bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain
Authors: Lim David , Gregorio G. Glenn , Bingman Craig , Martinez-Hackert Erik , Hendrickson Wayne A. , Goff Stephen P.
Published: August 2006

A crystallographic study of the Moloney murine leukemia virus (Mo-MLV) RNase H domain was performed to provide information about its structure and mechanism of action. These efforts resulted in the crystallization of a mutant Mo-MLV RNase H lacking the putative helix C (ΔC). The 1.6-Å resolution structure resembles the known structures of the human immunodeficiency virus type 1 (HIV-1) and
Escherichia coli
RNase H. The structure revealed the coordination of a magnesium ion within the catalytic core comprised of the highly conserved acidic residues D524, E562, and D583. Surface charge mapping of the Mo-MLV structure revealed a high density of basic charges on one side of the enzyme. Using a model of the Mo-MLV structure superimposed upon a structure of HIV-1 reverse transcriptase bound to an RNA/DNA hybrid substrate, Mo-MLV RNase H secondary structures and individual amino acids were examined for their potential roles in binding substrate. Identified regions included Mo-MLV RNase H β1-β2, αA, and αB and residues from αB to αD and its following loop. Most of the identified substrate-binding residues corresponded with residues directly binding nucleotides in an RNase H from
Bacillus halodurans
as observed in a cocrystal structure with RNA/DNA. Finally, superimposition of RNases H of Mo-MLV,
E. coli
, and HIV-1 revealed that a loop of the HIV-1 connection domain resides within the same region of the Mo-MLV and
E. coli
C-helix. The HIV-1 connection domain may serve to recognize and bind the RNA/DNA substrate major groove.
Crimean-Congo Hemorrhagic Fever Virus Genomics and Global Diversity
Authors: Deyde Varough M. , Khristova Marina L. , Rollin Pierre E. , Ksiazek Thomas G. , Nichol Stuart T.
Published: August 2006

Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high case fatality that occurs in Africa, Europe, the Middle East, and Asia. The complete genomes of 13 geographically and temporally diverse virus strains were determined, and CCHF viruses were found to be highly variable with 20 and 8%, 31 and 27%, and 22 and 10% nucleotide and deduced amino acid differences detected among virus S (nucleocapsid), M (glycoprotein), and L (polymerase) genome segments, respectively. Distinct geographic lineages exist, but with multiple exceptions indicative of long-distance virus movement. Discrepancies among the virus S, M, and L phylogenetic tree topologies document multiple RNA segment reassortment events. An analysis of individual segment datasets suggests genetic recombination also occurs. For an arthropod-borne virus, the genomic plasticity of CCHF virus is surprisingly high.
West Nile Virus 5′-Cap Structure Is Formed by Sequential Guanine N-7 and Ribose 2′-O Methylations by Nonstructural Protein 5
Authors: Ray Debashish , Shah Aaloki , Tilgner Mark , Guo Yi , Zhao Yiwei , Dong Hongping , Deas Tia S. , Zhou Yangsheng , Li Hongmin , Shi Pei-Yong
Published: August 2006

Many flaviviruses are globally important human pathogens. Their plus-strand RNA genome contains a 5′-cap structure that is methylated at the guanine N-7 and the ribose 2′-OH positions of the first transcribed nucleotide, adenine (m
7
GpppAm). Using West Nile virus (WNV), we demonstrate, for the first time, that the nonstructural protein 5 (NS5) mediates both guanine N-7 and ribose 2′-O methylations and therefore is essential for flavivirus 5′-cap formation. We show that a recombinant full-length and a truncated NS5 protein containing the methyltransferase (MTase) domain methylates GpppA-capped and m
7
GpppA-capped RNAs to m
7
GpppAm-RNA, using
S
-adenosylmethionine as a methyl donor. Furthermore, methylation of GpppA-capped RNA sequentially yielded m
7
GpppA- and m
7
GpppAm-RNA products, indicating that guanine N-7 precedes ribose 2′-O methylation. Mutagenesis of a K
61
-D
146
-K
182
-E
218
tetrad conserved in other cellular and viral MTases suggests that NS5 requires distinct amino acids for its N-7 and 2′-O MTase activities. The entire K
61
-D
146
-K
182
-E
218
motif is essential for 2′-O MTase activity, whereas N-7 MTase activity requires only D
146
. The other three amino acids facilitate, but are not essential for, guanine N-7 methylation. Amino acid substitutions within the K
61
-D
146
-K
182
-E
218
motif in a WNV luciferase-reporting replicon significantly reduced or abolished viral replication in cells. Additionally, the mutant MTase-mediated replication defect could not be
trans
complemented by a wild-type replicase complex. These findings demonstrate a critical role for the flavivirus MTase in viral reproduction and underscore this domain as a potential target for antiviral therapy.
Marek's Disease Virus Encodes MicroRNAs That Map to
meq
and the Latency-Associated Transcript
Authors: Burnside Joan , Bernberg Erin , Anderson Amy , Lu Cheng , Meyers Blake C. , Green Pamela J. , Jain Neeta , Isaacs Grace , Morgan Robin W.
Published: August 2006

