bluuebunny/crossref_metadata_2025 huggingface dataset:
A Simple Construction to Illustrate Lissajous Figures
Authors: Criado C. , Alamo N.
Published: March 2004

In a recent and interesting paper in The Physics Teacher, Thomas B. Greenslade Jr. presents a nice collection of devices that have been developed to display Lissajous figures.1 In this paper we discuss a very simple construction to illustrate the Lissajous figures using a method described by V.I. Arnold.2
Preheating Primes Pruners
Authors: Beckman Mary
Published: March 2004

Volunteers fill sandbags while storm clouds are brewing so the sacks will be ready when floodwaters rush in. Similarly, skin cells prepare for a flood of molten proteins by reinforcing a protein-chopping system, according to new research. This boost might explain how cells and organisms protect themselves from severe stress.
The Flavor of Aging
Authors: Davenport R. John
Published: March 2004

For the elderly, food turns bland and odors fade. Aging's undermining of the chemical senses makes meals uninspiring and sidetracks healthy eating habits. The changes also dampen awareness of spoiled food or malodorous--and potentially noxious--chemicals. Researchers are gaining a clearer view of how aging takes a toll on the senses of smell and taste, and they are hoping to find ways to revive them. Scientists are also investigating why neurodegenerative diseases often cripple the sense of smell and whether that failing might presage dementia.
Focus Issue: Targeting Signaling Pathways for Drug Discovery
Authors: Gough Nancy R. , Adler Elizabeth M. , Ray L. Bryan
Published: March 2004

This STKE Focus Issue on processes, targets, and opportunities in drug discovery is part of a coordinated effort to cover a broad range of topics related to drug discovery in
Science
's multiple online products and in a special issue of
Science
itself. STKE features three Perspectives and one Review that highlight drug development and signaling targets for therapeutic development. Shen describes the production of natural bioactive products by combinatorial biosynthesis in bacteria. Philips describes anticancer therapies aimed at the oncogenic guanosine triphosphatase Ras, and Kaelin discusses whether common cancers are likely to yield to single anticancer agents and echo the rousing success of the kinase inhibitor Gleevec. Charney and Manji discuss how an increased understanding of the underlying pathways could lead to novel potential therapies for treating depression.
Gleevec: Prototype or Outlier?
Authors: Kaelin William G.
Published: March 2004

The protein kinase inhibitor Gleevec has proven to be spectacularly effective in the treatment of chronic myelogenous leukemia (CML). But can success such as this be achieved for genetically complex neoplasms with other drugs targeted at hyperactive oncoproteins? Although only time will tell, both theoretical and empirical arguments suggest that the success of Gleevec in CML need not be a special case. As the molecular basis of various cancers is further defined, it should be possible to develop other new drugs that, like Gleevec, specifically target cancer cells by inhibiting early events that are integral to progression to the transformed phenotype. Encouraging in this regard are cell culture experiments and animal models that suggest that cancer cells often remain dependent on, and may become addicted to, the signals resulting from such early genetic changes.
Methotrexate and Ras Methylation: A New Trick for an Old Drug?
Authors: Philips Mark R.
Published: March 2004

Ras plays a central role in the development and progression of human cancer. Ras function depends on its ability to associate with cellular membranes. Nascent Ras is targeted to membranes by virtue of a series of posttranslational modifications of a C-terminal "CAAX" motif that include farnesylation, proteolysis, and carboxyl methylation. This pathway is an attractive target for anti-Ras drug development. Farnesyltransferase inhibitors have been developed and are in clinical trials. Their success has prompted interest in developing pharmacologically useful inhibitors of the other two enzymes in the Ras processing pathway. Ironically, it now appears that methotrexate, one of the oldest chemotherapeutic drugs, may work, in part, by inhibiting carboxyl methylation of Ras.
Interaction of the New Ketolide ABT-773 (Cethromycin) with Human Polymorphonuclear Neutrophils and the Phagocytic Cell Line PLB-985 In Vitro
Authors: Labro Marie Thérèse , Abdelghaffar Houria , Babin-Chevaye Catherine
Published: March 2004

A classical velocity centrifugation technique was used to study the in vitro uptake of the new ketolide ABT-773 by human polymorphonuclear neutrophils (PMNs) and a myelomonoblastic cell line, PLB-985, which can be differentiated into PMNs under certain culture conditions, compared to that of HMR 3004. ABT-773 was rapidly taken up by PMNs (cellular concentration to extracellular concentration ratio [C/E], about 34 at 30 s and up to 207 at 5 min), and uptake plateaued from 30 to 180 min (C/E, about 300). ABT-773 was accumulated significantly better than HMR 3004 from 5 to 180 min. Nondifferentiated PLB-985 cells (ND-PLB) accumulated significantly less ABT-773 and HMR 3004 than PMNs and PLB-985 cells differentiated into PMNs (D-PLB). Whatever the cell type and in contrast to the results obtained with HMR 3004, ABT-773 was mainly located in the cytosol (about 75%) and was rapidly released from loaded cells (about 40% at 5 min), followed by a plateau, likely owing to avid reuptake. Verapamil and H89, an inhibitor of protein kinase A, increased drug efflux. Uptake was sensitive to external pH, and the activation energy was moderate (about 50 kJ/mol). The existence of an active transport system on the PMN membrane was suggested by the following findings: concentration-dependent and saturable uptake (Vmax, about 10 000 ng/2.5 × 106PMNs/5 min;Km, about 60 μg/ml) the inhibitory effects of PMN activators or inhibitors (phorbol myristate acetate, verapamil, Ni2+) and the significantly decreased levels of accumulation by killed cells and cells treated at low temperatures. In addition, various macrolides impaired ABT-773 uptake, contrary to the findings for the quinolone levofloxacin. ND- and D-PLB also presented saturation kinetics that defined an active transport system (VmaxandKmvalues were similar to those obtained with PMNs), but the activation pathway of the carrier system did not seem to be fully functional in ND-PLB. As has been observed with other erythromycin A derivatives, ABT-773 impaired oxidant production by phagocytes in a time- and concentration-dependent manner. These data extend our previous results on the existence of an active transport system common to all macrolides and ketolides, at least in PMNs.
Efficacy of BAL5788, a Prodrug of Cephalosporin BAL9141, in a Mouse Model of Acute Pneumococcal Pneumonia
Authors: Azoulay-Dupuis E. , Bédos J. P. , Mohler J. , Schmitt-Hoffmann A. , Schleimer M. , Shapiro S.
Published: March 2004

