bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence and Consequence of Porcine Endogenous Retrovirus Recombination
Authors: Bartosch Birke , Stefanidis Dimitrios , Myers Richard , Weiss Robin , Patience Clive , Takeuchi Yasuhiro
Published: November 2004

The genetic nature and biological effects of recombination between porcine endogenous retroviruses (PERV) were studied. An infectious molecular clone was generated from a high-titer, human-tropic PERV isolate, PERV-A 14/220 (B. A. Oldmixon, et al. J. Virol.
76:
3045-3048, 2002; T. A. Ericsson et al. Proc. Natl. Acad. Sci. USA
100:
6759-6764, 2003). To analyze this sequence and 15 available full-length PERV nucleotide sequences, we developed a sequence comparison program, LOHA
TM
to calculate local sequence homology between two sequences. This analysis determined that PERV-A 14/220 arose by homologous recombination of a PERV-C genome replacing an 850-bp region around the
pol
-
env
junction with that of a PERV-A sequence. This 850-bp PERV-A sequence encompasses the
env
receptor binding domain, thereby conferring a wide host range including human cells. In addition, we determined that multiple regions derived from PERV-C are responsible for the increased infectious titer of PERV-A 14/220. Thus, a single recombination event may be a fast and effective way to generate high-titer, potentially harmful PERV. Further, local homology and phylogenetic analyses between 16 full-length sequences revealed evidence for other recombination events in the past that give rise to other PERV genomes that possess the PERV-A, but not the PERV-B,
env
gene. These results indicate that PERV-A
env
is more prone to recombination with heterogeneous backbone genomes than PERV-B
env
. Such recombination events that generate more active PERV-A appear to occur in pigs rather frequently, which increases the potential risk of zoonotic PERV transmission. In this context, pigs lacking non-human-tropic PERV-C would be more suitable as donor animals for clinical xenotransplantation.
Experimental Infection of NOD/SCID Mice Reconstituted with Human CD34
+
Cells with Epstein-Barr Virus
Authors: Islas-Ohlmayer Miguel , Padgett-Thomas Angela , Domiati-Saad Rana , Melkus Michael W. , Cravens Petra D. , Martin Maria del P. , Netto George , Garcia J. Victor
Published: November 2004

Epstein-Barr virus (EBV)-induced lymphoproliferative disease is an important complication in the context of immune deficiency. Impaired T-cell immunity allows the outgrowth of transformed cells with the subsequent production of predominantly B-cell lymphomas. Currently there is no in vivo model that can adequately recapitulate EBV infection and its association with B-cell lymphomas. NOD/SCID mice engrafted with human CD34
+
cells and reconstituted mainly with human B lymphocytes may serve as a useful xenograft model to study EBV infection and pathogenesis. We therefore infected reconstituted mice with EBV. High levels of viral DNA were detected in the peripheral blood of all infected mice. All infected mice lost weight and showed decreased activity levels. Infected mice presented large visible tumors in multiple organs, most prominently in the spleen. These tumors stained positive for human CD79a, CD20, CD30, and EBV-encoded RNAs and were light chain restricted. Their characterization is consistent with that of large cell immunoblastic lymphoma. In addition, tumor cells expressed EBNA1, LMP1, and LMP2a mRNAs, which is consistent with a type II latency program. EBV
+
lymphoblastoid cell lines expressing human CD45, CD19, CD21, CD23, CD5, and CD30 were readily established from the bone marrow and spleens of infected animals. Finally, we also demonstrate that infection with an enhanced green fluorescent protein (EGFP)-tagged virus can be monitored by the detection of infected EGFP
+
cells and EGFP
+
tumors. These data demonstrate that NOD/SCID mice that are reconstituted with human CD34
+
cells are susceptible to infection by EBV and accurately recapitulate important aspects of EBV pathogenesis.
Fitness Costs Limit Viral Escape from Cytotoxic T Lymphocytes at a Structurally Constrained Epitope
Authors: Peyerl Fred W. , Bazick Heidi S. , Newberg Michael H. , Barouch Dan H. , Sodroski Joseph , Letvin Norman L.
Published: November 2004

The intense selection pressure exerted by virus-specific cytotoxic T lymphocytes (CTL) on replicating human immunodeficiency virus and simian immunodeficiency virus results in the accumulation of CTL epitope mutations. It has been assumed that fitness costs can limit the evolution of CTL epitope mutations. However, only a limited number of studies have carefully examined this possibility. To explore the fitness costs associated with viral escape from p11C, C-M-specific CTL, we constructed a panel of viruses encoding point mutations at each position of the entire p11C, C-M epitope. Amino acid substitutions at positions 3, 4, 5, 6, 7, and 9 of the epitope significantly impaired virus replication by altering virus production and Gag protein expression as well as by destabilizing mature cores. Amino acid substitutions at position 2 of the epitope were tolerated but required reversion or additional compensatory mutations to generate replication-competent viruses. Finally, while amino acid substitutions at positions 1 and 8 of the p11C, C-M epitope were functionally tolerated, these substitutions were recognized by p11C, C-M-specific CTL and therefore provided no selection advantage for the virus. Together, these data suggest that limited sequence variation is tolerated by the region of the capsid encoding the p11C, C-M epitope and therefore that only a very limited number of mutations can allow successful viral escape from the p11C, C-M-specific CTL response.
Inhibition of Parainfluenza Virus Type 3 and Newcastle Disease Virus Hemagglutinin-Neuraminidase Receptor Binding: Effect of Receptor Avidity and Steric Hindrance at the Inhibitor Binding Sites
Authors: Porotto Matteo , Murrell Matthew , Greengard Olga , Lawrence Michael C. , McKimm-Breschkin Jennifer L. , Moscona Anne
Published: November 2004