MicroRNAs (miRNAs) are a class of small (∼22-nucleotide) regulatory molecules that block translation or induce degradation of target mRNAs. These have been identified in a wide range of organisms, including viruses. In particular, the oncogenic gammaherpesviruses Kaposi's sarcoma herpesvirus and Epstein-Barr virus encode miRNAs that could potentially regulate either viral or host genes. To determine if Marek's disease virus (MDV), an oncogenic alphaherpesvirus of chickens, encodes miRNAs, we isolated small RNAs from MDV-infected chicken embryo fibroblasts (CEF) and used the 454 Life Sciences sequencing technology to obtain the sequences of 13,679 candidate host and viral small RNAs. Eight miRNAs were found, five of which flank the
meq
oncogene and three that map to the latency-associated transcript (LAT) region of the genome. The
meq
gene is unique to pathogenic serotypes of MDV and is transcriptionally active during latency and transformation, and the LAT region of the MDV genome is antisense to the immediate-early gene ICP4. Secondary structure analysis predicted that the regions flanking the miRNAs could form hairpin precursors. Northern blot analysis confirmed expression of all miRNAs in MDV-infected CEF, MDV-induced tumors, and MDV lymphoblastoid cell lines. We propose that the MDV miRNAs function to enable MDV pathogenesis and contribute to MDV-induced transformation of chicken T cells.
Tertiary Structural and Functional Analyses of a Viroid RNA Motif by Isostericity Matrix and Mutagenesis Reveal Its Essential Role in Replication
Authors: Zhong Xuehua , Leontis Neocles , Qian Shuiming , Itaya Asuka , Qi Yijun , Boris-Lawrie Kathleen , Ding Biao
Published: August 2006

RNA-templated RNA replication is essential for viral or viroid infection, as well as for regulation of cellular gene expression. Specific RNA motifs likely regulate various aspects of this replication. Viroids of the
Pospiviroidae
family, as represented by the
Potato spindle tuber viroid
(PSTVd), replicate in the nucleus by utilizing DNA-dependent RNA polymerase II. We investigated the role of the loop E (sarcin/ricin) motif of the PSTVd genomic RNA in replication. A tertiary-structural model of this motif, inferred by comparative sequence analysis and comparison with nuclear magnetic resonance and X-ray crystal structures of loop E motifs in other RNAs, is presented in which core non-Watson-Crick base pairs are precisely specified. Isostericity matrix analysis of these base pairs showed that the model accounts for the reported natural sequence variations and viable experimental mutations in loop E motifs of PSTVd and other viroids. Furthermore, isostericity matrix analysis allowed us to design disruptive, as well as compensatory, mutations of PSTVd loop E. Functional analyses of such mutants by in vitro and in vivo experiments demonstrated that loop E structural integrity is crucial for replication, specifically during transcription. Our results suggest that the PSTVd loop E motif exists and functions in vivo and provide loss-of-function genetic evidence for the essential role of a viroid RNA three-dimensional motif in rolling-circle replication. The use of isostericity matrix analysis of non-Watson-Crick base pairing to rationalize mutagenesis of tertiary motifs and systematic in vitro and in vivo functional assays of mutants offers a novel, comprehensive approach to elucidate the tertiary-structure-function relationships for RNA motifs of general biological significance.
Antiviral Potency of APOBEC Proteins Does Not Correlate with Cytidine Deamination
Authors: Bishop Kate N. , Holmes Rebecca K. , Malim Michael H.
Published: August 2006

The human cytidine deaminases APOBEC3G (hA3G) and APOBEC3F (hA3F) are intracellular antiretroviral factors that can hypermutate nascent reverse transcripts and inhibit the replication of human immunodeficiency virus type 1 (HIV-1). Both enzymes have two cytidine deaminase motifs, although only the C-terminal motif is catalytic. Current models of APOBEC protein function imply editing is the principal mechanism of antiviral activity. In particular, hA3G is a more potent inhibitor of HIV-1 infectivity than hA3F and also induces a greater frequency of mutations in HIV-1 cDNA. We used hA3G/hA3F chimeric proteins to investigate whether cytidine deaminase potential reflects antiviral potency. We show here that the origin of the C-terminal deaminase motif is sufficient to determine the degree of mutation induced in a bacterial assay that measures mutations in chromosomal DNA. In contrast, this was not the case in the context of HIV-1 infection where the N-terminal deaminase motif also modulated the editing capabilities of the chimeras. Surprisingly, although three of the chimeric proteins induced levels of mutation that approximated those of parental hA3F, they displayed lower levels of antiviral activity. Most importantly, real-time PCR experiments revealed that the quantity of reverse transcripts detected in target cells, rather than the mutational burden carried by such DNAs, corresponded closely with viral infectivity. In other words, the antiviral phenotype of APOBEC proteins correlates with their ability to prevent the accumulation of reverse transcripts and not with the induction of hypermutation.
Role of Bim in Regulating CD8+T-Cell Responses during Chronic Viral Infection
Authors: Grayson Jason M. , Weant Ashley E. , Holbrook Beth C. , Hildeman David
Published: August 2006

