian Immunodeficiency Virus Sequence Variation
Authors: O'Connor David H. , McDermott Adrian B. , Krebs Kendall C. , Dodds Elizabeth J. , Miller Jacqueline E. , Gonzalez Edna J. , Jacoby Timothy J. , Yant Levi , Piontkivska Helen , Pantophlet Ralph , Burton Dennis R. , Rehrauer William M. , Wilson Nancy , Hughes Austin L. , Watkins David I.
Published: November 2004

CD8+T lymphocytes (CD8-TL) select viral escape variants in both human immunodeficiency virus and simian immunodeficiency virus (SIV) infections. The frequency of CD8-TL viral escape as well as the contribution of escape to overall virus diversification has not been assessed. We quantified CD8-TL selection in SIV infections by sequencing viral genomes from 35 SIVmac239-infected animals at the time of euthanasia. Here we show that positive selection for sequences encoding 46 known CD8-TL epitopes is comparable to the positive selection observed for the variable loops ofenv. We also found that >60% of viral variation outside of the viral envelope occurs within recognized CD8-TL epitopes. Therefore, we conclude that CD8-TL selection is the dominant cause of SIV diversification outside of the envelope.
Clinical Latency and Reactivation of AIDS-Related Mycobacterial Infections
Authors: Shen Yun , Shen Ling , Sehgal Prabhat , Huang Dan , Qiu Liyou , Du George , Letvin Norman L. , Chen Zheng W.
Published: November 2004

The immune mechanisms associated with the evolution from latent to clinically active mycobacterial coinfection in human immunodeficiency virus type 1 (HIV-1)-infected humans remain poorly understood. Previous work has demonstrated that macaques infected with simian immunodeficiency virus (SIVmac) can develop persistentMycobacterium bovisBCG coinfection and a fatal SIV-related tuberculosis-like disease by 4 months after BCG inoculation. In the present study, SIVmac-infected monkeys that developed clinically quiescent mycobacterial infection after BCG inoculation were followed prospectively for the reactivation of the BCG and the development of SIV-related tuberculosis-like disease. The development of clinically latent BCG coinfection in these SIVmac-infected monkeys was characterized by a change from high to undetectable levels of bacterial organisms, with or without measurable BCG mRNA expression in lymph node cells. The reactivation of clinically latent BCG coinfection and development of SIV-related tuberculosis-like disease were then observed in these SIVmac-BCG-coinfected monkeys during a 21-month period of follow-up. The reactivation of SIV-related tuberculosis-like disease in these animals coincided with a severe depletion of CD4 T cells and a loss of BCG-specific T-cell responses. Interestingly, bacterial superantigen challenge of the SIVmac-BCG-coinfected monkeys resulted in an up-regulation of clinically latent BCG coinfection, suggesting that infection with superantigen-producing microbes may increase the susceptibility of individuals to the reactivation of AIDS-related mycobacterial coinfection. Thus, reactivation of latent mycobacterial infections in HIV-1-infected individuals may result from a loss of T-cell immunity or from a superimposed further compromise of the immune system.
Infectious Molecular Clone of a Recently Transmitted Pediatric Human Immunodeficiency Virus Clade C Isolate from Africa: Evidence of Intraclade Recombination
Authors: Grisson Ricky D. , Chenine Agnès-Laurence , Yeh Lan-Yu , He Jun , Wood Charles , Bhat Ganapati J. , Xu Weidong , Kankasa Chipepo , Ruprecht Ruth M.
Published: November 2004