BAL5788 is a water-soluble prodrug of BAL9141, a new broad-spectrum cephalosporin with high levels of in vitro activity against methicillin- and vancomycin-resistant staphylococci and penicillin-resistant streptococci. In plasma BAL5788 is rapidly converted to BAL9141. We studied the activity of BAL5788 in a mouse model of acute pneumococcal pneumonia. Leukopenic female Swiss albino mice were challenged intratracheally with 10
7
CFU of clinical
Streptococcus pneumoniae
strains P-52181 (Pen
s
Cro
s
Ctx
s
), P-15986 (Pen
r
Cro
s
Ctx
s
), P-40422 (Pen
r
Cro
r
Ctx
r
), and P-40984 (Pen
r
Cro
r
Ctx
r
). Infected mice received subcutaneous (s.c.) injections of BAL5788 or ceftriaxone starting 3 h after pneumococcal challenge. Uninfected nonleukopenic mice received single s.c. doses of BAL5788 to determine the BAL9141 concentration-time profiles in serum and lungs. Untreated control mice died within 5 days postinfection. Ten-day cumulative survival rates for infected mice receiving BAL5788 (total daily doses of BAL9141 equivalents, 2.1 to 75 mg/kg of body weight) ranged from 57 to 100%, whereas with ceftriaxone (total daily doses, 10 to 400 mg/kg), the survival rates varied between 13 and 100%. In mice infected with P-15986, the survival rates achieved with BAL5788 (BAL9141 equivalent, 8.4 mg/kg) and those achieved with ceftriaxone (50 mg/kg) were significantly different (93 versus 13%;
P
< 0.0001) in favor of BAL5788; the outcomes of the trials with all other strains were not significantly different between the two antibiotics, but markedly lower doses of BAL5788 than ceftriaxone were required to obtain similar survival rates. Pharmacokinetic data showed that BAL9141 was effective against the four pneumococcal strains tested at very low values of the time above the MIC (
T
> MIC), which ranged from 9 to 18% of the dosing interval, whereas the values of
T
> MICs for ceftriaxone ranged from 30 to 50% of the dosing interval.
Aspergillus fumigatusVariant with Decreased Susceptibility to Multiple Antifungals
Authors: Balajee S. Arunmozhi , Weaver Molly , Imhof Alexander , Gribskov Jennifer , Marr Kieren A.
Published: March 2004

Isolates ofAspergillus fumigatusthat demonstrate resistance to itraconazole (ITZ) have been described previously; however, the prevalence and clinical significance of ITZ resistance are not completely understood. In this study we assessed the ITZ susceptibilities of 128A. fumigatusisolates that caused invasive infection in 82 stem cell transplant patients before and after the use of ITZ in our institution (study period, 1991 to 2000). The MICs for 10 isolates obtained from seven patients were high, ≥1 μg/ml. The average ITZ MIC increased after institutional use of the drug began in 1995. The majority of the isolates for which MICs were high (6 of 10) and one isolate for which the MIC was low (0.06 μg/ml) demonstrated an unusual phenotype, appearing as predominantly white colonies. For all seven atypical isolates, voriconazole MICs were high (≥2 μg/ml), and minimal effective concentrations of caspofungin were high (≥4 μg/ml). For two of the seven atypical isolates, amphotericin B MICs were high (≥2 μg/ml). The isolates appeared white due to slow sporulation; however, after prolonged incubations, the isolates sporulated with no difference in conidial color or conidiophore morphology compared with typical isolates. Randomly amplified polymorphic DNA-PCR patterns of these isolates were distinct compared with those of otherA. fumigatusisolates. Sequencing of 18S rRNA genes confirmed that all wereA. fumigatus; however, the mitochondrial cytochromebgene sequences of all the atypical isolates were unique. These data suggest the potential presence of a genetically unique, poorly sporulating variant ofA. fumigatusthat demonstrates decreased susceptibilities to several antifungals.
Dissemination of CTX-M-Type β-Lactamases among Clinical Isolates of
Enterobacteriaceae
in Paris, France
Authors: Eckert C. , Gautier V. , Saladin-Allard M. , Hidri N. , Verdet C. , Ould-Hocine Z. , Barnaud G. , Delisle F. , Rossier A. , Lambert T. , Philippon A. , Arlet G.
Published: March 2004