Apoptosis is critical for the development and maintenance of the immune system. The proapoptotic Bcl-2 family member Bim is important for normal immune system homeostasis. Although previous experiments have shown that Bim is critical for the apoptosis of antigen-specific CD8+T cells during acute viral infection, the role of Bim during chronic viral infection is unclear. Using lymphocytic choriomeningitis virus clone 13 infection of mice, we demonstrate a role for Bim in CD8+T-cell apoptosis during chronic viral infection. Enumeration of antigen-specific CD8+T cells by major histocompatibility complex class I tetramer staining revealed that CD8+DbNP396-404+T cells, which undergo extensive deletion in wild-type mice, exhibited almost no decrease in Bim mutant mice. This contrasts with CD8+DbGP33-41+and CD8+DbGP276-286+T cells that underwent similar decreases in numbers in both Bim mutant and wild-type mice. Increased numbers of CD8+DbNP396-404+T cells in Bim mutant mice were due to lack of apoptosis and could not be explained by altered proliferation, differential homing to tissues, or increased help from CD4+T cells. When viral titers were examined, high levels were initially observed in both groups, but in Bim mutant mice, clearance from the spleen and sera was slightly accelerated. These experiments demonstrate the critical role of Bim during chronic viral infection to down-regulate CD8+T-cell responses and have implications for designing strategies for optimizing immunotherapies during situations where antigen persists, such as chronic infection, autoimmune syndromes, and cancer.
Intra- and Intersubtype Alternative Pak2-Activating Structural Motifs of Human Immunodeficiency Virus Type 1 Nef
Authors: O'Neill Eduardo , Baugh Laura L. , Novitsky Vladimir A. , Essex Myron E. , Garcia J. Victor
Published: August 2006

The design of antiviral strategies against human immunodeficiency virus type 1 (HIV-1) has been largely derived from studies of subtype B viruses, although they constitute only 12% of infections worldwide. At 50% of all HIV-1 infections worldwide, subtype C viruses are the most predominant. Here, we present evidence that subtype C Nefs display functional Pak2-activating motifs that differ from those found in subtype B and E Nefs. The identification of multiple Pak2-activating structural motifs that singly affect one Nef activity revealed a functional plasticity that has implications for future drug and vaccine design aimed at HIV-1 Nef and its effects on the deregulation of the immune system.
Poxviral Regulation of the Host NF-κB Response: the Vaccinia Virus M2L Protein Inhibits Induction of NF-κB Activation via an ERK2 Pathway in Virus-Infected Human Embryonic Kidney Cells
Authors: Gedey Roderick , Jin Xiao-Lu , Hinthong Olivia , Shisler Joanna L.
Published: August 2006

Exposure of eukaryotic cells to viruses will activate the host NF-κB transcription factor, resulting in proinflammatory and immune protein production. Vaccinia virus (VV), the prototypic orthopoxvirus, expresses products that inhibit this antiviral event. To identify novel mechanisms responsible for this effect, we made use of a VV deletion mutant (MVA) that stimulates NF-κΒ activation in infected 293T cells. In this virus-host system, the extents of NF-κΒ-regulated gene expression and nuclear translocation were reduced in the presence of either PD 98059 or U0126, two compounds capable of blocking ERK1 and ERK2 phosphorylation. A similar repression was also observed in cells that contained a dominant, nonactive form of ERK2 but not in cells where ERK1 phosphorylation was inhibited via overexpression of a dominant-negative mutant MEK1 protein. Presumably, proteins expressed from a wild-type VV that block ERK2 activity would also inhibit MVA-induced NF-κB activation. Indeed, the expression of one such open reading frame, M2L, supported this prediction. First, ectopic M2L expression hampered ERK2 phosphorylation induced by exposure to phorbol myristate acetate. Second, viral M2L expression via infection of cells with a recombinant MVA construct that stably expressed M2L decreased the phosphorylation of ERK2 compared to that in cells infected with the parental MVA strain. Finally, the recombinant M2L-expressing virus restored the “wild-type” NF-κB-inhibitory phenotype, as indicated by decreased NF-κB migration to infected cell nuclei and interference in transcription. Thus, in 293T cells, VV apparently utilizes its M2L protein to interfere with a step(s) that would otherwise enable ERK2 phosphorylation and the consequential activation of an NF-κΒ response.
Inducible Yeast System for Viral RNA Recombination Reveals Requirement for an RNA Replication Signal on Both Parental RNAs
Authors: Garcia-Ruiz Hernan , Ahlquist Paul
Published: August 2006

To facilitate RNA recombination studies, we tested whether
Saccharomyces cerevisiae
, which supports brome mosaic virus (BMV) replication, also supports BMV RNA recombination. Yeast strains expressing BMV RNA replication proteins 1a and 2a
pol
were engineered to transiently coexpress two independently inducible, overlapping, nonreplicating derivatives of BMV genomic RNA3. B3Δ3′ lacked the coat protein gene and negative-strand RNA promoter. B3Δ5′ lacked the positive-strand RNA promoter and had the coat gene replaced by the selectable
URA3
gene. After 12 to 72 h of induction, B3Δ3′ and B3Δ5′ transcription was repressed and Ura
+
yeast cells were selected. All Ura
+
cells contained recombinant RNA3 replicons expressing
URA3
. Most replicons arose by intermolecular homologous recombination between B3Δ3′ and B3Δ5′. Such recombinants were isolated only when 1a and 2a
pol
were expressed and after transient transcription of both B3Δ3′ and B3Δ5′, showing that recombination occurred at the RNA, not DNA, level. A minority of
URA3
-expressing replicons were derived from B3Δ5′, independently of B3Δ3′, by 5′ truncation and modification, generating novel positive-strand promoters and demonstrating that BMV can give rise to subgenomic RNA replicons. Intermolecular B3Δ3′-B3Δ5′ recombination occurred only when both parental RNAs bore a functional,
cis
-acting template recognition and recruitment element targeting viral RNAs to replication complexes. The results imply that recombination occurred in RNA replication complexes to which parental RNAs were independently recruited. Moreover, the ability to obtain intermolecular recombinants at precisely measurable, reproducible frequencies, to control genetic background and induction conditions, and other features of this system will facilitate further studies of virus and host functions in RNA recombination.
Mobility of Human Immunodeficiency Virus Type 1 Pr55
Gag
in Living Cells
Authors: Gomez Candace Y. , Hope Thomas J.
Published: August 2006