Although human immunodeficiency virus type 1 (HIV-1) clade C continues to dominate the pandemic, only two infectious clade C proviral DNA clones have been described (N. Mochizuki, N. Otsuka, K. Matsuo, T. Shiino, A. Kojima, T. Kurata, K. Sakai, N. Yamamoto, S. Isomura, T. N. Dhole, Y. Takebe, M. Matsuda, and M. Tatsumi, AIDS Res. Hum. Retrovir.
15:
1321-1324, 1999; T. Ndung'u, B. Renjifo, and M. Essex, J. Virol.
75:
4964-4972, 2001). We have generated an infectious molecular clone of a pediatric clade C strain, HIV1084i, which was isolated from a Zambian infant infected either intrapartum or through breastfeeding. HIV1084i is an R5, non-syncytium-inducing isolate that bears all known clade C signatures;
gag
,
pol
, and
env
consistently mapped within clade C. Interestingly,
gag
resembled Asian isolates, whereas
pol
and
env
resembled African isolates, indicating that HIV1084i probably arose from an intraclade recombination. As a recently transmitted clade C strain, HIV1084i will be a useful vaccine development tool.
Abnormally high serum ferritin levels among professional road cyclists
Authors: Zotter H , Robinson N , Zorzoli M , Schattenberg L , Saugy M , Mangin P
Published: November 2004

Background:An international, longitudinal medical follow up examination of male professional road cyclists revealed excessively elevated serum ferritin levels.

Objective:To evaluate the importance of elevated ferritin values among professional cyclists, their relationship with age and nationality, and their evolution over 3 years.

Methods:Over 1000 serum ferritin values were collected. Other parameters were included in order to exclude conditions which might have increased ferritin levels without changing body iron stores.

Results:In 1999, over 45% of riders displayed ferritin values above 300 ng/ml and one fourth levels over 500 ng/ml. These percentages had decreased to 27% and 9%, respectively, 3 years later, while the overall average, which was above the normal limits in 1999, had decreased by 33% in 3 years. Older cyclists had higher ferritin values than younger cyclists. There was also a relationship between ferritin levels and the nationality of the cyclists. Analysis of 714 riders in 2000 and 2002 showed only a slight and insignificant decrease in the mean ferritin value although those with initially elevated iron stores had a much greater decrease.

Conclusion:Professional road cyclists used excessive iron supplementation leading to high serum ferritin levels correlating with increased body iron stores. Although the situation progressively improved over 3 years, it remains worrying as increased body iron stores are related to health complications. Therefore, prevention in addition to the fight against doping should be a main goal of the UCI. Aggressive therapy for athletes with excessive ferritin values should be carried out at or before the end of their careers.
Weight changes, medical complications, and performance during an Ironman triathlon
Authors: Sharwood K A , Collins M , Goedecke J H , Wilson G , Noakes T D
Published: November 2004

Background:Subjects exercising without fluid ingestion in desert heat terminated exercise when the total loss in body weight exceeded 7%. It is not known if athletes competing in cooler conditions with free access to fluid terminate exercise at similar levels of weight loss.

Objectives:To determine any associations between percentage weight losses during a 224 km Ironman triathlon, serum sodium concentrations and rectal temperatures after the race, and prevalence of medical diagnoses.

Methods:Athletes competing in the 2000 and 2001 South African Ironman triathlon were weighed on the day of registration and again immediately before and immediately after the race. Blood pressure and serum sodium concentrations were measured at registration and immediately after the race. Rectal temperatures were also measured after the race, at which time all athletes were medically examined. Athletes were assigned to one of three groups according to percentage weight loss during the race.

Results:Body weight was significantly (p<0.0001) reduced after the race in all three groups. Serum sodium concentrations were significantly (p<0.001) higher in athletes with the greatest percentage weight loss. Rectal temperatures were the same in all groups, with only a weak inverse association between temperature and percentage weight loss. There were no significant differences in diagnostic indices of high weight loss or incidence of medical diagnoses between groups.

Conclusions:Large changes in body weight during a triathlon were not associated with a greater prevalence of medical complications or higher rectal temperatures but were associated with higher serum sodium concentrations.
Evidence for complex system integration and dynamic neural regulation of skeletal muscle recruitment during exercise in humans
Authors: St Clair Gibson A , Noakes T D
Published: November 2004

A model is proposed in which the development of physical exhaustion is a relative rather than an absolute event and the sensation of fatigue is the sensory representation of the underlying neural integrative processes. Furthermore, activity is controlled as part of a pacing strategy involving active neural calculations in a “governor” region of the brain, which integrates internal sensory signals and information from the environment to produce a homoeostatically acceptable exercise intensity. The end point of the exercise bout is the controlling variable. This is an example of a complex, non-linear, dynamic system in which physiological systems interact to regulate activity before, during, and after the exercise bout.
The role of serum insulin-like growth factor I (IGF-I) in neonatal outcome
Authors: Hayati A R , Cheah F C , Yong J F , Tan A E , Norizah W M
Published: November 2004

Aims:To determine the role of serum insulin-like growth factor I (IGF-I) in predicting the occurrence of septal hypertrophic cardiomyopathy in infants of mothers with diabetes.

