bluuebunny/crossref_metadata_2025 huggingface dataset:
IPSE/alpha‐1, a major secretory glycoprotein antigen from schistosome eggs, expresses the Lewis X motif on core‐difucosylated N‐glycans
Authors: Wuhrer Manfred , Balog Crina I. A. , Catalina M. I. , Jones Frances M. , Schramm Gabriele , Haas Helmut , Doenhoff Michael J. , Dunne David W. , Deelder André M. , Hokke Cornelis H.
Published: April 2006

Schistosomes are parasitic flatworms that infect millions of people in (sub)tropical areas around the world. Glycoconjugates of schistosomes play a critical role in the interaction of the different developmental stages of the parasite with the host. In particular, glycosylated components of the eggs produced by the adult worm pairs living in the bloodstream are strongly immunogenic. We have investigated the glycosylation of interleukin‐4‐inducing factor from schistosome eggs (IPSE/alpha‐1), a major secretory egg antigen from Schistosoma mansoni that triggers interleukin‐4 production in human basophils, by MS analysis of tryptic glycopeptides. Nanoscale LC‐MS(/MS) and MALDI‐TOF(/TOF)‐MS studies combined with enzymatic degradations showed that monomeric IPSE/alpha‐1 contains two N‐glycosylation sites, which are each occupied for a large proportion with core‐difucosylated diantennary glycans that carry one or more Lewis X motifs. Lewis X has been reported as a major immunogenic glycan element of schistosomes. This is the first report both on the expression of Lewis X on a specific schistosome egg protein and on a protein‐specific glycosylation analysis of schistosome eggs.
Solar Hydrogen Production by a Two-Step Cycle Based on Mixed Iron Oxides
Authors: Roeb Martin , Sattler Christian , Klüser Ruth , Monnerie Nathalie , de Oliveira Lamark , Konstandopoulos Athanasios G. , Agrafiotis Christos , Zaspalis V. T. , Nalbandian L. , Steele Andrew , Stobbe Per
Published: April 2006

A promising method for the conversion and storage of solar energy into hydrogen is the dissociation of water into oxygen and hydrogen, carried out via a two-step process using metal oxide redox systems such as mixed iron oxides, coated upon multi-channeled honeycomb ceramic supports capable of absorbing solar irradiation, in a configuration similar to that encountered in automobile exhaust catalytic converters. With this configuration, the whole process can be carried out in a single solar energy converter, the process temperature can be significantly lowered compared to other thermo-chemical cycles and the recombination of oxygen and hydrogen is prevented by fixing the oxygen in the metal oxide. For the realization of the integrated concept, research work proceeded in three parallel directions: synthesis of active redox systems, manufacture of ceramic honeycomb supports and manufacture, testing and optimization of operating conditions of a thermochemical solar receiver-reactor. The receiver-reactor has been developed and installed in the solar furnace in Cologne, Germany. It was proven that solar hydrogen production is feasible by this process demonstrating that multicycling of the process was possible in principle.
Initial Analysis of PCM Integrated Solar Collectors
Authors: Alva S. L. H. , González J. E. , Dukhan N.
Published: April 2006

This paper investigates the technical feasibility of innovative solar collectors. The proposed collectors have a phase change material (PCM) integrated into them as the storage mechanism. The PCM-integrated solar collector eliminates the need of conventional storage tanks, thus reducing cost and space. The present work uses a paraffin-graphite composite as the PCM to increase the conductivity of the PCM matrix. The paraffin’s melting point is around 89°C, which is appropriate for use in single-effect absorption systems. The mathematical model that describes the thermal process in the PCM is presented and differs from the analysis of conventional flat plate solar collectors making use of the lumped capacitance method which neglects spatial variations. The proposed model is calibrated favorably with a more detailed mathematical model that uses finite differences and considers temporal and spatial variations. Results for the collectors’ thermal performance are presented along with the effects of the composition of the PCM. The results for the PCM integrated collector proposed here are very encouraging. Therefore, there is an indication that conventional storage tanks may be replaced for the PCM integrated in the solar collector.
Solar Cooling Economic Considerations: Centralized Versus
Decentralized Options
Authors: García-Casals Xavier
Published: April 2006