We analyzed 19 clinical isolates of the family
Enterobacteriaceae
(16
Escherichia coli
isolates and 3
Klebsiella pneumoniae
isolates) collected from four different hospitals in Paris, France, from 2000 to 2002. These strains had a particular extended-spectrum cephalosporin resistance profile characterized by a higher level of resistance to cefotaxime and aztreonam than to ceftazidime. The
bla
CTX-M
genes encoding these β-lactamases were involved in this resistance, with a predominance of
bla
CTX-M-15
. Ten of the 19 isolates produced both TEM-1- and CTX-M-type enzymes. One strain (
E. coli
TN13) expressed CMY-2, TEM-1, and CTX-M-14.
bla
CTX-M
genes were found on large plasmids. In 15 cases the same insertion sequence, IS
Ecp1
, was located upstream of the 5′ end of the
bla
CTX-M
gene. In one case we identified an insertion sequence designated IS
26
. Examination of the other three
bla
CTX-M
genes by cloning, sequencing, and PCR analysis revealed the presence of a complex
sul1
-type integron that includes open reading frame ORF513, which carries the
bla
gene and the surrounding DNA. Five isolates had the same plasmid DNA fingerprint, suggesting clonal dissemination of CTX-M-15-producing strains in the Paris area.
Comparative Activities of Doripenem versus Isolates, Mutants, and Transconjugants of
Enterobacteriaceae
and
Acinetobacter
spp. with Characterized β-Lactamases
Authors: Mushtaq Shazad , Ge Yigong , Livermore David M.
Published: March 2004

Doripenem (S-4661), a new parenteral carbapenem, was tested against over 250 clinical isolates, mutants, and transconjugants of
Enterobacteriaceae
and
Acinetobacter
spp., selected or derived for their β-lactamase expression characteristics. Imipenem, meropenem, and ertapenem were tested as comparators, along with cephalosporins and piperacillin-tazobactam, by using National Committee for Clinical Laboratory Standards agar dilution methodology. Doripenem MICs were from 0.03 to 0.25 μg/ml for
Klebsiella
isolates, irrespective of the presence of extended-spectrum β-lactamases (ESBLs) or plasmid-mediated AmpC or hyperproduced K1 β-lactamase. Similarly, MICs of doripenem for both AmpC-inducible and -derepressed
Enterobacter
isolates were 0.06 to 0.5 μg/ml. ESBL production did not raise the MICs of doripenem for
Escherichia coli
transconjugants, and studies with known expression mutants confirmed that neither inducible nor depressed AmpC β-lactamase expression was protective in
Enterobacter cloacae
,
Citrobacter freundii
,
Serratia marcescens
, or
Morganella morganii
. In all of these respects, doripenem resembled meropenem and imipenem, whereas the MICs of ertapenem were raised (but still ≤1 μg/ml) for many ESBL-producing klebsiellas and AmpC-derepressed
E. cloacae
and
C. freundii
strains. Resistance to all carbapenems, including doripenem (MICs of mostly 16 to 64 μg/ml, compared with 0.25 to 1 μg/ml for typical strains), was seen in
Acinetobacter
isolates with metallo-β-lactamases or OXA-carbapenemases. Isolates of
Klebsiella
and
Serratia
spp. with IMP, KPC, and SME β-lactamases also were resistant to doripenem (MICs, 8 to >64 μg/ml) and to other carbapenems, although the continued apparent susceptibility (MICs, ≤0.5 μg/ml) of
E. coli
derivatives with cloned IMP-1 and NMC-A β-lactamases suggested that carbapenem resistance might require other factors besides the enzymes.
Transactivator Protein BICP0 of Bovine Herpesvirus 1 (BHV-1) Is Blocked by Prostaglandin D2(PGD2), Which Points to a Mechanism for PGD2-Mediated Inhibition of BHV-1 Replication
Authors: Saydam Okay , Abril Carlos , Vogt Bernd , Ackermann Mathias , Schwyzer Martin
Published: March 2004

The immediate-early protein, BICP0, of bovine herpesvirus 1 (BHV-1) transactivates a variety of viral and cellular genes. In a yeast two-hybrid cDNA library screening, we found that lipocalin-type prostaglandin D synthase, which catalyzes the production of prostaglandin D2(PGD2), is a cellular target of BICP0. We observed that, during wild-type BHV-1 infection, PGD2levels were increased intracellularly and decreased in the medium. These effects were absent upon infection with recombinant BHV-1 expressing β-galactosidase instead of BICP0 (A2G2). Transient-expression assays showed that BICP0 alone caused a significant increase in PGD2levels in the cell. PGD2repressed BHV-1 replication in cultured cells. Antiviral activities of prostaglandins have been documented long ago, but their mode of action remains to be clarified. Here we provide evidence that PGD2impairs the transactivation ability of BICP0 that is necessary for efficient virus replication.
Long-Lived Poxvirus Immunity, Robust CD4 Help, and Better Persistence of CD4 than CD8 T Cells
Authors: Amara Rama Rao , Nigam Pragati , Sharma Sunita , Liu Jinyan , Bostik Vanda
Published: March 2004

The currently used smallpox vaccine is associated with a high incidence of adverse events, and there is a serious need for a safe and effective alternative vaccine. Here, we carried out a longitudinal evaluation of vaccinia virus-specific CD4 and CD8 T cells in smallpox-vaccinated individuals by using a highly sensitive intracellular cytokine staining assay. Our results demonstrate that, in addition to the CD8 response, the smallpox vaccinations raised a robust CD4 response with a Th1-dominant cytokine profile. These CD4 T cells were stable and exhibited only a twofold contraction between peak effector and memory phases compared with an approximate sevenfold contraction for CD8 cells. A significant proportion of vaccinated individuals lost detectable CD8 memory while maintaining CD4 memory. After a booster immunization, these individuals generated a robust CD8 response, which some of them rapidly lost. Thus, the current smallpox vaccine provides long-lasting CD4 help that may be critical for long-lived B-cell memory. We suggest that the provision of adequate CD4 help for CD8 and humoral effector functions will be critical to the success of the next generation of smallpox vaccines.
RoXaN, a Novel Cellular Protein Containing TPR, LD, and Zinc Finger Motifs, Forms a Ternary Complex with Eukaryotic Initiation Factor 4G and Rotavirus NSP3
Authors: Vitour Damien , Lindenbaum Pierre , Vende Patrice , Becker Michelle M. , Poncet Didier
Published: March 2004