Zanamivir (4-guanidino-Neu5Ac2en [4-GU-DANA]) inhibits not only the neuraminidase activity but also the receptor interaction of the human parainfluenza virus type 3 (HPIV3) hemagglutinin-neuraminidase (HN), blocking receptor binding and subsequent fusion promotion. All activities of the HPIV3 variant ZM1 HN (T193I/I567V) are less sensitive to 4-GU-DANA's effects. The T193I mutation in HN confers both increased receptor binding and increased neuraminidase activity, as well as reduced sensitivities of both activities to 4-GU-DANA inhibition, consistent with a single site on the HN molecule carrying out both catalysis and binding. We now provide evidence that the HPIV3 variant's resistance to receptor-binding inhibition by 4-GU-DANA is related to a reduced affinity of the HN receptor-binding site for this compound as well as to an increase in the avidity of HN for the receptor. Newcastle disease virus (NDV) HN and HPIV3 HN respond differently to inhibition in ways that suggest a fundamental distinction between them. NDV HN-receptor binding is less sensitive than HPIV3 HN-receptor binding to 4-GU-DANA, while its neuraminidase activity is highly sensitive. Both HPIV3 and NDV HNs are sensitive to receptor-binding inhibition by the smaller molecule DANA. However, for NDV HN, some receptor binding cannot be inhibited. These data are consistent with the presence in NDV HN of a second receptor-binding site that is devoid of enzyme activity and has a negligible, if any, affinity for 4-GU-DANA. Avidity for the receptor contributes to resistance by allowing the receptor to compete effectively with inhibitors for interaction with HN, while the further determinant of resistance is the reduced binding of the inhibitor molecule to the binding pocket on HN. Based upon our data and recent three-dimensional structural information on the HPIV3 and NDV HNs, we propose mechanisms for the observed sensitivity and resistance of HN to receptor-binding inhibition and discuss the implications of these mechanisms for the distribution of HN functions.
Genetic Screen for Monitoring Severe Acute Respiratory Syndrome Coronavirus 3C-Like Protease
Authors: Parera Mariona , Clotet Bonaventura , Martinez Miguel Angel
Published: November 2004

A novel coronavirus (SCoV) is the etiological agent of severe acute respiratory syndrome. Site-specific proteolysis plays a critical role in regulating a number of cellular and viral processes. Since the main protease of SCoV, also termed 3C-like protease, is an attractive target for drug therapy, we have developed a safe, simple, and rapid genetic screen assay to monitor the activity of the SCoV 3C-like protease. This genetic system is based on the bacteriophage lambda regulatory circuit, in which the viral repressor cI is specifically cleaved to initiate the lysogenic-to-lytic switch. A specific target for the SCoV 3C-like protease, P1/P2 (SAVLQ/SGFRK), was inserted into the lambda phage cI repressor. The target specificity of the SCoV P1/P2 repressor was evaluated by coexpression of this repressor with a chemically synthesized SCoV 3C-like protease gene construct. Upon infection of
Escherichia coli
cells containing the two plasmids encoding the cI. SCoV P1/P2-cro and the β-galactosidase-SCoV 3C-like protease constructs, lambda phage replicated up to 2,000-fold more efficiently than in cells that did not express the SCoV 3C-like protease. This simple and highly specific assay can be used to monitor the activity of the SCoV 3C-like protease, and it has the potential to be used for screening specific inhibitors.
Sports related maxillofacial injuries: the first maxillofacial trauma database in Switzerland
Authors: Exadaktylos A K , Eggensperger N M , Eggli S , Smolka K M , Zimmermann H , Iizuka T
Published: November 2004

Background:With the increase in the amount of medical data handled by emergency units, advances in computerisation have become necessary. New computer technology should have a major influence on accident analysis and prevention and the quality of research in the future.

Objectives:To investigate the occurrence of sports related maxillofacial injuries using a newly installed relational database. To establish the first sports trauma database in Switzerland.

Methods:The Qualicare databank was used to prospectively review 57 248 case histories of patients treated in the Department of Emergency Medicine between January 2000 and December 2002. Pre-defined key words were used to collect data on sports related maxillofacial injuries.

Results:A total of 750 patients with maxillofacial injuries were identified. Ninety (12%) were sports related maxillofacial fractures. Most (27%) were sustained during skiing and snowboarding, 22% during team sports such as soccer or ice hockey, and 21% were from cycling accidents. Sixty eight per cent of the cyclists, 50% of the ice hockey players and soccer players, and 48% of the skiers and snowboarders had isolated fractures of the midface. Fractures of the mandible were noted predominantly in contact sports.

Conclusions:Computerisation of trauma and emergency units and the introduction of customised software can significantly reduce the workload of researchers and doctors. The effective use of new computer technology should have a considerable influence on research and the quality of future prospective and retrospective studies.
Three year follow up of a self certification system for the assessment of fitness to dive in Scotland
Authors: Glen S
Published: November 2004

Background:The need for routine medical examinations of sport divers in the Scottish Sub-Aqua Club (Scot-SAC) was revised in March 2000, and a new system using a self administered screening questionnaire was developed to allow divers to be assessed when necessary by doctors with diving medicine experience.