Human immunodeficiency virus type 1 (HIV-1) assembly requires the converging of thousands of structural proteins on cellular membranes to form a tightly packed immature virion. The Gag polyprotein contains all of the determinants important for viral assembly and must move around in the cell in order to form particles. This work has focused on Gag mobility in order to provide more insights into the dynamics of particle assembly. Key to these studies was the use of several fluorescently labeled Gag derivatives. We used fluorescence recovery after photobleaching as well as photoactivation to determine Gag mobility. Upon expression, Gag can be localized diffusely in the cytoplasm, associated with the plasma membrane, or in virus-like particles (VLPs). Here we show that Gag VLPs are primarily localized in the plasma membrane and do not colocalize with CD63. We have shown using full-length Gag as well as truncation mutants fused to green fluorescent protein that Gag is highly mobile in live cells when it is not assembled into VLPs. Results also showed that this mobility is highly dependent upon cholesterol. When cholesterol is depleted from cells expressing Gag, mobility is significantly decreased. Once cholesterol was replenished, Gag mobility returned to wild-type levels. Taken together, results from these mobility studies suggest that Gag is highly mobile and that as the assembly process proceeds, mobility decreases. These studies also suggest that Gag assembly must occur in cholesterol-rich domains in the plasma membrane.
Role of the Envelope Genetic Context in the Development of Enfuvirtide Resistance in Human Immunodeficiency Virus Type 1-Infected Patients
Authors: Labrosse Béatrice , Morand-Joubert Laurence , Goubard Armelle , Rochas Séverine , Labernardière Jean-Louis , Pacanowski Jerôme , Meynard Jean-Luc , Hance Allan J. , Clavel François , Mammano Fabrizio
Published: August 2006

Acquired human immunodeficiency virus type 1(HIV-1) resistance to the fusion inhibitor enfuvirtide (ENF) is primarily associated with mutations within the highly conserved first heptad repeat (HR1) region of gp41. Viralenvsequences, however, are remarkably variable, and the envelope genetic background could have an important impact on optimal expression of HR1 mutations. We have examined the genetic evolution ofenvsequences, ENF susceptibility, and Env replicative capacity in patients failing ENF treatment. Sequential plasma-derived virus populations, obtained from six patients initiating ENF treatment as part of a salvage therapy, were studied using a recombinant phenotypic assay evaluating the entire gp120 and the gp41 ectodomains. Regardless of major differences in the baseline ENF susceptibilities, viral populations with similar phenotypic ENF resistance (50% inhibitory concentration, >3,000 ng/ml) were selected under treatment in four of six patients. As expected, in all patients ENF-resistant viruses harbored one or more HR1 mutations (positions 36, 38, and 43). Interestingly, in five patients the emergence of resistance mutations was not associated with reduced Env replicative capacity. Phylogenetic analysis ofenvsequences in sequential samples from two patients showed that the HR1 mutations had emerged in the context ofenvquasi-species that were different from those prevalent at baseline. Thus, the envelope genetic context appears to play a critical role in the selection of HR1 mutations and the expression of ENF resistance, thereby conditioning the evolution of HIV-1 under fusion inhibitor selective pressure.
AN ANALYSIS AND MEASUREMENT OF CONFIDENCE OF STOCK INVESTORS IN INDIA
Authors: SRIVASTAVA AMAN
Published: August 2006

This paper intends to establish the importance of expectations and confidence of Indian investors on the financial market in India. Previous research of investors in other countries has shown that both of these attitudes manifest clear tendencies to change through time and strongly influence the behavior of the pragmatic markets. The field of behavioral finance — an emerging field in financial analysis that takes explicit account of psychological factors — is the driving force of this research. This research is based on information obtained through a survey process in India.
PROJECTING THE FORWARD RATE FLOW ONTO A FINITE DIMENSIONAL MANIFOLD
Authors: BAYRAKTAR ERHAN , CHEN LI , POOR H. VINCENT
Published: August 2006

Given a Heath–Jarrow–Morton (HJM) interest rate model [Formula: see text] and a parametrized family of finite dimensional forward rate curves [Formula: see text], this paper provides a technique for projecting the infinite dimensional forward rate curve rt given by [Formula: see text] onto the finite dimensional manifold [Formula: see text]. The Stratonovich dynamics of the projected finite dimensional forward curve are derived and it is shown that, under the regularity conditions, the given Stratonovich differential equation has a unique strong solution. Moreover, this projection leads to an efficient algorithm for implicit parametric estimation of the infinite dimensional HJM model. The feasibility of this method is demonstrated by applying the generalized method of moments.
VALUES OF MORTGAGES WITH TOP-UP PAYMENT OPTIONS
Authors: LAI ROSE NENG , ONG SEOW ENG , SING TIEN FOO
Published: August 2006