Rotavirus mRNAs are capped but not polyadenylated, and viral proteins are translated by the cellular translation machinery. This is accomplished through the action of the viral nonstructural protein NSP3, which specifically binds the 3′ consensus sequence of viral mRNAs and interacts with the eukaryotic translation initiation factor eIF4G I. To further our understanding of the role of NSP3 in rotavirus replication, we looked for other cellular proteins capable of interacting with this viral protein. Using the yeast two-hybrid assay, we identified a novel cellular protein-binding partner for rotavirus NSP3. This 110-kDa cellular protein, named RoXaN (rotavirus X protein associated with NSP3), contains a minimum of three regions predicted to be involved in protein-protein or nucleic acid-protein interactions. A tetratricopeptide repeat region, a protein-protein interaction domain most often found in multiprotein complexes, is present in the amino-terminal region. In the carboxy terminus, at least five zinc finger motifs are observed, further suggesting the capacity of RoXaN to bind other proteins or nucleic acids. Between these two regions exists a paxillin leucine-aspartate repeat (LD) motif which is involved in protein-protein interactions. RoXaN is capable of interacting with NSP3 in vivo and during rotavirus infection. Domains of interaction were mapped and correspond to the dimerization domain of NSP3 (amino acids 163 to 237) and the LD domain of RoXaN (amino acids 244 to 341). The interaction between NSP3 and RoXaN does not impair the interaction between NSP3 and eIF4G I, and a ternary complex made of NSP3, RoXaN, and eIF4G I can be detected in rotavirus-infected cells, implicating RoXaN in translation regulation.
Superinfection Prevents Recombination of the Alphaherpesvirus Bovine Herpesvirus 1
Authors: Meurens François , Schynts Frédéric , Keil Günther M. , Muylkens Benoît , Vanderplasschen Alain , Gallego Pierre , Thiry Etienne
Published: March 2004

Homologous recombination between strains of the same alphaherpesvirus species occurs frequently both in vitro and in vivo. This process has been described between strains of herpes simplex virus type 1, herpes simplex virus type 2, pseudorabies virus, feline herpesvirus 1, varicella-zoster virus, and bovine herpesvirus 1 (BoHV-1). In vivo, the rise of recombinant viruses can be modulated by different factors, such as the dose of the inoculated viruses, the distance between inoculation sites, the time interval between inoculation of the first and the second virus, and the genes in which the mutations are located. The effect of the time interval between infections with two distinguishable BoHV-1 on recombination was studied in three ways: (i) recombination at the level of progeny viruses, (ii) interference induced by the first virus infection on β-galactosidase gene expression of a superinfecting virus, and (iii) recombination at the level of concatemeric DNA. A time interval of 2 to 8 h between two successive infections allows the establishment of a barrier, which reduces or prevents any successful superinfection needed to generate recombinant viruses. The dramatic effect of the time interval on the rise of recombinant viruses is particularly important for the risk assessment of recombination between glycoprotein E-negative marker vaccine and field strains that could threaten BoHV-1 control and eradication programs.
Identification of Epstein-Barr Virus (EBV) Nuclear Antigen 2 (EBNA2) Target Proteins by Proteome Analysis: Activation of EBNA2 in Conditionally Immortalized B Cells Reflects Early Events after Infection of Primary B Cells by EBV
Authors: Schlee Martin , Krug Tanja , Gires Olivier , Zeidler Reinhard , Hammerschmidt Wolfgang , Mailhammer Reinhard , Laux Gerhard , Sauer Guido , Lovric Josip , Bornkamm Georg W.
Published: March 2004

The Epstein-Barr virus (EBV) is a ubiquitous B-lymphotropic herpesvirus associated with several malignant tumors, e.g., Burkitt's lymphoma and Hodgkin's disease, and is able to efficiently immortalize primary B lymphocytes in vitro. The growth program of infected B cells is initiated and maintained by the viral transcription factor EBV nuclear antigen 2 (EBNA2), which regulates viral and cellular genes, including the proto-oncogene c-myc. In our study, patterns of protein expression in B cells with and without EBNA2 were analyzed by two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. For this purpose, we used a conditional immortalization system for EBV, a B cell line (EREB2-5) that expresses an estrogen receptor-EBNA2 fusion protein. In order to discriminate downstream targets of c-Myc from c-Myc-independent EBNA2 targets, we used an EREB2-5-derived cell line, P493-6, in which c-Myc is expressed under the control of a tetracycline-regulated promoter. Of 20 identified EBNA2 target proteins, 11 were c-Myc dependent and therefore most probably associated with proliferation, and one of these proteins was a posttranslationally modified protein, i.e., hypusinylated eIF5a. Finally, to estimate the relevance of EBNA2 targets during early EBV infection, we analyzed the proteomes of primary B cells before and after infection with EBV. The protein expression pattern induced upon EBV infection was similar to that following EBNA2 activation. These findings underscore the value of EREB2-5 cells as an appropriate model system for the analysis of early events in the process of EBV-mediated B-cell immortalization.
Selective Modification of Variable Loops Alters Tropism and Enhances Immunogenicity of Human Immunodeficiency Virus Type 1 Envelope
Authors: Yang Zhi-yong , Chakrabarti Bimal K. , Xu Ling , Welcher Brent , Kong Wing-pui , Leung Kwanyee , Panet Amos , Mascola John R. , Nabel Gary J.
Published: March 2004