Objective:To assess the effect of the new medical system on medical referee workload, diver exclusion rates, and diving incident frequency.

Methods:All divers were required to complete a questionnaire to screen for conditions that might affect fitness to dive. Divers answering “Yes” to any of the questions had their medical background assessed by a diving doctor, and, if necessary, received a clinical examination or investigation. The rate of diver exclusions based on the questionnaire response was recorded in conjunction with analysis of the incident reports.

Results:The number of forms requiring review by diving doctors increased from 1.2% to 5.7% (p<0.0001, 95% confidence interval (CI) −0.06 to −0.03) in the year after the introduction of the new medical system and gradually increased in subsequent years to 7.7% (p<0.0001, 95% CI −0.08 to −0.05). The number of divers failing to be certified fit to dive increased slightly from 0.7% to 1.0% after one year (p  =  0.26, 95% CI −0.01 to 0.00) and subsequently to 2.0% (p  =  0.0003, 95% CI 0.02 to −0.01) after three years. Most divers were certified fit to dive on the basis of the questionnaire alone, and only 0.9% required objective investigation (such as exercise testing or echocardiography). Analysis of the incidents during three years of follow up confirmed that no incident occurred because of an undetected pre-existing medical condition. Two incidents involved divers with hypertension, but both had received medical examinations and investigation based on their responses to the questionnaire.

Conclusion:The new self administered questionnaire system appears to be an effective screening tool for the detection of divers requiring detailed assessment by doctors with diving medicine experience.
Exercise following a sport induced concussion
Authors: Gall B , Parkhouse W S , Goodman D
Published: November 2004

Objective:To determine if an athlete’s capacity to perform exercise is impaired following concussion and whether this would be reflected by an altered heart rate response.

Methods:Of the 14 concussed athletes, nine missed playing time as a direct result of their concussion and five did not. The concussed athletes performed an exercise protocol on a cycle ergometer within 72 hours of being asymptomatic at rest and a second test at 5 days following the previous assessment. Matched controls (n = 14) were tested using the same time line. The exercise protocol consisted of a 2 minute warm up, 10 minute, low−moderate intensity, steady state exercise session, and a high intensity interval protocol. The interval protocol consisted of a 40 second high intensity bout, followed by a 40 second rest period. This protocol continued until the participant had reached volitional fatigue.

Results:The number of exercise bouts completed was not significantly different from their matched controls. However, concussed athletes who missed playing time had a significantly higher heart rate during the steady state exercise session. During this same period, they also exhibited a greater rise in heart rate over time.

Conclusion:These findings indicate that exercise capacity is unaffected in concussed athletes who are asymptomatic at rest. However, their heart rate response to submaximal exercise is increased.
Paraplegia secondary to fracture-subluxation of the thoracic spine sustained playing rugby union football: Figure 1
Authors: Walsh A J , Shine S , McManus F
Published: November 2004

Fractures of the spinal column during rugby matches of all codes are rare but catastrophic, especially when associated with spinal cord injury. The cervical spine is vulnerable during trauma to the head and neck in contact sports. Spinal injuries reported during rugby matches have almost exclusively involved the cervical region, often with neurological sequelae. This is the first reported case of paraplegia caused by a fracture-dislocation of the thoracic spine resulting from a low velocity rugby union injury.
Blood borne infections in sport: risks of transmission, methods of prevention, and recommendations for hepatitis B vaccination
Authors: Kordi R , Wallace W A
Published: November 2004

Athletes are at risk of blood borne infections through bleeding injuries or injection of drugs with contaminated syringes. Prevention should focus on reducing non-sport associated risky behaviour, as well as dealing appropriately with bleeding injuries. The risk of transmission of hepatitis B virus is particularly high in athletes in contact and collision sports, those who live in or travel to endemic regions, injecting drug abusers, and those who practice first aid when there is no healthcare practitioner available. It is recommended that such athletes, and also adolescent athletes, should be vaccinated against the virus as a routine.
Primary intratesticular leiomyosarcoma in a mixed race man: a case report
Authors: Singh R , Chandra A , O’Brien T S
Published: November 2004

Primary leiomyosarcoma of the testis is an extremely rare condition with only a few reported cases in the literature. None has been reported in men of afrocaribean descent. This report describes the first case of a primary leiomyosarcoma in a mixed race man. Several different immunostains were used to confirm the morphological suggestion of a primary intratesticular smooth muscle tumour. Scrotal ultrasound and abdominal computed tomography imaging were used to exclude paratesticular and retroperitoneal pathology. Where reported, primary intratesticular leiomyosarcoma is described as an indolent tumour with the potential for distant metastases. Its occurrence in younger men is usually associated with anabolic steroid abuse. Although the number of reported cases is very few, radical orchidectomy followed by surveillance appears to be the treatment of choice.
Unusual cardiac tumour with perivascular myoid differentiation: a case report
Authors: Orlandi A , Ferlosio A , Ciucci A , Pellegrino A , Spagnoli L G
Published: November 2004