The right of lenders to request for top-ups of negative equity when the property value falls below the loan outstanding is a little known, yet widely adopted provision in mortgage documents in many Asian markets. We analyze the effect of the top-up option by appealing to a contingent claim framework. Specifically, we model the top-up option as a synthetic option comprising a long put to request for a top-up, a short put that cancels out the first option in the event of a default, and a binary put option once triggered will yield a value equivalent to the difference between the mortgage outstanding and the property value. The results of comparative analyses show that the lender's right to request for top-ups is valuable when the negative mortgage equity increases, especially in a market where price is highly volatile. The top-up clause fundamentally affects the mortgage values for both the borrower and the lender. We show that lender's inaction by not calling for top-ups when negative mortgage equity occurs is suboptimal. On the other hand, the lenders' exercise of the in-the-money top-up options may lead to early default by the mortgagor. This is one of the reasons why lenders exercise this option only very sparingly in practice. This mortgage design has economic value to the lenders, it is, however, not optimal in time of volatile market. The policy implication of the findings is that the sub-optimal top-up feature should be removed from the mortgage contract, and it will not severely jeopardize the lender's ability to enforce payments in the mortgages.
TWO-COMPONENT EXTREME VALUE DISTRIBUTION FOR ASIA-PACIFIC STOCK INDEX RETURNS
Authors: ANÉ THIERRY
Published: August 2006

Financial risk management typically deals with low-probability events in the tails of asset return distributions. To better capture the behavior of these tails, several studies have clearly highlighted that one should rely on a methodology that directly focuses on the tails of the distribution rather than getting the tails as an outcome of modelling the entire density function. Traditional Extreme Value Theory (EVT) distributions, however, provide a good fit for the bulk of the extreme data but usually underestimate a small amount of observations considered as "outliers".

Since the main objective of risk management analysis is to estimate the size and probability of very large price movements, these "outliers" are by definition the very events we need to investigate. In this paper we suggest the use of a Two-Component Extreme Value (TCEV) distribution where a 'basic distribution' generates ordinary extremes (more frequent and less severe in the mean) while an "outlying distribution" generates rarer but severe extremes.

Goodness-of-fit tests show the superiority of this distribution to capture the extremes of eleven MSCI Indices of the Pacific-Basin region relative to traditional EVT densities. Measures of accuracy and efficiency used to assess the performance of VaR forecasts also indicate that the additional flexibility brought by the TCEV model provides strong improvements for risk management.
NEURAL CLASSIFICATION OF MASS ABNORMALITIES WITH DIFFERENT TYPES OF FEATURES IN DIGITAL MAMMOGRAPHY
Authors: PANCHAL R. , VERMA B.
Published: August 2006

Early detection of breast abnormalities remains the primary prevention against breast cancer despite the advances in breast cancer diagnosis and treatment. Presence of mass in breast tissues is highly indicative of breast cancer. The research work presented in this paper investigates the significance of different types of features using proposed neural network based classification technique to classify mass type of breast abnormalities in digital mammograms into malignant and benign. 14 gray level based features, four BI-RADS features, patient age feature and subtlety value feature have been explored using the proposed research methodology to attain maximum classification on test dataset. The proposed research technique attained a 91% testing classification rate with a 100% training classification rate on digital mammograms taken from the DDSM benchmark database.
INTEGRATED ALGORITHMS FOR IMAGE ANALYSIS AND CLASSIFICATION OF NUCLEAR DIVISION FOR HIGH-CONTENT CELL-CYCLE SCREENING
Authors: PHAM TUAN D. , TRAN DAT T. , ZHOU XIAOBO , WONG STEPHEN T. C.
Published: August 2006

Advances in fluorescent probing and microscopic imaging technology provide important tools for biomedical research in studying the structures and functions of cells and molecules. Such studies require the processing and analysis of huge amounts of image data, and manual image analysis is very time consuming, thus costly, and also potentially inaccurate and poor reproducibility. In this paper, we present and combine several advanced computational, probabilistic, and fuzzy-set methods for the computerized classification of cell nuclei in different mitotic phases. We tested our proposed methods with real image sequences recorded over a period of twenty-four hours at every fifteen minutes with a time-lapse fluorescence microscopy. The experimental results have shown that the proposed methods are effective for the task of classification.
WEIGHTED THRESHOLD-BASED CLUSTERING FOR INTRUSION DETECTION SYSTEMS
Authors: NIKULIN VLADIMIR
Published: August 2006

Signature-based intrusion detection systems look for known, suspicious patterns in the input data. In this paper we explore compression of labeled empirical data using threshold-based clustering with regularization. The main target of clustering is to compress training dataset to the limited number of signatures, and to minimize the number of comparisons that are necessary to determine the status of the input event as a result. Essentially, the process of clustering includes merging of the clusters which are close enough. As a consequence, we will reduce original dataset to the limited number of labeled centroids. In a complex with k-nearest-neighbor (kNN) method, this set of centroids may be used as a multi-class classifier. Clearly, different attributes have different importance depending on the particular training database and given cost matrix. This importance may be regulated in the definition of the distance using linear weight coefficients. The paper introduces special procedure to estimate above weight coefficients.