Although the B clade of human immunodeficiency virus type 1 (HIV-1) envelopes (Env) includes five highly variable regions, each of these domains contains a subset of sequences that remain conserved. The V3 loop has been much studied for its ability to elicit neutralizing antibodies, which are often restricted to a limited number of closely related strains, likely because a large number of antigenic structures are generated from the diverse amino acid sequences in this region. Despite these strain-specific determinants, subregions of V3 are highly conserved, and the effects of different portions of the V3 loop on Env tropism and immunogenicity have not been well delineated. For this report, selective deletions in V3 were introduced by shortening of the stem of the V3 loop. These mutations were explored in combination with deletions of selected V regions. Progressive shortening of the stem of V3 abolished the immunogenicity as well as the functional activity of HIV Env; however, two small deletions on both arms of the V3 stem altered the tropism of the dualtropic 89.6P viral strain so that it infected only CXCR4+cells. When this smaller deletion was combined with removal of the V1 and V2 loops and used as an immunogen in guinea pigs, the antisera were able to neutralize multiple independent clade B isolates with a higher potency. These findings suggest that highly conserved subregions within V3 may be relevant targets for eliciting neutralizing antibody responses, affecting HIV tropism, and increasing the immunogenicity of AIDS vaccines.
Herpes Simplex Virus 1 Gene Products Occlude the Interferon Signaling Pathway at Multiple Sites
Authors: Chee Ana Virginia , Roizman Bernard
Published: March 2004

Earlier studies have shown that herpes simplex virus 1 (HSV-1) blocks the interferon response pathways, at least at two sites, by circumventing the effects of activation of protein kinase R by double-stranded RNA and interferon and through the degradation of promyelocytic leukemia protein (PML) since interferon has no antiviral effects in PML−/−cells. Here we report on two effects of viral genes on other sites of the interferon signaling pathway. (i) In infected cells, Jak1 kinase associated with interferon receptors and Stat2 associated with the interferon signaling pathway rapidly disappear from infected cells. The level of interferon alpha receptor is also reduced, albeit less drastically at times after 4 h postinfection. Other members of the Stat family of proteins were either decreased in amount or posttranslationally processed in a manner different from those of mock-infected cells. The decrease in the levels of Jak1 and Stat2 may account for the decrease in the formation of complexes consisting of Stat1 or ISGF3 and DNA sequences containing the interferon-stimulated response elements after exposure to interferon. (ii) The disappearance of Jak1 and Stat2 was related at least in part to the function of the virion host shutoff protein, the product of the viral UL41 gene. Consistent with this observation, a mutant lacking the UL41 gene and treated with interferon produced lesser amounts of a late protein (UL38) than the wild-type parent. We conclude that HSV-1 blocks the interferon signaling pathways at several sites.
Early Activation of the Kaposi's Sarcoma-Associated Herpesvirus RTA, RAP, and MTA Promoters by the Tetradecanoyl Phorbol Acetate-Induced AP1 Pathway
Authors: Wang Shizhen Emily , Wu Frederick Y. , Chen Honglin , Shamay Meir , Zheng Qizhi , Hayward Gary S.
Published: March 2004

Kaposi's sarcoma-associated herpesvirus (KSHV) maintains a latent infection in primary effusion lymphoma (PEL) cells, but treatment with tetradecanoyl phorbol acetate (TPA) can trigger the full lytic-cycle replication in some of these cells. During lytic-cycle replication, the KSHV-encoded replication and transcription activator (RTA or ORF50), the mRNA transport and accumulation protein (MTA), and the replication-associated protein (RAP) all play crucial roles in expression of downstream viral genes as well as in mediation of viral DNA replication. The cellular CCAAT/enhancer-binding protein alpha (C/EBPα) is induced in TPA-treated PEL cells and contributes to transactivation of the promoters for all of these genes through both direct binding and cooperative interactions with RTA and RAP targeted to upstream C/EBP sites. However, little is known about how RTA expression is triggered initially at the earliest stages after TPA induction when the C/EBPα levels are still limited. Treatment with TPA proved to significantly induce both AP1 DNA-binding activity and levels of activated phosphorylated cJUN in PEL cells and ectopic expression of cJUN-plus-cFOS-induced RTA protein expression in PEL cells. Cotransfected cJUN plus cFOS or TPA treatment transactivated the KSHV RTA, RAP, and MTA promoters in an AP1-binding site-dependent manner in all three promoters. Chromatin immunoprecipitation assays confirmed that cJUN associates with these KSHV target promoters in PEL cells as early as 4 h after TPA treatment. Furthermore, the KSHV RTA and RAP proteins both interact with cJUN or both cJUN and cFOS in vitro or by coimmunoprecipitation from induced PEL cells and enhance cJUN-plus-cFOS-mediated transactivation of these viral promoters. Both increased phosphorylated cJUN and AP1 DNA-binding activity was detected as early as 1 h after TPA treatment in PEL cells, suggesting that AP1 activity may be crucial for very early activation of the RAP, MTA, and RTA promoters during the KSHV lytic cycle. Finally, expression of RTA alone increased cJUN protein levels severalfold in DG75 cells but did not induce cJUN phosphorylation. Therefore, we suggest that the initiating effects of TPA via the AP1 pathway in PEL cells need to be amplified by RTA for full lytic-cycle induction.
The Leader Protein of Theiler's Virus Interferes with Nucleocytoplasmic Trafficking of Cellular Proteins
Authors: Delhaye Sophie , van Pesch Vincent , Michiels Thomas
Published: March 2004

The leader protein of Theiler's virus was previously shown to block the production of alpha/beta interferon by infected cells. Here, we observed that expression of the leader protein in infected cells triggered subcellular redistribution of a nucleus-target green fluorescent protein. It enhanced redistribution of the nuclear polypyrimidine tract-binding protein but had no influence on the localization of the nuclear splicing factor SC-35. The leader protein also interfered with trafficking of the cytoplasmic interferon regulatory factor 3, a factor critical for transcriptional activation of alpha/beta interferon genes.
DNA Vaccines: Influenza Virus Challenge of a Th2/Tc2 Immune Response Results in a Th2/Tc1 Response in the Lung
Authors: Oran Alp E. , Robinson Harriet L.
Published: March 2004