A previously healthy 70 year old woman was admitted for fatigue and dyspnoea on exertion and cough. A two dimensional echocardiography revealed a mass in the right atrium, which obstructed filling and infiltrated the cardiac chamber wall. Postsurgical histological examination revealed an unusual tumour with prevalent myoid glomangiopericytoma-type and haemangiopericytoma-like patterns. Mitosis and necrosis were absent. A computed tomography scan excluded the presence of metastasis to distant organs or, conversely, metastatic involvement of the heart. Therefore, a diagnosis of tumour with perivascular myoid differentiation was made. This new entity, recently described in soft tissues, can easily recur. Its recognition helps to differentiate from metastasis and other primitive cardiac tumours sharing some morphological features but a different clinical behaviour, with consequent improvement to the management of patient care.
THE WORD PROBLEM OF ACD-GROUND THEORIES IS UNDECIDABLE
Authors: MARCHÉ CLAUDE
Published: November 2004

We prove that there exists an ACD-ground theory, i.e., an equational theory defined by a set of ground equations plus the associativity and commutativity of two binary symbols * and +, and the distributivity of * over +, for which the word problem is undecidable.
ON LEARNING LIMITING PROGRAMS
Authors: CASE JOHN , JAIN SANJAY , SHARMA ARUN
Published: November 2004

Machine learning of limit programs (i.e., programs allowed finitely many mind changes about their legitimate outputs) for computable functions is studied. Learning of iterated limit programs is also studied. To partially motivate these studies, it is shown that, in some cases, interesting global properties of computable functions can be proved from suitable (n+1)-iterated limit programs for them which can not be proved from any n-iterated limit programs for them. It is shown that learning power is increased when (n+1)-iterated limit programs rather than n-iterated limit programs are to be learned. Many trade-off results are obtained regarding learning power, number (possibly zero) of limits taken, program size constraints and information, and number of errors tolerated in final programs learned.
TEMPORAL LOGICS FOR COMMUNICATING SEQUENTIAL AGENTS: I
Authors: LODAYA KAMAL , RAMANUJAM R. , THIAGARAJAN P.S.
Published: November 2004

We introduce a class of distributed systems called Communicating Sequential Agents (CSAs). Sound and complete axiomatizations are provided for various subclasses using a family of indexed temporal logics. Some of the important features of these logics are:

• Both the formulas and the structures for the logics reflect the fact that a system is composed out of a number of participating sequential agents.

• Formulas of the logics are interpreted only at local states.

• An agent makes a definite assertion about another agent only if it has received — directly or indirectly — some communication from that agent supporting that assertion.
MAKING SOME ISSUES OF IMPLICIT KNOWLEDGE EXPLICIT
Authors: VAN DER HOEK W. , MEYER J.-J. CH.
Published: November 2004

We discuss issues of expressibility and completeness of the logic of implicit knowledge (I) and “everybody’s knowledge” (E), as introduced in a system with a number m of epistemic agents by Halpern & Moses. The operator E is defined as a conjunction and corresponds semantically to the union of the m accessibility relations. Dually, the operator I is semantically associated with an intersection, but it is, surprisingly, not equivalent with a disjunction. From the view of Kripke structures there is a related asymmetry: although union can be modally defined, intersection cannot! We discuss consequences (in terms of (in)expressibility, correspondence and completeness) of this property for the epistemic logic under consideration and also present an extension of modal logic in which intersection is expressible.
ITERATION ALGEBRAS
Authors: BLOOM STEPHEN L. , ÉSIK ZOLTÁN
Published: November 2004

We assume the reader has some familiarity with theories and iteration theories. The main topic of the paper is properties of varieties of iteration algebras. After a preliminary section which contains all of the necessary definitions, we spend some time on a coproduct construction which is needed to prove a fundamental lemma: for each iteration theory T, any T-algebra is a retract of a T-iteration algebra. The proof of the lemma shows that only one property of iteration theories is used: the parameter identity. Hence, the lemma applies to any preiteration theory in which this identity is valid. It follows from this fact that the variety of all T-iteration algebras has “nice” properties only when every T-algebra is an iteration algebra. Some of the possible pathology in varieties of iteration algebras is demonstrated. It is shown that for each set Z of non-negative integers there is a variety of iteration algebras having an n-generated free algebra iff n∈Z. Also given is a theorem characterizing certain functors between varieties of iteration theories which are induced by iteration theory morphisms. We find an explicit description of all of the theory congruences on theories of partial functions. The last section is connected with the strong iteration algebras introduced in a paper by Ésik (1983).
UNSUPERVISED LEARNING PROCEDURES FOR NEURAL NETWORKS
Authors: Becker Suzanna
Published: November 2004

Supervised learning procedures for neural networks have recently met with considerable success in learning difficult mappings. However, their range of applicability is limited by their poor scaling behavior, lack of biological plausibility, and restriction to problems for which an external teacher is available. A promising alternative is to develop unsupervised learning algorithms which can adaptively learn to encode the statistical regularities of the input patterns, without being told explicitly the correct response for each pattern. In this paper, we describe the major approaches that have been taken to model unsupervised learning, and give an in-depth review of several examples of each approach.
A FAST NEURAL ALGORITHM FOR PRINCIPAL COMPONENT ANALYSIS AND SINGULAR VALUE DECOMPOSITION
Authors: Sirat J. Ariel
Published: November 2004