The experiments on the KDD-99 intrusion detection dataset have confirmed the effectiveness of the proposed methods.
APPLICATION OF SICoNNETS TO HANDWRITTEN DIGIT RECOGNITION
Authors: TIVIVE FOK HING CHI , BOUZERDOUM ABDESSELAM
Published: August 2006

In this paper, we apply a new neural network model, namely shunting inhibitory convolutional neural networks, or SICoNNets for short, to the problem of handwritten digit recognition. This type of networks has a generic and flexible architecture, where the processing is based on the physiologically plausible mechanism of shunting inhibition. A hybrid first-order training method, called QRProp, is developed based on the three training algorithms Rprop, Quickprop, and SuperSAB. The MNIST database is used to train and evaluate the performance of SICoNNets in handwritten digit recognition. A network with 24 feature maps and 2722 free parameters achieves a recognition accuracy of 97.3%.
APPEARANCE FEATURE EXTRACTION VERSUS IMAGE TRANSFORM-BASED APPROACH FOR VISUAL SPEECH RECOGNITION
Authors: SAGHEER ALAA , TSURUTA NAOYUKI , TANIGUCHI RIN-ICHIRO , MAEDA SAKASHI
Published: August 2006

In this paper we propose a new appearance based system which consists of two stages: visual speech feature extraction and classification, followed by recognition of the extracted feature, thereby the result is a complete lip-reading system. This lip-reading system employs our Hyper Column Model (HCM) approach to extract and classify the visual features and uses the Hidden Markov Model (HMM) for recognition. This paper addresses mainly the first stage; i.e. feature extraction and classification. We investigate the HCM performance to achieve feature extraction and classification and then compare the performance when replacing HCM with Fast Discrete Cosine Transform (FDCT). Unlike FDCT, HCM could extract the entire features without any loss. Also the experiments have shown that HCM is generally better than FDCT and provides a good distribution of the phonemes in the feature space for recognition purposes. For fair comparison, two databases are exploited with three different sets of resolution for each database. One of these two databases is designed to include shifted and scaled objects. Experiments reveal that HCM is capable of recovering and dealing with such image restrictions whereas the effectiveness of FDCT drops drastically especially for new subjects.
GENETIC PROGRAMMING APPROACH FOR MULTI-CATEGORY PATTERN CLASSIFICATION APPLIED TO NETWORK INTRUSIONS DETECTION
Authors: FARAOUN K. M. , BOUKELIF A.
Published: August 2006

The present paper describes a new approach of classification using genetic programming. The proposed technique consists of genetically co-evolve a population of nonlinear transformations on the input data to be classified, and map them to a new space with reduced dimension in order to get a maximum inter-classes discrimination. It is much easier to classify the new samples from the transformed data. Contrary to the existing GP-classification techniques, the proposed one uses a dynamic repartition of the transformed data in separated intervals, the efficiency of a given intervals repartition is handled by the fitness criterion, with a maximum classes discrimination. Experiments were performed using the Fisher's Iris dataset. After that, the KDD'99 Cup dataset was used to study the intrusion detection and classification problem. The results demonstrate that the proposed genetic approach outperforms the existing GP-classification methods, and provides improved results compared to other existing techniques.
Living History of Physiology: Carl Gans
Authors: Dudley Robert , Huey Raymond B. , Carrier David R.
Published: August 2006

In 2005, The American Physiological Society initiated The Living History of Physiology Project to recognize senior members who have made extraordinary contributions during their career to the advancement of the discipline and profession of physiology. Each Eminent Physiologist will be interviewed for archival purposes, and the video tape will be available from the American Physiological Society Headquarters. In addition, a biographical profile of the recipient will be published in Advances in Physiology Education.
Teaching skeletal muscle adaptations to aerobic exercise using an American Physiological Society classic paper by Dr. Philip Gollnick and colleagues
Authors: Brown Gregory A.
Published: August 2006

The use of primary research in the classroom enhances the critical thinking abilities of students. The present article describes a strategy for using the American Physiological Society classic paper “Enzyme activity and fiber composition in skeletal muscle of untrained and trained men” by Dr. Philip D. Gollnick and colleagues to enhance the students’ ability to understand research, increase their knowledge of the adaptations to exercise, and learn computer skills in data analysis and presentation. By having students read, study, prepare graphs, and discuss the data from a classic paper, they gain an improved understanding of the factors that influence aerobic exercise ability. This study is especially useful for illuminating the exercise-specific differences in bioenergetic enzymes, muscle fiber type, and fitness characteristics that exist between untrained and trained individuals.
Mammalian Target of Rapamycin Inhibition Promotes Response to Epidermal Growth Factor Receptor Kinase Inhibitors in PTEN-Deficient and PTEN-Intact Glioblastoma Cells
Authors: Wang Maria Y. , Lu Kan V. , Zhu Shaojun , Dia Ederlyn Q. , Vivanco Igor , Shackleford Gregory M. , Cavenee Webster K. , Mellinghoff Ingo K. , Cloughesy Timothy F. , Sawyers Charles L. , Mischel Paul S.
Published: August 2006

The epidermal growth factor receptor (EGFR) is commonly amplified, overexpressed, and mutated in glioblastoma, making it a compelling molecular target for therapy. We have recently shown that coexpression of EGFRvIII and PTEN protein by glioblastoma cells is strongly associated with clinical response to EGFR kinase inhibitor therapy. PTEN loss, by dissociating inhibition of the EGFR from downstream phosphatidylinositol 3-kinase (PI3K) pathway inhibition, seems to act as a resistance factor. Because 40% to 50% of glioblastomas are PTEN deficient, a critical challenge is to identify strategies that promote responsiveness to EGFR kinase inhibitors in patients whose tumors lack PTEN. Here, we show that the mammalian target of rapamycin (mTOR) inhibitor rapamycin enhances the sensitivity of PTEN-deficient tumor cells to the EGFR kinase inhibitor erlotinib. In two isogenic model systems (U87MG glioblastoma cells expressing EGFR, EGFRvIII, and PTEN in relevant combinations, and SF295 glioblastoma cells in which PTEN protein expression has been stably restored), we show that combined EGFR/mTOR kinase inhibition inhibits tumor cell growth and has an additive effect on inhibiting downstream PI3K pathway signaling. We also show that combination therapy provides added benefit in promoting cell death in PTEN-deficient tumor cells. These studies provide strong rationale for combined mTOR/EGFR kinase inhibitor therapy in glioblastoma patients, particularly those with PTEN-deficient tumors. (Cancer Res 2006; 66(16): 7864-9)
Sequence Variants in Cell Cycle Control Pathway, X-ray Exposure, and Lung Cancer Risk: A Multicenter Case-Control Study in Central Europe
Authors: Hung Rayjean J. , Boffetta Paolo , Canzian Federico , Moullan Norman , Szeszenia-Dabrowska Neonila , Zaridze David , Lissowska Jolanta , Rudnai Peter , Fabianova Eleonora , Mates Dana , Foretova Lenka , Janout Vladimir , Bencko Vladimir , Chabrier Amelie , Landi Stefano , Gemignani Federica , Hall Janet , Brennan Paul
Published: August 2006