For this study, we used DNA-based immunizations to elicit gamma interferon-producing (Tc1) or interleukin 4 (IL-4)-producing (Tc2) CD8 T cells to the influenza virus nucleoprotein. We examined the response of these cells to an intranasal viral challenge. Both the Tc2- and Tc1-biased responses were present in mice with predominantly IL-4-producing (Th2) CD4 T cells. After viral challenge, Tc1 cells underwent more efficient expansion than did Tc2 cells, and only Tc1 cells were detected at the site of infection. In contrast, the CD4 response remained IL-4 biased. However, only a limited number of CD4 cells appeared in the postchallenge lung, and these were strongly enriched for the Th1 phenotype. Thus, the type of memory T-cell response induced by DNA vaccination does not determine the type of response that will predominate at the site of an infection.
ON AN EXTENSION OF TRIVIALIZABLE GRAPHS
Authors: TAMURA NAOKO
Published: March 2004

In this paper, we define edge sum of some trivializable graphs. The main theorem of this paper is that an edge sum of some trivializable graphs at handle edges is trivializable and using this theorem we actually construct a larger class of trivializable graphs.
QSPR MODELING OF ENTHALPIES OF FORMATION FROM ELEMENTS OF COORDINATION COMPOUNDS BY CORRELATION WEIGHTING OF NEAREST NEIGHBORING CODES
Authors: CASTRO EDUARDO A. , DUCHOWICZ PABLO R. , FERNANDEZ FRANCISCO M. , TOROPOV ANDREY A. , NESTEROVA ALEXANDRA I. , NAZAROV AZIZBEK U.
Published: March 2004

We have obtained the enthalpies of formation from elements of a representative set of 158 coordination compounds resorting to the QSPR theory. The basic variables to determine the regression equations are the correlation weights of the nearest neighboring codes. Both linear and quadratic fitting relationships were determined as well as an optimal exponent method. Statistical parameters are quite satisfactory and they show the suitability of this sort of methodology to predict molecular enthalpies of formation.
AN MMX STUDY OF BENZENE ISOMERS AND THE HYDROGENATION PRODUCTS OF BENZENE
Authors: ZUO TIANMING , HUANG THOMAS
Published: March 2004

We have calculated the structures, the heats of hydrogenation and the resonance energies of benzene isomers. All structures and energies were calculated by using the MMX force fields. Using PC model, the calculated structure parameters of benzene's 8 isomers are generally in good agreements with the experimental data. The heats of hydrogenation and resonance energy of benzene isomers are parallel to those experimental data and need a systematic adjustment of 4.5 kJ/mol.
NONADDITIVE EFFECTS IN H2 AND HF TETRAMERS
Authors: LI JINSHAN , JING FUQIAN
Published: March 2004

Nonadditive three- and four-body interaction energies have been calculated for HF tetramer at the MP2/aug-cc-pVTZ level and for H 2 tetramer at the MP4(SDTQ)/aug-cc-pVTZ level using the so-called fifteen-point method. Calculated results show that with intermolecular distances decreasing from 3.0 to 1.7 Å the nonadditive three- and four-body interactions may be: (a) more and more attractive; (b) more and more repulsive; or (c) extremely weak. Strangely the minimum point of nonadditive three- and four-body interaction potentials has not been found up to now. For both H 2 and HF tetramers the nonadditive four-body interaction energy makes a negligible contribution to total binding energy when intermolecular distances are compressed from 3.0 to 1.7 Å.
ON THE DETERMINATION OF CAUSTICS
Authors: OLOYEDE PONMILE , MIL'NIKOV GENNADY , NAKAMURA HIROKI
Published: March 2004

This paper presents a numerical method which locates caustics of classical trajectories on-the-fly. The method is conceptually simple and is applicable to a system of arbitrary dimensions. The efficiency of the method is demonstrated by determining caustics of trajectories in the 2-D Henon–Heiles potential and of trajectories used to simulate a triatomic reaction process for J (total angular momentum) = 0.
TIME DEPENDENT DENSITY FUNCTIONAL METHODS AND THEIR APPLICATION TO CHEMICAL PHYSICS
Authors: YOSHIMORI AKIRA
Published: March 2004

This article reviews microscopic development of time dependent functional method and its application to chemical physics. It begins with the formulation of density functional theory. The time dependent extension is discussed after the equilibrium formulation. Its application is explained by solvation dynamics. In addition, it reviews studies of nonlinear effects on polar liquids and simple mixtures.
THE ESTIMATIONS OF INNER-SHELL IONIZATION ENERGIES FOR ALKYL HALIDES: A DESIGNATED SINGLE-CONFIGURATION CASSCF APPROACH AND ADVANCED CORRECTION
Authors: YU CHIN-HUI , YU JEN-SHIANG K. , CHEN WEI-CHEN
Published: March 2004

Based on the Franck–Condon principle, vertical ionization energies regarding the inner-shell valence electrons of alkyl halides and their unsaturated analogues were evaluated with a designated single-configuration complete active self-consistent field (CASSCF) approach as well as the advanced correction with configuration interaction. Excitations corresponding to the elimination of one electron from a specific molecular orbital of these species were calculated by the deviation between the energy of the SCF-optimized neutral structure and of its cation. The freezing over the outer orbitals with identical symmetry was achieved while performing the CASSCF ionization calculation for the inner orbitals. These energy evaluations utilized Pople's 6-31G*, 6-311G** and Roos' ANO basis sets. Computed results agreed well with the experimental data. The characters for the molecular orbitals of corresponding vertical ionizations could be qualitatively assigned by the MOLDEN visualization program.
FULL AB INITIO COMPUTATION OF PROTEIN-WATER INTERACTION ENERGIES
Authors: ZHANG D. W. , ZHANG J. Z. H.
Published: March 2004