Methods/materials:In this prospective study, 100 pregnant women (50 with diabetes and 50 controls), matched for age and race, were studied. One intrapartum blood sample was taken at 28 weeks of gestation from both groups of mothers and another sample at delivery. All samples were analysed for maternal IGF-I by an enzyme linked immunosorbent assay method. A chest radiograph and an electrocardiogram were performed on the babies of the mothers with diabetes within the first 24 hours of life. An echocardiogram was performed in the first 3 days of life to look for septal hypertrophy and to measure the myocardial thickness.

Results:In the six cases of neonatal septal hypertrophic cardiomyopathy, all the mothers had greatly raised IGF-I concentrations of more than 400 ng/ml at the time of delivery compared with a mean (SD) of 302 (25) ng/ml in control mothers.

Conclusions:In the present study a crude analysis revealed that increased IGF-I concentrations correlate with neonatal septal hypertrophic cardiomyopathy.
Design of a real time quantitative PCR assay to assess global mRNA amplification of small size specimens for microarray hybridisation
Authors: Choesmel V , Foucault F , Thiery J P , Blin N
Published: November 2004

Background:Low RNA yields from clinical samples are a limiting step for microarray technology.

Aims:To design an accurate real time quantitative polymerase chain reaction (PCR) assay to assess the crucial step of global mRNA amplification performed before microarray hybridisation, using less than 1 µg total RNA.

Methods:Three RNA extraction procedures were compared for small size samples. Total RNA was amplified from universal RNA or the BC-H1 breast cancer micrometastatic cell line using three different protocols. Real time quantitative PCR technology was used for accurate measurement of urokinase plasminogen activator receptor and cytokeratin 8 RNA amplification rates and ratios, using primer sets binding at various distances from the 3′ end of transcripts. A 50 mer oligomeric array targeting 87 genes potentially involved in breast cancer metastatic progression was built and hybridised with amplified RNA.

Results:Eighteen nanograms of total RNA could be purified from 1000 BC-H1 micrometastatic cells. Amplification rates of 25 000 to 100 000 were achieved with as little as 10 ng of starting material. However, results were highly variable, depending on the amount of starting material, gene characteristics, sample quality, and protocols used. Oligomeric array hybridisation with 20 µg reference RNA resulted in specific and reproducible signals for 83% of the genes, whereas mRNA amplification from less than 400 ng of starting material resulted in selective detection of signals from highly expressed genes.

Conclusions:Improvements in the design of global mRNA amplification procedures and oligomeric arrays are needed to extract informative gene expression data from clinical samples containing limited cell numbers.
Aneuploidy and malignancy: an unsolved equation
Authors: Dey P
Published: November 2004

Aneuploidy is frequently noted in malignant tumours. There is much controversy about its cause and effect in relation to malignant tumours. Failure of the spindle checkpoint caused by mutation of the responsible genes may be one of the important factors for the development of aneuploidy. Telomere dysfunction may also be a possible source of failure of cytokinesis resulting in aneuploidy. Evidence such as tumour specific aneuploidy, presence of aneuploidy in various preneoplastic conditions, increased frequency of genetic instability in aneuploid cell lines compared with diploid cells, and mutation of mitotic checkpoint genes suggests that aneuploidy possibly plays an active role in carcinogenesis. In this brief review, the various aspects of aneuploidy with special emphasis on its mechanism of development and impact on progression of cancer are discussed.
ON PVchunk OPERATIONS AND MATROGENIC GRAPHS
Authors: DE AGOSTINO SERGIO , PETRESCHI ROSSELLA
Published: November 2004