Exposure to ionizing radiation (IR) results in various types of DNA damage and is a suspected cause of lung cancer. An essential cellular machinery against DNA damage is cell cycle control, which is regulated by several genes, including TP53, CCND1, and CDKN2A. Therefore, we hypothesized that the genetic variants in these three genes influence the predisposition of lung cancer (i.e., CCND1 G870A, CDKN2A Ala148Thr, TP53 Arg72Pro, and 16-bp repeat in intron 3) and that the effect of X-ray on lung cancer risk can be modified by the presence of these genetic variations. The study was conducted in 15 centers in 6 countries of Central Europe between 1998 and 2002. A total of 2,238 cases and 2,289 controls were recruited and provided DNA samples. Cases with positive family history were analyzed separately. The joint effect of X-ray and previous risk genotypes was assessed, and modification by sequence variants on X-ray dose-response relationship with lung cancer risk was evaluated. We found an overall effect of TP53 intron 3 16-bp repeats [odds ratio (OR), 1.99; 95% confidence interval (95% CI), 1.27-3.13], which was stronger among cases with family history of lung cancer (OR, 2.98; 95% CI, 1.29-6.87). In addition, our results suggested an interaction that was greater than multiplicativity between TP53 intron 3 16-bp repeats and multiple X-ray exposures (interaction OR, 5.69; 95% CI, 1.33-24.3). We did not observe a main effect of CCND1 G870A polymorphism; however, the dose-response relationship between lung cancer risk and X-ray exposures was modified by CCND1 genotype with no risk from X-ray exposures among subjects who carried G/G genotype, intermediate risk [trend OR for X-ray, 1.16; 95% CI, 1.05-1.27) among subjects with G/A genotype, and highest risk [trend OR for X-ray, 1.29; 95% CI, 1.12-1.49) among subjects with A/A genotype. Sequence variants in cell cycle control pathway may increase the risk of lung cancer and modify the risk conferred by multiple X-ray exposures. However, a definite conclusion can only be drawn on replication by different studies among individuals who are highly exposed to IR. (Cancer Res 2006; 66(16): 8280-6)
Transforming Growth Factor-β Promotes Invasion in Tumorigenic but not in Nontumorigenic Human Prostatic Epithelial Cells
Authors: Ao Mingfang , Williams Karin , Bhowmick Neil A. , Hayward Simon W.
Published: August 2006

Transforming growth factor-β (TGF-β) is a pleiotropic growth factor with actions that are dependent on circumstances, including dose, target cell type, and context. TGF-β can elicit both growth-promoting and growth-suppressive activities. In normal tissues, TGF-β generally acts to restrict growth and maintain differentiation. However, during tumorigenesis, changes in TGF-β expression and cellular responses can promote tumorigenesis. The present study examines the effects of TGF-β on the nontumorigenic human prostatic epithelial cell line BPH1 and on three derivative tumorigenic sublines BPH1CAFTD1, BPH1CAFTD3, and BPH1CAFTD5. The data show that TGF-β has different effects on the nontumorigenic and tumorigenic cells. The nontumorigenic cells are growth inhibited by TGF-β. In contrast, the tumorigenic sublines are not growth inhibited but instead undergo an epithelial to mesenchymal transformation (EMT) in response to TGF-β. The tumorigenic lines show constitutively elevated levels of phosphorylated Akt, which modulates their response to TGF-β by blocking Smad3 and p21 nuclear translocation. On TGF-β stimulation of the tumorigenic sublines, the activated Akt allows the cell to escape cell cycle arrest. The phosphatidylinositol 3-kinase/Akt pathway is also involved in TGF-β-induced EMT, defined here by induction of vimentin expression and enhanced cellular motility. In vivo, tumorigenic cells with constitutively active TGF-β signaling show increased invasion with EMT, which express vimentin, located specifically at the invasive front of the tumor. These data indicate that following malignant transformation TGF-β can play a direct role in promoting prostatic cancer and further that these responses are context specific in vivo. (Cancer Res 2006; 66(16): 8007-16)
Inhibition of 7,12-Dimethylbenz(a)anthracene-Induced Skin Tumorigenesis in C57BL/6 Mice by Sulforaphane Is Mediated by Nuclear Factor E2–Related Factor 2
Authors: Xu Changjiang , Huang Mou-Tuan , Shen Guoxiang , Yuan Xiaoling , Lin Wen , Khor Tin Oo , Conney Allan H. , Kong Ah-Ng Tony
Published: August 2006