A method to perform full quantum mechanical (ab initio) calculation of interaction energy involving a macromolecule like protein has recently been developed. This new scheme, named molecular fractionation with conjugate caps (MFCC), decomposes a protein molecule into amino acid-based fragments. These individual fragments are properly treated to preserve the chemical property of the bonds that are cut. Through proper combination of interaction energies between the molecule and individual fragments and their conjugate caps, the full protein-molecule interaction energy can be obtained to a high degree-of-accuracy by full ab initio calculations. Here we report a benchmark full ab initio calculation of interaction energy between a HIV-1 gp41 protein (with 982 atoms) and a water molecule at various geometries using HF (Hartree Fock), DFT (density functional theory) and MP2 (second-order Moller-Plesset perturbation theory) methods on a standard workstation.
A THEORETICAL COMPARISON OF CONFORMATIONAL FEATURES OF CALIX[4]AROMATICS
Authors: WANG DI-FEI , WU YUN-DONG
Published: March 2004

Although there are tremendous studies about the conformational feature of calix[4]arenes and its analogies, no theoretical study has been done systematically about why some structural modifications could completely lead to a change of conformational preference. For example, calix[4]arene 1 adopts a cone conformation while its analogue calix[4]pyrrole 7 only adopts a 1,3-alternate conformation. So if this is only because of the effect of OH—OH hydrogen bonds, then why does O-methyl substituted calix[4]arene 2 still has cone conformation? In this paper, the conformational features of a series of seven calix[4]aromatics, calix[4]arene and calix[4]pyrrole related structures, have been investigated at BLYP/6–31G* level both in the gas phase and in CH 2 Cl 2 solution. The calculations demonstrated that three main factors influence the conformational preference of these calix[4]aromatics, i.e. the intramolecular hydrogen bond, the adjacent ring-ring electrostatic interaction and the intrinsic flexibility of the [14] metacyclophane framework. Calix[4]benzene 3 and calix[4]pyridine 4 have little conformational preferences due to their flexible [14] metacyclophane framework, the lack of hydrogen-bonding interactions and weak ring-ring electrostatic interactions. In contrast, calix[4]aromatics 1 and 5–7 have either intramolecular hydrogen bonds (1) or ring-ring electrostatic interactions (5–7). Consequently, calix[4]arene 1 has the cone preference and calix[4]pyrrole, calix[4]furan, and calixthiophene (5–7) have the 1,3-alternate preference. Methoxy calix[4]arene prefers a cone or partial cone conformation, because the 1,3-alternate and 1,2-alternate conformations are destabilized by electrostatic repulsions involving the methoxy group and the adjacent phenyl ring.
Formulating Knowledge Management Infrastructure Based on Strategic Management and Total Quality Management
Authors: Lin Cheng Ming , Wei Chiu-Chi
Published: March 2004

Due to the rapid change in technology environments, creating value through Knowledge Management (KM) has become a new research area. The organization must continuously learn, share, expand and apply knowledge in order to maintain business advantage in this highly competitive age.

This study first investigates the evolution and practical application of the Strategic Management (SM) and Total Quality Management (TQM), and then constructs an adequate framework for establishing the KM system.

The objective of this study is to address the importance of SM and TQM on KM from the methodological viewpoint. A few points are discussed to explore the key factors for establishing the most effective management structure to optimize the KM value.
Impact of User's Internal Flexibility and Expectations on Information Systems Usage
Authors: Palanisamy Ramaraj
Published: March 2004

Information Systems (IS) usage has been a primary focus in the IS implementation research. The focus of this study is to examine the influence of user characteristics on IS usage. User characteristics were considered in terms of a user's internal flexibility, user expectations from information systems, and perceived personal usefulness. IS maturity was considered as the intervening variable moderating the effect of perceived personal usefulness on IS usage. A questionnaire survey was conducted to collect empirical data about research variables to examine the relationship. 296 users from forty-two organizations participated in the survey. Moderated regression analysis was used to examine the proposed model. The study results validate the relationship between user characteristics and IS usage. But, it does not support the moderation effect of IS maturity on the relationship with perceived personal usefulness on IS usage.
Semantic Search Engine
Authors: Manjula D. , Geetha T. V.
Published: March 2004

Currently existing search engines index documents only by words and as a result, when a query can be interpreted in different senses, the irrelevant results are obtained in the midst of relevant results. A semantic search engine is proposed here which indexes documents both by words and senses and as a result tries to avoid the irrelevant results. The "crawler" traverses the worldwide web and the normalized documents are sent to the disambiguator module, which identifies the top few sense(s) of ambiguous words by employing a weighted disambiguation algorithm. The documents are then indexed by the words and the senses. The query is also disambiguated in a similar manner and retrieval is performed by matching both the sense and the word. The performance of the semantic search engine is compared against traditional word based indexing and also against the commercial search engines like Google, Yahoo, Hotbot and Lycos. The results show an impressive precision for the semantic search engine compared to other engines, particularly for ambiguous queries.
Cloning, Expression, Activity and Folding Studies of Serine Hydroxymethyltransferase: A Target Enzyme for Cancer Chemotherapy
Authors: Agrawal Shipra , Kumar Ajay , Srivastava Vivek , Mishra B.N.
Published: March 2004