We propose a fast neural algorithm to perform Principal Component Analysis (PCA) of a set of examples. It is obtained by simplification of current neural learning rules for PCA. First, we use a single binary neuron to extract a given component by a Hebb-type learning rule (Self-Organized Perceptron). This rule rapidly yields the first principal component. Moreover, as the neuron is binary, convergence is easily interpreted in terms of geometry and trajectory. Then successive components are obtained after projection of examples on the subspace which is supplementary to already learnt components. This avoids mixing the components as in, for example, the “Subspace Method” recently proposed by Oja.11

We have tested this approach on a gaussian distribution of examples: the quality of results is identical to that obtained with methods which diagonalize the correlation matrix computed from the set of examples. A variant of the algorithm is also proposed to perform the Singular Value Decomposition (SVD) which “diagonalizes” an asymmetrical matrix. Performances are as satisfactory as for PCA. Complexity and performances of a VLSI implementation are then estimated from the specifications of the neural VLSI developed in our laboratory. Comparison with hardware implementations of non-neural approaches (SVD) seems to favor neatly the neural approach: the expected speed increase is at least two orders of magnitude for a 100-dimensional SVD calculation.
PRINCIPLES OF THE DESIGN OF D-NEURONAL NETWORKS I: NET REPRESENTATION FOR COMPUTER SIMULATION OF A MELODY COMPOSITIONAL PROCESS
Authors: FEDOR PETER
Published: November 2004

We present a deterministic neural network model for the processing of temporal sequences of tones. Several types of model neural units are defined in a form suitable for the digital computer simulation of their nets. On the basis of the proposed units, we set up prediction trees which serve for recognition and prediction of pitches that emerge in single-lined diatonic melodies. The prediction tree also evaluates the surprise evoked by a processed melody in regard to the pitch sequences currently memorized in this tree.
PRINCIPLES OF THE DESIGN OF D-NEURONAL NETWORKS II: COMPOSING SIMPLE MELODIES
Authors: FEDOR PETER
Published: November 2004

Digital computer simulation of the prediction trees introduced in Part I of this series is performed. We define the simplest prediction tree arrangements for the analysis and composition of diatonic single-lined melodies. A measure of surprise is defined as the weighted sum of the outputs of the tree surprise-evaluating units. The melody composing process is then considered as an optimization task, the goal of which is to find the tone sequences elicited in trees of as great a mean level of surprise as possible.
A NODE PRUNING ALGORITHM FOR BACKPROPAGATION NETWORKS
Authors: CHUNG F.L. , LEE T.
Published: November 2004

Backpropagation (BP) networks are a class of artificial neural network model that has been widely used in many areas of interest. One difficulty in adopting this model is the need to predetermine a suitable network size, particularly, the number of hidden nodes. A common approach is to start with an oversized network and then the size is reduced by eliminating unnecessary nodes and links. In this paper, starting from the viewpoint of pattern classification theory, a study on the characteristics of hidden nodes in oversized networks is reported. The study shows that four categories of excessive hidden nodes can be found in an oversized network. A new node pruning algorithm to attain appropriate size BP networks is then proposed by detecting and removing those excessive nodes. Moreover, the algorithm is extended to cater for the larger class of problems, i.e. real-to-real mapping. Unlike previous works, the concept of “excessiveness” advocated here has strong indications whether a node can be removed without impairing the performance of original network and hence the proposed algorithm is useful in obtaining a network that is optimized with both the network size and performance. The effectiveness of the proposed algorithm has been demonstrated through the N-bit parity problems and the experiment in predicting the chaotic time series.
BUILDING A ROBUST NEAREST NEIGHBOR CLASSIFIER CONTAINING ONLY A SMALL NUMBER OF PROTOTYPES
Authors: YAN HONG
Published: November 2004

A robust nearest neighbor classifier with only a small number of prototypes can be designed if the prototypes contain distinctive features that have a high classification power. We present in this paper an interset and intraset distance based method for reducing the number of prototypes and a neural network based technique for optimizing the prototypes of a nearest neighbor classifier. It is shown that the prototypes can be modified with a learning algorithm in such a way that useful features are created or enhanced to improve the matching capability of the classifier.
DYNAMIC PROPERTIES OF A BIOLOGICALLY MOTIVATED NEURAL NETWORK MODEL
Authors: BLONDEAU FRANÇOIS CHAPEAU , CHAUVET GILBERT
Published: November 2004

We develop a neural network model based on prominent basic features of biological neural networks. The description keeps a simple but coherent link between the subneuronal, neuronal and network levels. In addition, the variables of the model are endowed with realistic numerical values together with their physical units. This permits to reach quantitative significance for the results. To describe the operation of the neuron, a transfer function is used that is believed to convey more biological significance compared to the usual sigmoid transfer function. It is shown that the dynamic properties of the network, which can vary from stability to chaos, are significantly influenced by the choice of the neuron transfer function. Constraints on the synaptic efficacies, as imposed by Dale’s rule, are also shown to modify the dynamic properties by increasing the stability of the network. A simple neural architecture is presented that leads to a controllable time evolution of the network activities.
WHEN IS A POTENTIAL FUNCTION ACCURATE ENOUGH FOR PROTEIN STRUCTURE PREDICTION?
Authors: Bryngelson Joseph D.
Published: November 2004

Attempts to predict protein tertiary structure, through neural network or other means, generally try to optimize some potential function or other “score” over a set of structures. This paper develops a formalism that addresses the question: What are the accuracy requirements for a potential function that predicts protein structure? The results of a simple model calculation with this formalism are also presented. The paper closes with a discussion of the implications of these results for practical structure prediction.
NEURAL NETWORKS FOR PHYSICS ANALYSIS IN DELPHI
Authors: De Angelis Alessandro , Ciuchini Marco , Giudice Paolo Del
Published: November 2004