Sulforaphane, a dietary isothiocyanate, possesses potent chemopreventive effects through the induction of cellular detoxifying/antioxidant enzymes via the transcription factor nuclear factor E2–related factor 2 (Nrf2). To investigate carcinogenesis mechanisms related to the regulation of Nrf2, we examined the tumor incidence and tumor numbers per mouse in Nrf2 wild-type (+/+) and Nrf2 knockout (−/−) mice. 7,12-Dimethylbenz(a)anthracene/12-O-tetradecanoylphorbol-13-acetate treatments resulted in an increase in the incidence of skin tumors and tumor numbers per mouse in both genotypes; however, both indices were markedly higher in Nrf2(−/−) mice as compared with Nrf2(+/+) mice. Western blot analysis revealed that Nrf2 as well as heme oxygenase-1, a protein regulated by Nrf2 were not expressed in skin tumors from mice of either genotype, whereas expression of heme oxygenase-1 in Nrf2(+/+) mice was much higher than that in Nrf2(−/−) mice in nontumor skin samples. Next, we examined the chemopreventive efficacy of sulforaphane in mice with both genotypes. Topical application of 100 nmol of sulforaphane once a day for 14 days prior to 7,12-dimethylbenz(a)anthracene/12-O-tetradecanoylphorbol-13-acetate applications decreased the incidence of skin tumor in the Nrf2(+/+) mice when compared with the vehicle-treated group. Importantly, there was no chemoprotective effect elicited by sulforaphane pretreatment in the Nrf2(−/−) mice group. Taken together, our results show for the first time that Nrf2(−/−) mice are more susceptible to skin tumorigenesis and that the chemopreventive effects of sulforaphane are mediated, at least in part, through Nrf2. (Cancer Res 2006; 66(16): 8293-6)
Targeting Mitogen-Activated Protein Kinase/Extracellular Signal–Regulated Kinase Kinase in the Mutant (V600E) B-Raf Signaling Cascade Effectively Inhibits Melanoma Lung Metastases
Authors: Sharma Arati , Tran Melissa A. , Liang Shile , Sharma Arun K. , Amin Shantu , Smith Charles D. , Dong Cheng , Robertson Gavin P.
Published: August 2006

Malignant melanoma has a high propensity for metastatic spread, making it the most deadly form of skin cancer. B-RAF has been identified as the most mutated gene in these invasive cells and therefore an attractive therapeutic target. However, for uncertain reasons, chemotherapy inhibiting B-Raf has not been clinically effective. This has raised questions whether this pathway is important in melanoma metastasis or whether targeting a protein other than B-Raf in the signaling cascade could more effectively inhibit this pathway to reduce lung metastases. Here, we investigated the role played by V600EB-Raf in melanoma metastasis and showed that targeting this signaling cascade significantly reduces lung metastases. Small interfering RNA (siRNA)–mediated inhibition was used in mice to reduce expression (activity) of each member of the signaling cascade and effects on metastasis development were measured. Targeting any member of the signaling cascade reduced metastasis but inhibition of mitogen-activated protein kinase/extracellular signal–regulated kinase kinase (Mek) 1 and Mek 2 almost completely prevented lung tumor development. Mechanistically, metastatic inhibition was mediated through reduction of melanoma cell extravasation through the endothelium and decreased proliferative capacity. Targeting B-Raf with the pharmacologic inhibitor BAY 43-9006, which was found ineffective in clinical trials and seems to act primarily as an angiogenesis inhibitor, did not decrease metastasis, whereas inhibition of Mek using U0126 decreased cellular proliferative capacity, thereby effectively reducing number and size of lung metastases. In summary, this study provides a mechanistic basis for targeting Mek and not B-Raf in the mutant V600EB-Raf signaling cascade to inhibit melanoma metastases. (Cancer Res 2006; 66(16): 8200-9)
Autocrine/Paracrine Platelet-Derived Growth Factor Regulates Proliferation of Neural Progenitor Cells
Authors: Erlandsson Anna , Brännvall Karin , Gustafsdottir Sigrun , Westermark Bengt , Forsberg-Nilsson Karin
Published: August 2006

Growth factors play an important role in regulating neural stem cell proliferation and differentiation. This study shows that platelet-derived growth factor (PDGF) induces a partial differentiation of neural stem/progenitor cells (NSPCs) in the absence of other mitogens in vitro. NSPCs thus acquire an immature morphology and display markers for both neurons and glia. In addition, these cells do not readily mature in the absence of further stimuli. When NSPC cultures treated with PDGF were exposed to additional differentiation factors, however, the differentiation proceeded into neurons, astrocytes, and oligodendrocytes. We find that NSPC cultures are endowed with an endogenous PDGF-BB production. The PDGF-BB expression peaks during early differentiation and is present both in cell lysates and in conditioned medium, allowing for autocrine as well as paracrine signaling. When the NSPC-derived PDGF was inhibited, progenitor cell numbers decreased, showing that PDGF is involved in NSPC expansion. Addition of a PDGF receptor (PDGFR) inhibitor resulted in a more rapid differentiation. Neurons and oligodendrocytes appeared earlier and had more elaborate processes than in control cultures where endogenous PDGFR signaling was not blocked. Our observations point to PDGF as an inducer of partial differentiation of NSPC that also sustains progenitor cell division. Such an intermediate stage in stem cell differentiation is of relevance for the understanding of brain tumor development because autocrine PDGF stimulation is believed to drive malignant conversion of central nervous system progenitor cells. (Cancer Res 2006; 66(16): 8042-8)