A system of asynchronous parallel processes is represented by an exclusion graph in which a vertex is a process and an edge is a pair of mutually excluding processes. The mutual exclusion problem can be managed by simple entrance and exit protocols using PVchunk operations on a single shared variable when the graph is a threshold one. Ordman wonders if an efficient way exists for managing mutual exclusion situations modeled by more complex graphs than the threshold ones. A start is made on that here: we present a solution of the problem when the model is in the class of matrogenic graphs, which properly contains the threshold graphs.
PETRI NETS AND STEP TRANSITION SYSTEMS
Authors: MUKUND MADHAVAN
Published: November 2004

Labelled transition systems are a simple yet powerful formalism for describing the operational behaviour of computing systems. They can be extended to model concurrency faithfully by permitting transitions between states to be labelled by a collection of actions, denoting a concurrent step.

Petri nets (or Place/Transition nets) give rise to such step transition systems in a natural way—the marking diagram of a Petri net is the canonical transition system associated with it. In this paper, we characterize the class of PN-transition systems, which are precisely those step transition systems generated by Petri nets.

We express the correspondence between PN-transition systems and Petri nets in terms of an adjunction between a category of PN-transition systems and a category of Petri nets in which the associated morphisms are behaviour-preserving in a strong and natural sense.
RELATIVE UNCERTAINTY LEARNING THEORY: AN ESSAY
Authors: FIORI SIMONE
Published: November 2004

The aim of this manuscript is to present a detailed analysis of the algebraic and geometric properties of relative uncertainty theory (RUT) applied to neural networks learning. Through the algebraic analysis of the original learning criterion, it is shown that RUT gives rise to principal-subspace-analysis-type learning equations. Through an algebraic-geometric analysis, the behavior of such matrix-type learning equations is illustrated, with particular emphasis to the existence of certain invariant manifolds.
A NOVEL APPROACH FOR SHORT-TERM LOAD FORECASTING USING SUPPORT VECTOR MACHINES
Authors: TIAN LIANG , NOORE AFZEL
Published: November 2004

A support vector machine (SVM) modeling approach for short-term load forecasting is proposed. The SVM learning scheme is applied to the power load data, forcing the network to learn the inherent internal temporal property of power load sequence. We also study the performance when other related input variables such as temperature and humidity are considered. The performance of our proposed SVM modeling approach has been tested and compared with feed-forward neural network and cosine radial basis function neural network approaches. Numerical results show that the SVM approach yields better generalization capability and lower prediction error compared to those neural network approaches.
ADVANCES IN BLIND SOURCE SEPARATION (BSS) AND INDEPENDENT COMPONENT ANALYSIS (ICA) FOR NONLINEAR MIXTURES
Authors: JUTTEN CHRISTIAN , KARHUNEN JUHA
Published: November 2004

In this paper, we review recent advances in blind source separation (BSS) and independent component analysis (ICA) for nonlinear mixing models. After a general introduction to BSS and ICA, we discuss in more detail uniqueness and separability issues, presenting some new results. A fundamental difficulty in the nonlinear BSS problem and even more so in the nonlinear ICA problem is that they provide non-unique solutions without extra constraints, which are often implemented by using a suitable regularization. In this paper, we explore two possible approaches. The first one is based on structural constraints. Especially, post-nonlinear mixtures are an important special case, where a nonlinearity is applied to linear mixtures. For such mixtures, the ambiguities are essentially the same as for the linear ICA or BSS problems. The second approach uses Bayesian inference methods for estimating the best statistical parameters, under almost unconstrained models in which priors can be easily added. In the later part of this paper, various separation techniques proposed for post-nonlinear mixtures and general nonlinear mixtures are reviewed.
STABILITY OF MULTILAYERED NEURAL NETWORKS
Authors: Miller M. , Miranda E.N.
Published: November 2004

Stability of a multilayered neural network architecture against synaptic changes has been studied numerically. We have found that the average change goes to zero as the number N of input neurons is N≫1. If a fixed fraction of output mistakes is allowed, then the synapses may be changed within some limits even for large N.
EXACT CLASSIFICATION WITH TWO-LAYERED PERCEPTRONS
Authors: Zwietering P.J. , Aarts E.H.L. , Wessels J.
Published: November 2004