All the members of pyridoxal-5′-phosphate-dependent enzymes are involved in the metabolism of amino acids. The sequence homology studies further divide this family into three distinct groups. A fine scrutiny of the reactions catalyzed by these enzymes shows their regio specificity; they have been considered as the largest group of enzymes having tendency to affect the valency of the same carbon atom that carries the amino group forming an amine linkage with the coenzyme. Thus, this group was named ‘α-class of enzymes’. Serine hydroxymethyltransferase (SHMT) is a member of this α-class; it reversibly catalyses the conversion of serine into glycine while the hydroxymethyl group is transferred to 5,6,7,8-tetrahydrofolate. The resultant compound is the sole precursor of purine biosynthesis. Henceforth, this enzyme greatly affects nucleic acid biosynthesis in all the organisms. It is obvious that SHMT plays an indispensable role in nucleic acid biosynthesis; therefore, designing and developing a repressor/inhibitor of the SHMT gene/protein may resolve the problem of drug resistance to cancer chemotherapy. SHMT has been widely studied in many living systems (e.g. Escherichia coli, humans, sheep, rabbits, Trypanosoma,Arabidopsis, peas, tobacco) in terms of its structure, cloning, expression, purification and folding patterns. Such studies have enabled one to assess the pattern of overall kinetic and activity behaviour of the enzyme, which may further help in developing a suitable cancer therapeutic molecule.
Studies on the Mechanism of Allergic Contact Dermatitis: The Reaction of α-Methylene-γ-Butyrolactone with Peptide-Bound Lysine
Authors: Pickert J. , Hartert C. , Raddatz H. , Henle T.
Published: March 2004

The binding of low-molecular-weight compounds to nucleophilic side-chains of amino acids bound within a protein, resulting in a hapten-modified macromolecule, is discussed to represent the very first step within the development of allergic contact dermatitis. For one of the best-known occupational dermatoses in the field of plant breeding, the so-called tulip fingers, α-methylene-γ-butyrolactone (tulipalin A) was proved to be the causative agent. In this paper, the reaction of tulipalin A with Nα-hippuryl-L-lysine as a model for peptide-bound lysine was studied. After the incubation of the α-methylene-γ-butyrolactone with the dipeptide in varying molar ratios in methanolic solution at 37°C up to 3 weeks, the reaction was monitored using reversed-phase high-performance liquid chromatography with UV detection. Tulipalin A was found to react with the Ε-amino group, resulting in the formation of one characteristic reaction product. After isolation, the structure of this addition product was unambiguously characterised by nuclear magnetic resonance spectroscopy as 2-(2-benzoylamino-acetylamino)-6-[(2-oxo-tetrahydro-furan-3-ylmethyl)amino] hexanoic acid (Hip-LysTu). After incubation of bovine serum albumin with tulipalin A, followed by acid hydrolysis and amino acid analysis, LysTu was found as addition product, thus representing the first known amino acid derivative resulting from the conjugation of the electrophilic α-methylene-γ-butyrolactone to protein.
Bilateral Pallidotomy for Severe Dystonia in an 18-Month-Old Child with Glutaric Aciduria
Authors: Rakocevic Goran , Rakocevic Goran , Lyons Kelly E. , Lyons Kelly E. , Wilkinson Steven B. , Wilkinson Steven B. , Overman John W. , Overman John W. , Pahwa Rajesh , Pahwa Rajesh
Published: March 2004

Glutaric aciduria type 1 is an inborn error of metabolism due to deficiency of glutaryl-CoA dehydrogenase. This disorder mainly affects children. The majority of patients develop a dystonic-dyskinetic syndrome. The dystonia is painful and can cause significant disability. This report documents an 18-month-old child, the youngest reported, who underwent pallidotomy for disabling dystonia. The surgery improved dystonic symptoms, especially pain in this child with minor complications related to the procedure. Pallidotomy is a reasonable option for children with dystonic symptoms secondary to glutaric aciduria.
Gamma Knife Stereotactic Radiosurgical Boost for Patients Treated Primarily with Neutron Radiotherapy for Salivary Gland Neoplasms
Authors: Douglas James G. , Douglas James G. , Silbergeld Daniel L. , Silbergeld Daniel L. , Laramore George E. , Laramore George E.
Published: March 2004

Object: To determine the feasibility of utilizing a Gamma Knife stereotactic boost for patients at high risk of local recurrence from minor salivary gland tumors invading the base of skull. Methods: Eight patients with minor salivary gland tumors invading the base of skull were treated with primary neutron radiotherapy followed by a Gamma Knife radiosurgical boost to the base of skull. Patients had the following characteristics: (1) primary site of disease: paranasal sinuses (n = 3), nasopharynx (n = 3), hard palate (n = 1), pterygopalatine fossa (n = 1); (2) median age 59 years (range 37–80); (3) interval from completion of neutron radiotherapy to Gamma Knife boost 4 weeks (range 2–8 weeks); (4) median stereotactic dose delivered 10 Gy (prescribed to 50% isodose line, range 8–12 Gy), and (5) median number of isocenters treated 16 (range 14–21). Dosimetry from the neutron radiotherapy was used to determine both the volume boosted and the dose utilized. The median follow-up interval from the time of Gamma Knife treatment was 21.5 months (range 16–23 months). Results: All patients tolerated the procedure well. Acute side effects were minimal and included 1 patient with a delayed fatigue reaction at 2 months, 1 patient with vertigo of limited duration, and a third patient with prolonged nausea requiring steroid use. All patients were placed on a tapering dose of steroids after the procedure. One patient suffered a local relapse, with a 2-year actuarial disease-free survival rate of 80%. Conclusions: Gamma Knife radiosurgical boost following primary neutron radiotherapy for patients with a high risk of local failure is feasible and well tolerated acutely. Careful attention must be given to the previously treated regions in regard to volume treated and dose delivered. Further follow-up will be necessary to determine the long-term effectiveness and complications of such a boost in these high-risk patients.