The use of Artificial Neural Networks in physics analysis by the DELPHI experiment at LEP is reviewed. DELPHI has used Neural Networks to tag the primary flavour of hadronic Z0 decays, to enhance the sensitivity of the searches for new particles, to measure properties of quark and gluon jets, and to identify final state particles.
A SECOND LEVEL NEURAL NETWORK TRIGGER IN THE H1 EXPERIMENT AT HERA
Authors: Fent J. , Gruber A. , Kiesling C. , Oberlack H. , Ribarics P.
Published: November 2004

At the HERA e-p collider the expected machine background rates are typically 105 times higher than the rates from physics. The greatest challenge in the trigger is finding methods which suppress the machine background without using lengthy pattern recognition algorithms with prohibitive computing times. This task is optimally suited to a neural network solution. Our present investigations show that feed-forward networks, trained on the topological energy sums from the H1 calorimeter and on first level tracking trigger information, provide an additional background suppression factor compared to the traditional method which operates with fixed thresholds. The neural network algorithm — implemented by special purpose fast matrix-vector multiplier chips at the second level of the trigger — allows the lowering of the first level thresholds which is shown to be important to get good efficiencies for specific physics event classes.
JET CLASSIFICATION AT CDF
Authors: Bianchin S. , Domini A. , Dall’Agata M. , De Nardi M. , Zara F. , Denby B. , Wainer N. , Dickson M.
Published: November 2004

Results for the classification of jets obtained with the use feed-forward neural networks are reviewed with particular attention to model-dependence, flavor sensitivity and Et-dependence. First results obtained with a Kohonen-type network are also presented and both are compared with those obtained with a Fisher discriminant.
THE TAKIZAWA PIXE FACILITY COMBINED WITH A BABY CYCLOTRON FOR POSITRON NUCLEAR MEDICINE
Authors: SERA K. , YANAGISAWA T. , TSUNODA H. , FUTATSUGAWA S. , HATAKEYAMA S. , SUZUKI S. , ORIHARA H.
Published: November 2004

A new PIXE facility combined with a small cyclotron (alias Baby Cyclotron) established exclusively for medical use is described. Sufficient amount of 2.9-MeV protons can be extracted from the cyclotron by accelerating H2+-ions with acceleration parameters for 8.3-MeV deuterons. Some technical problems for applying the cyclotron to PIXE analysis, such as elimination of deuteron contamination from proton beams and radiation shielding of the PIXE room during radioisotope production in the cyclotron vault, are reported.
TRACE ANALYSIS OF ALUMINUM METAL REFERENCE STANDARDS BY PIXE METHOD
Authors: HIROKAWA TAKESHI , TANAKA SHINJI , YOSHIDA SATOSHI , NISHIYAMA FUMITAKA , KISO YOSHIYUKI , ITO KAZUAKI , SHOTO EIJI
Published: November 2004

Trace elements in thick samples of aluminum metal reference standards were analyzed by means of PIXE and ICP-AES. The samples were SRM1258 and SRM1259 from National Institute of Standards and Technology (U.S.A.) and 1-A, 3, 4-A and 83 from Japan light metal association. The observed PIXE spectrum was converted “into that of a hypothetical thin target and it was analyzed using a relative intensity database for thin target. A good agreement was obtained between the certified and the found amount of the trace elements. The analytical results for SRM1258 and SRM1259 obtained by ICP-AES method also agreed well with the present results confirming the analytical accuracy.
APPLICATIONS OF PIXE ANALYSIS TO STUDIES IN CELL BIOLOGY
Authors: MATSUMOTO SHINJI , FURUSE MASAKO , KITAO KENSUKE , ISHIHARA TOYOYUKI , SHIMA KUNIHIRO , CHIBA REN
Published: November 2004

PIXE application to the measurement of cellular elements is outlined on characteristic variations of the contents of yeast, CHO, V79 and MM46 cultured mammalian cells according to environmental changes. Cellular elements from P to Br were successfully analyzed at these cells after cautious preparation of samples in filtration steps with as possible as less deterioration. We confirmed linear relationships between the X-ray yields and these element contents. The experiment was extended to an analysis of cellular substances at molecular level by scanning of specimens. Preliminary results were included.
APPLICATION OF AAS AND NAA FOR DETERMINATION OF TIN IN SRMs, AND IN ANIMAL AND HUMAN ORGANS
Authors: CHIBA MOMOKO , IYENGAR VENKATESH G.
Published: November 2004

Tin (Sn) is one of the causative elements of the environmental pollution. As no certified reference materials for Sn are presently available, existing reference materials were analyzed for Sn by two independent analytical techniques; atomic absorption spectrometry (AAS) and neutron activation analysis (NAA). The results obtained by both methods were in agreement except for mixed diet which contains Sn in the range of 50 μ g/g. Further, tin concentrations in human and animal organs have been examined by AAS. Among organs tested tin concentrations in testes were the highest, 2.08±0.62 μ g/g dry weight (mean ±SD, n=12) in humans, and 1.45±0.55 μ g/g (n=8) in mice.
AN ATOMIC BASIS STUDY ON CANCER: - HERB MEDICINE ADDITIVE LANTHANIDE-HPD LOCALIZATION IN ANIMAL TUMOR -
Authors: WEI CHAU-CHIN , TOMINAGA YASUO , TSAI JUI-CHANG , CHAI CHEE-YIN , WU WU-SIUNG
Published: November 2004