We study the capabilities of two-layered perceptrons for classifying exactly a given subset. Both necessary and sufficient conditions are derived for subsets to be exactly classifiable with two-layered perceptrons that use the hard-limiting response function. The necessary conditions can be viewed as generalizations of the linear-separability condition of one-layered perceptrons and confirm the conjecture that the capabilities of two-layered perceptrons are more limited than those of three-layered perceptrons. The sufficient conditions show that the capabilities of two-layered perceptrons extend beyond the exact classification of convex subsets. Furthermore, we present an algorithmic approach to the problem of verifying the sufficiency condition for a given subset.
A SINGLE-LAYER NEURAL NETWORK FOR PARALLEL THINNING
Authors: WU REI-YAO , TSAI WEN-HSIANG
Published: November 2004

A single-layer recurrent neural network is proposed to perform thinning of binary images. This network iteratively removes the contour points of an object shape by template matching. The set of templates is specially designed for a one-pass parallel thinning algorithm. The proposed neural network produce the same results as the algorithm. Neurons in the neural network performs a sigma-pi function to collect inputs. To obtain this function, the templates used in the algorithm are transformed to equivalent Boolean expressions. After the neural network converges, a perfectly 8-connected skeleton is derived. Good experimental results show the feasibility of the proposed approach.
PROCESSING OF SENSORY INFORMATION BY A NETWORK OF OSCILLATORS WITH MEMORY
Authors: Sompolinsky Haim , Tsodyks Michail
Published: November 2004

We propose a model of coupled oscillators with noise that performs binding and segmentation of objects using a set of stored images each consisting of figures and a background. The amplitudes of the oscillators encode the spatial and featural distribution of the external stimulus. In the learning stage the couplings between the phases are modified in a Hebb-like manner. By meanfield analysis and simulations we show that an external stimulus whose local features resemble those of one or several of the stored figures causes a selective phase coherence that retrieves the stored pattern of segmentation.
ENTROPY MINIMIZATION: A DESIGN PRINCIPLE FOR SENSORY PERCEPTION?
Authors: Atick Joseph J.
Published: November 2004

We speculate on how computational strategies suggested by Information theory could be useful for knowledge acquisition in sensory systems. The focus of our exploration is the idea that perception is a data reduction problem and as such sensory transformations should be predictable from the data reduction problem and as such sensory transformations should be predictable terms of variational principles involving the minimization of two types of entropy. The analysis suggests a scheme in which the two can be combined to produce a predictive design principle for sensory pathways.
Cortical Cells Do NOT Perform Temporal Integration of Small EPSPs
Authors: Softky William , Koch Christof
Published: November 2004

The standard theory of a leaky integrator with stochastic spike input predicts that cortical cells should fire regularly. We tested interspike-interval histograms from awake, behaving macaque visual cortex (V1 and MT), and found high levels of variability (CV>0.5) characteristic of a nearly random (Poisson) process. A simple integrate-and-fire model, using accepted biophysical parameters, fails by more than a factor of ten to account for the high CV. We also simulated a biophysically detailed compartment-model of an anatomically reconstructed and physiologically characterized layer V pyramidal cell; again, at high firing rate, CV values are low, in disagreement with the data. Only a few situations could account for this discrepency: very large EPSP’s, a very short membrane time constant (τm<0.3 msec), highly synchronized input, or spikes in excitable dendrites. Our analysis suggests that cortical computation may occur at a time-scale much faster than previously realized.
A FAST METHOD TO SEARCH FOR PROTEIN HOMOLOGIES USING NEURAL NETWORKS
Authors: Ferrán Edgardo A. , Ferrara Pascual
Published: November 2004

In a previous work we have described a method, based on Kohonen’s unsupervised-learning algorithm, to cluster a set of known protein sequences into families. We show here some examples of how a network, trained with 1758 human protein sequences, can correctly classify nonlearned sequences (nonhuman sequences and small fragments or random amino acid mutations of human sequences) in a very fast way.
A STUDY OF TRACK FINDING WITH A NEURAL NETWORK ALGORITHM
Authors: Barbagli Giuseppe , Castellini Guido , Landi Gregorio , Vettori Stefano
Published: November 2004

We have investigated the problem of track finding with a recurrent neural network algorithm based on the Hopfield model and considered the possibility of a hardware implementation with DSP’s. Starting from a set of signal points we define track segments and set a cut on the length to keep the size of the network reasonable. Those segments surviving the cut are associated to neurons. A geometric coupling of neighbouring segments is used to select smooth combinations of them. Given random initial conditions the network converges to a solution. The method may be applied to a variety of curves.
ELECTRON AND PION IDENTIFICATION BY NEURAL NETWORKS AND STANDARD METHODS
Authors: Teykal Helmut F.
Published: November 2004

The identification of electrons and pions in a calorimeter was studied with Feed Forward Networks and standard χ2-methods. The analysis was carried out with experimental data. The results of one and two hidden layer networks and the χ2-methods turned out to be compatible. However, their methodical advantages are demonstrated in the case of more complex event topologies like superimposed electron and pion events and simultaneous reconstruction of the incident angle of the particles.
HUMAN HAIR ANALYSIS BY PIXE
Authors: VALKOVIC V.
Published: November 2004

Hair is the unique biological material which, because of its growth, reflects the biomedical and environmental history of the subject. Because of convenience in handling and sampling and relatively high concentrations of metals, trace-element analysis of human hair has been applied widely for different purposes.

Although even the measurements of the bulk trace element levels contain some information, the real meaning is contained in longitudinal and radial concentration profiles. This is best achievable by X-ray emission spectroscopy measurements.
OPTIMIZATION OF THE SENSITIVITY IN PIXE ANALYSIS
Authors: JOHANSSON SVEN A.E.
Published: November 2004

This paper reports on an attempt to investigate how much the sensitivity in PIXE analysis could be improved by optimization of the experimental procedure. The composition and origin of the spectral background in proton excitation of thin plastic foils were studied. It was found that the background could be reduced by good collimation of the beam and efficient shielding of the detector. Minimum detection limits of the order of 0.05–0.2 ppm were obtained. Further improvement with detection limits in the range 0.02–0.03 ppm was achieved by using 5 MeV α-particles for excitation.
STUDIES OF ATOMIC PHYSICS AT RIKEN
Authors: AWAYA YOHKO , KAMBARA TADASHI
Published: November 2004

Experimental studies of atomic physics are performed with heavy-ion beams from accelerators at RIKEN. The variety of ion species and wide range of velocities and charge states enable us to study atomic collision processes and spectroscopy of highly charged ions. An overview of the works is presented.
Bio-PIXE AT THE TAKIZAWA FACILITY (Bio-PIXE WITH A BABY CYCLOTRON)
Authors: SERA K. , YANAGISAWA T. , TSUNODA H. , FUTATSUGAWA S. , HATAKEYAMA S. , SAITOH Y. , SUZUKI S. , ORIHARA H.
Published: November 2004

For the developement of bio-PIXE, two problems remain to be solved; one in accelerator availability and the other in data analysis. To improve the former, a method of applying baby cyclotrons to PIXE has been developed. To solve the latter, the computer program SAPIX for x-ray spectrum analysis ,which runs on ordinary personal computers and is fairly easy to operate has been developed. Examples of spectral fitting by the SAPIX and a description of the program are given. Further, the two-detector measuring system which we have employed for the simultaneous determination of all elements is reported.
BIO-PIXE BY MICRO BEAM
Authors: YAO HUIYING , REN CHIGANG , YANG FUJIA , ZHU JIEQING , LI MINQIN , ZHANG JINGXIA , HUANG PING
Published: November 2004

The paper shows the availability of micro beam on biological and medical fields, the particular application on the elemental composition concentration and distribution in cell. The prospect of application is disscussed as well.
APPLICATION OF PIXE ANALYSIS TO FORENSIC INVESTIGATION
Authors: Yuanxun ZHANG , Min ZHI , Wei ZHOU , Quisun ZHUANG , Yuandi CHENG
Published: November 2004