The particle induced X-ray emission analysis is applied to mark (or to localize) a cancer lesion from its benign environment in animal experiments. As a photosensitiser, we have used hematoporphyrin derivative (HPD) and in order to make HPD visible to PIXE, we synthesize HPD with rare earth metals to form lanthanide-HPD to enhance the localizing efficiency tremendously and PIXE is used as a straightforward detection method to find the successfulness of the synthesis. In theory, this approach can be used to probe carcinogenesis at cell levels. To increase the cure effects of lanthanide-HPD, we add ZYX to enhance the pharmaceutical effectiveness. ZYX, our code name for a group of drugs and chemicals, is mostly of the Chinese herb extraxctions but some has different origin. We explain the present approach with a specific experiment, Dysprosium-HPD (Dy-HPD) as a localizer, and conclude this article with some comments and perspectives.
DESIGN AUTOMATION FOR MULTICHIP MODULE — ISSUES AND STATUS
Authors: CHAN PHILIP C.
Published: November 2004

In this paper we will review the current state of commercial electronic design automation (EDA) tools for the design of multichip modules. MCM can be classified in terms of its substrate technology. The choice of substrate technology has important implications for the selection of design automation tools. A PCB EDA system seems more appropriate for MCMs with stacked via substrate which closely resembles the through-hole printed circuit board (PCB). A chip layout system may be more appropriate for MCMs with low-cost thin-film silicon substrate which typically uses staircase vias. The cofired ceramic substrate MCM which evolved from the hybrid integrated circuit technology may use the specialized hybrid EDA software packages available for the designing of hybrid integrated circuits. Historically, printed circuit board and integrated circuit design automation software evolved separately. There exists a boundary between the printed circuit board and integrated circuit design automation tools in the physical design hierarchy. This boundary can be an important limitation for the repartitioning of the physical design hierarchy within the MCM.

We shall discuss in detail the impact of MCM on various aspects of EDA. In the area of physical design, we must face the traditional placement and routing problem for any high speed design. Problems such as system clock skew and tight timing requirements must be considered. As one push clock frequency higher, one also must consider discontinuities due to vias and bends besides the classical transmission line effect due to long wires. Other traditional physical design problems such as ground and power plane generation, physical design verification and mask tooling must be revisited in the context of various MCM substrate technologies. The thermal aspects of MCM design are strongly influenced by the placement of chips on the MCM substrate. Thermal design is especially important for high density MCMs using the flip-chip mounting technology. Here, the heat must be dissipated through the back of the substrate via thermal pillars or bumps. We still need to deal with the traditional coupled transmission line problems. Due to the small cross section, high performance MCM substrate interconnects are resistive and the transmission lines they form are lossy. Noise is another main problem for MCM design. For high speed MCM with many CMOS buffers, the ground bouncing noise resulting from simultaneous switching of a large number of CMOS drivers must be controlled through proper substrate and package design. We will conclude the paper by comparing existing VLSI and PCB EDA tools for MCM design.
PERFORMANCE DRIVEN LAYOUT FOR THIN-FILM MULTICHIP MODULES
Authors: DAI WAYNE WEI-MING
Published: November 2004

This paper addresses some of the problems encountered in propagating high speed signals on lossy transmission lines on the substrates of thin-film multichip modules. The interconnect lines on thin-film substrate are relatively lossy in the respect that the total resistance of such a line is typically comparable to its characteristic impedance. If such a line were terminated with a load resistor appropriately valued to minimize signal reflections and resonances, the voltage divider formed by the terminating resistance and line resistance causes undesirable attenuation of the output signals. In addition, each terminating resistor dissipates quiescent power on a high density substrate, generating a substantial amount of heat in a small area. Instead of being terminated by resistors, the distributed resistance of the lines are used to critically damp out the signal resonances. With the flexibility of the rubber-band routing and the efficiency of a dynamic data representation based on the constrained Delaunay triangulation, lossy and unterminated transmission lines can be generated to successfully propagate high speed signals. The SURF (Santa-Cruz ULSI Routing Framework) layout system is being developed specifically for thin-film MCM substrate design. The system is performance driven, featuring variable width, variable spacing, evenly distributed spacing, and thermal via insertion. A flexible topological routing model, called rubber-band sketch, together with a dynamic layer representation based on the constrained Delaunay triangulation, is used to control the reflected noise, coupled noise (crosstalk), simultaneous switching noise, and thermal resistance.
AFFINE VARIETIES AND STEIN MANIFOLDS
Authors: TOTARO BURT
Published: November 2004

We give some examples of Stein manifolds which are not diffeomorphic, as oriented manifolds, to any smooth affine algebraic variety. Some of these examples are in complex dimension 2.
STRONGLY MAXIMAL TRIANGULAR AF ALGEBRAS
Authors: VENTURA BELISARIO A.
Published: November 2004