This work is to analyse trace elements in skin and muscle of a broken woman leg. Using PIXE technique,tissues of skin and muscle from doubtful point and normal part were analysed quantitatively. As the results,the contents of Fe and Zn in the doubtful point are higher than those in normal part, while other elemental contents are not remarkably different. This fact suggests that the doubtful point in skin and muscle might contain extravasated blood after wounded by some tools.
SHORT-RANGE TRANSPORT OF AEROSOLS EMITTED BY A POINT SOURCE OF MIXED CHARACTER AT PÁLHÁZA, HUNGARY
Authors: KATOH T. , AMEMIYA S. , KOLTAY E. , BORBÉLY-KISS I. , SZABó GY. , BISWAS S.K.
Published: November 2004

Longitudinal distribution of ground level aerosol concentrations have been measured in the neighbourhood of an emission source of mixed character by the PIXE method. The source was located in a valley in hilly terrain. The elements observed are divided into two groups according to the magnitude of the fine-to-coarse concentration ratio. The elements of small ratios are crust-related elements and the concentration of these elements show strong decrease with transport distance. The elements of large ratios are oil-related elements and the concentration are relatively stable during short-range transport.
TEMPERATURE MODELING OF GaAs DCFL
Authors: CONGER JEFF , PECZALSKI ANDRZEJ , SHUR MICHAEL S.
Published: November 2004

Direct-Coupled FET Logic (DCFL) is an important logic family for LSI GaAs FET circuits because of its simple structure and good speed/power performance. Since it is especially sensitive to temperature shifts of performance, accurate temperature modeling is critical for design of DCFL circuits. Using a version of SPICE modified to include FET temperature dependence, the performance of DCFL is simulated over temperature and compared with measured results. In addition, an improved version of DCFL known as E-E Logic (Enhancement-Enhancement Logic) is modeled over temperature. The performance of E-E Logic is compared to DCFL with depletion-mode FET and saturated resistor loads over temperature. E-E Logic is found to offer improved yield, power dissipation and performance control compared to conventional DCFL.
INTEGRATION WITH RESPECT TO A WEIGHT
Authors: LEINERT MICHAEL
Published: November 2004

A simple approach to non-commutative integration for weights is described, following the lines of [7] i.e., using a natural upper integral (which is in fact an integral) and interpolation.

If [Formula: see text] is a von Neumann algebra on the Hilbert space H and φ is a faithful normal semifinite weight on [Formula: see text], the space D of all φ-bounded vectors in H is contained in the domain of every closed positive form coming from a positive self-adjoint operator T affiliated to [Formula: see text] with finite upper integral [Formula: see text]. The (classes of) linear combinations of such forms constitute [Formula: see text]. In an obvious sense, [Formula: see text] consists of forms, too (bounded ones). [Formula: see text] is the complex interpolation space [Formula: see text]. It is checked that [Formula: see text] is isometrically isomorphic to Vp in [10], so [Formula: see text] is what it ought to be.
COMMUTING TRANSFER MATRICES AND LINK POLYNOMIALS
Authors: JONES V.F.R.
Published: November 2004

Borrowing from an argument in statistical mechanics we give a machine for constructing pairs of links with the same skein polynomials. Examples are generally not mutants (Kauffman polynomials differ) and can have small crossing numbers, e.g. the coincidence V41 #41 = V89, is explained.
Ab-Initio Calculation of Migration Energies of Adatoms on the Si (100) Surface
Authors: BROCKS G. , KELLY P.J. , CAR R.
Published: November 2004

The binding sites for adsorption of a single Si atom on the reconstructed Si (100) surface are identified using first-principles total energy calculations. By mapping out the total energy as a function of the position of the adatom on the surface, we establish several saddle points for migration over the surface. Similar calculations for P and Al adatoms establish the most important chemical trend.
Educational Statistical Physics on the Computer
Authors: GISLÉN LARS
Published: November 2004

Three programs are included in this package: BOLTZMANN, ISING and CURIE. All programs are Mackintosh applications and have a very simple user interface.
BLOCKSPIN AND MULTIGRID FOR STAGGERED FERMIONS IN NON-ABELIAN GAUGE FIELDS
Authors: KALKREUTER T. , MACK G. , SPEH M.
Published: November 2004