We consider strongly maximal triangular subalgebras of AF algebras. These are the triangular algebras [Formula: see text] such that [Formula: see text] is dense in the ambient AF algebra. We prove that every isometric isomorphism between two strongly maximal triangular subalgebras of the AF algebra [Formula: see text] factors as the composition of two automorphsims of [Formula: see text], one induced by a homeomorphism of the Gelfand spectrum of the diagonal of [Formula: see text], and the other induced by a cocycle on the groupoid supporting [Formula: see text]. As a consequence we obtain that the partial order supporting [Formula: see text] is an isomorphism invariant for [Formula: see text]. Another result establishes conditions that if satisfied by a strongly maximal triangular subalgebra [Formula: see text] of a UHF algebra guarantee that [Formula: see text] is product type analytic. As a consequence we show that the two fundamental examples of triangular UHF algebras are product type analytic, and we exhibit cocycles implementing the analyticity.
SHIMIZU’S LEMMA FOR COMPLEX HYPERBOLIC SPACE
Authors: PARKER JOHN R.
Published: November 2004

Shimizu’s lemma gives a necessary condition for a discrete group of isometries of the hyperbolic plane containing a parabolic map to be discrete. Viewing the hyperbolic plane as complex hyperbolic 1-space we generalise Shimizu’s lemma to higher dimensional complex hyperbolic space In particular we give a version of Shimizu’s lemma for subgroups of PU (n, 1) containing a vertical translation Partial generalisation to groups containing either an ellipto-parabolic map or non-vertical translations are also given together with examples that show full generalisation is not possible in these cases
C*-ALGEBRAS WITH REAL RANK ZERO AND THEIR CORONA AND MULTIPLIER ALGEBRAS PART IV
Authors: ZHANG SHUANG
Published: November 2004

By proving various equivalent versions of the generalized Weyl-von Neumann theorem, we investigate the structure of projections in the multiplier algebra [Formula: see text] of certain C*-algebra [Formula: see text] with real rank zero. For example, we prove that [Formula: see text] if and only if any two projections in [Formula: see text] are simultaneously quasidiagonal. In case [Formula: see text] is a purely infinite simple C*-algebra, [Formula: see text] if and only if any two projections in [Formula: see text] are simultaneously quasidiagonal. If [Formula: see text] is one of the Cuntz algebras, or one of finite factors or type III factors, then any two projections in [Formula: see text] are simultaneously quasidiagonal. On the other hand, if [Formula: see text] is one of the Bunce-Deddens algebras or one of the irrational rotation algebras of real rank zero, then there exist two projections in [Formula: see text] which are not simultaneously quasidiagonal.
CLOSED MINIMAL HYPERSURFACES IN COMPACT SYMMETRIC SPACES
Authors: GORODSKI CLAUDIO
Published: November 2004

W.Y. Hsiang, W.T. Hsiang and P. Tomter conjectured that every simply-connected, compact symmetric space of dimension ≥4 must contain some minimal hypersurfaces of sphere type. With the aid of equivariant differential geometry, they showed that this is in fact the case for many symmetric spaces of rank one and two. Let M be one of the symmetric spaces: Sn(1)×Sn(1)(n≥4), SU(6)/Sp(3), E6/F4, ℍP2 (quaternionic proj. plane) or CaP2 (Cayley proj. plane). We prove the existence of infmitely many immersed, minimal hypersurfaces of sphere type in M which are invariant under a certain group G of isometries of M. Following Hsiang and the others, the equivariant method is also used here to reduce the problem to an investigation of geodesics in M/G equipped with a metric (with singularities) depending only on the orbital geometry of the transformation group (G, M). However, our constructions are based on area minimizing homogeneous cones, corresponding to a corner singularity of M/G with the local geometry of nodal type; this can be viewed as a variation of some of their constructions which depended on some unstable minimal cones of focal type. We further apply the equivariant method to construct a minimal embedding of S1×Sn−1×Sn−1 into Sn(1)×Sn(1)(n≥2) and a minimal, embedded hypersurface of sphere type in [Formula: see text], ℍPn×ℍPn (n≥2) and CaP2×CaP2.
Computer Simulation of Energy Relaxation and Recombination of Nonequilibrium Electrons in a Disordered System with Localized Electronic States
Authors: BARANOVSKII S.D. , LEVIN E.I. , RUZIN I.M. , FRITZSCHE H. , SHKLOVSKII B.I.
Published: November 2004

A new exact algorithm is developed for the simulation of simultaneous diffusion and recombination of nonequilibrium electrons. It is shown that the diffusion process is non-Markovian, and the exact value of the critical index s is found. The solution of the universal geometrical problem is used to describe many phenomena in disordered systems, such as photoconductivity, photoluminescence etc. The results coincide well with the experimental observations.
Computation of Nuclear Reactions with Light-Heavy Ions
Authors: BELYAEVA T.L. , ZELENSKAYA N.S.
Published: November 2004

The computer code OLYMPS for calculation of the inclusive cross sections for nuclear reactions induced by light heavy ions on medium-mass nuclei at beam energies of 10–20 MeV per nucleon is developed. Our calculations are based on the description of the massive transfer reactions in the spectator model. In view of the fact that most of the considered reactions have more than two particles in the final state and require an allowance for the continuum spectrum, the standard distorted wave Born approximation (DWBA) code fails to work. In our method the transition amplitude is witten in a prior-form of exact finite range DWBA and an exact numerical integration over the transfer momentum is carried out. This requires knowledge of the optical potentials between interacting light and heavy ions in a wide energy range. In addition, OLYMPS provides for the alternative ways of calculation of the wave functions of the relative motion of the heavy ions.