We discuss blockspins for staggered fermions, i. e. averaging and interpolation procedures which are needed in a real space renormalization group approach to gauge theories with staggered fermions and in a multigrid approach to the computation of gauge covariant propagators. The discussion starts from the requirement that the symmetries of the free action should be preserved by the blocking procedure in the limit of a pure gauge. A definition of an averaging kernel as a solution of a gauge covariant eigenvalue equation is proposed, and the properties of a corresponding interpolation kernel are examined in the light of general criteria for good choices of blockspins. Some results of multigrid computations of bosonic propagators in an SU(2) gauge field in 4 dimensions are also presented.
CALCULATING THE QUARK PROPAGATORS USING THE MIGDAL-KADANOFF TRANSFORMATION
Authors: VYAS VIKRAM
Published: November 2004

I discuss a multigrid algorithm for calculating fermionic propagators in the lattice gauge theories. In order to preserve the infrared physics on the coarse lattice the coarse grid operators are obtained by an approximate real-space renormalization-group transformation, namely the Migdal-Kadanoff transformation. The resulting projection and the interpolation operators have a simple interpretation in terms a path integral for a fermionic particle on the lattice. The method was tested in two-dimensions in the presence of U(1) gauge-field, where it reduces the critical slowing down for the large values of β. The algorithm was implemented on the Connection-Machine.
CALCULATING FRACTAL DIMENSIONS
Authors: GOSHEN S. , THIEBERGER R.
Published: November 2004

An algorithm for calculating fractal dimensions by the box counting method is described. Parallel implementation of the algorithm is presented.
CHERN-SIMONS TERM IN THE 4-DIMENSIONAL SU(2) HIGGS MODEL
Authors: KARSCH F. , LAURSEN M.L. , NEUHAUS T. , PLACHE B. , WIESE U.-J.
Published: November 2004

Using a variation of Lueschers geometric charge definition for SU(2) lattice gauge theory, we have managed to give a geometric expression for it’s Chern-Simons term. From this definition we have checked the periodic structure. We determined the Chern-Simons density for lattices L4 and L3×2, 4 with L=4, 6, and 8 near the critical region in the SU(2) Higgs model. The data indicate that tunneling is increased at high temperature.
PATTERN FORMATION IN FIRST-ORDER PHASE TRANSITIONS
Authors: BRENER E. , KASSNER K. , MÜLLER-KRUMBHAAR H. , TEMKIN D.
Published: November 2004

Recent developments in the theory of pattern formation in diffusional growth are reviewed. Asymptotic analysis and scaling arguments are used to construct a morphology diagram in parameter space. The relevant variables spanning this space are the anisotropy ∈ of the capillary length and the dimensionless undercooling Δ. Structures are classified according to whether they are compact or fractal and whether they possess orientational order or not. Explicit expressions for selected velocities and typical length scales are given in the scaling regime. For compact structures the theory provides a prescription how to go beyond scaling results.
FLUCTUATING INTERFACES, SURFACE TENSION, AND CAPILLARY WAVES: AN INTRODUCTION
Authors: PRIVMAN VLADIMIR
Published: November 2004

We present an introduction to modern theories of interfacial fluctuations and the associated interfacial parameters: surface tension and surface stiffness, as well as their interpretation within the capillary wave model. Transfer matrix spectrum properties due to fluctuation of an interface in a long-cylinder geometry are reviewed. The roughening transition and properties of rigid interfaces below the roughening temperature in 3d lattice models are surveyed with emphasis on differences in fluctuations and transfer matrix spectral properties of rigid vs. rough interfaces.
CHIRAL INTERFACE FOR QCD WITH DYNAMICAL FERMIONS
Authors: HACKEL M. , FABER M. , MARKUM H. , MÜLLER M.
Published: November 2004

The free energy distribution across the interface of coexisting quark and hadron mat-ter is studied in the framework of lattice QCD. We calculate the interface tension α with the “differential method” for pure SU(3) gauge theory and in the presence of dynamical quarks with four flavors. Using lattices with spatial volume 82×16 it turns out that α is very small and compatible with zero. The chiral condensate indicates the same width of the domain wall as the Polyakov loop distribution and the other thermodynamical observables.