In Spain, as in other Mediterranean and low-latitude countries, cooling loads of the same order of magnitude or even higher than heating loads coexist with high solar radiation resources. Cooling loads in most of these countries have, thus far, not been completely incorporated into the building sector energy demand because they arise after that DHW (domestic hot water) and heating loads have been satisfied and the living standard of the population reaches a given threshold. The increasing comfort demand in the cooling season from a population living in buildings that were developed without taking into account these considerations are bringing about a strong increase in the installation of domestic vapor compression air conditioning units, aimed to partially fulfil the thermal comfort demand in few rooms of these dwellings. This has a significant impact on the environment and the electricity distribution system, in a moment when strong environmental constraints are being imposed on the energy system to fulfil international agreements as the Kyoto protocol. Solar absorption cooling emerges as an interesting alternative to satisfy this growing energy demand for cooling applications with synergies with solar energy use for heating and DHW purposes. However, solar absorption cooling has been there already, for decades, without having a significant development, and still today presents some limitations that prevent its widespread application. Other solar cooling alternatives, such as the use of commercial vapor compression air conditioning equipment fed with electricity from centralized solar power plants could, in short, become available in these countries. In this paper, based on the experienced gained with the simulation of the most recent installations of absorption cooling installations in Spain, we perform a cost comparison between decentralized and centralized solar cooling options to give some insight into the development requirements and possibilities from both solar cooling options.
Study of Cubic Splines and Fourier Series as Interpolation Techniques for Filling in Short Periods of Missing Building Energy Use and Weather Data
Authors: Baltazar Juan-Carlos , Claridge David E.
Published: April 2006

A study of cubic splines and Fourier series as interpolation techniques for filling in missing hourly data in energy and meteorological time series data sets is presented. The procedure developed in this paper is based on the local patterns of the data around the gaps. Artificial gaps, or “pseudogaps,” created by deleting consecutive data points from the measured data sets, were filled using four variants of the cubic spline technique and 12 variants of the Fourier series technique. The accuracy of these techniques was compared to the accuracy of results obtained using linear interpolation to fill the same pseudogaps. The pseudogaps filled were 1–6 data points in length created in 18 year-long sets of hourly energy use and weather data. More than 1000 pseudogaps of each gap length were created in each of the 18 data sets and filled using each of the 17 techniques evaluated. Use of mean bias error as the selection criterion found that linear interpolation is superior to the cubic spline and Fourier series methodologies for filling gaps of dry bulb and dew point temperature time series data. For hourly building cooling and heating use data, the Fourier series approach with 24 data points before and after each gap and six terms was found to be the most suitable; where there are insufficient data points to apply this approach, simple linear interpolation is recommended.
Comparison of Photovoltaic Module Performance Measurements
Authors: Fanney A. Hunter , Davis Mark W. , Dougherty Brian P. , King David L. , Boyson William E. , Kratochvil Jay A.
Published: April 2006

Computer simulation tools used to predict the energy production of photovoltaic systems are needed in order to make informed economic decisions. These tools require input parameters that characterize module performance under various operational and environmental conditions. Depending upon the complexity of the simulation model, the required input parameters can vary from the limited information found on labels affixed to photovoltaic modules to an extensive set of parameters. The required input parameters are normally obtained indoors using a solar simulator or flash tester, or measured outdoors under natural sunlight. This paper compares measured performance parameters for three photovoltaic modules tested outdoors at the National Institute of Standards and Technology (NIST) and Sandia National Laboratories (SNL). Two of the three modules were custom fabricated using monocrystalline and silicon film cells. The third, a commercially available module, utilized triple-junction amorphous silicon cells. The resulting data allow a comparison to be made between performance parameters measured at two laboratories with differing geographical locations and apparatus. This paper describes the apparatus used to collect the experimental data, test procedures utilized, and resulting performance parameters for each of the three modules. Using a computer simulation model, the impact that differences in measured parameters have on predicted energy production is quantified. Data presented for each module includes power output at standard rating conditions and the influence of incident angle, air mass, and module temperature on each module’s electrical performance. Measurements from the two laboratories are in excellent agreement. The power at standard rating conditions is within 1% for all three modules. Although the magnitude of the individual temperature coefficients varied as much as 17% between the two laboratories, the impact on predicted performance at various temperature levels was minimal, less than 2%. The influence of air mass on the performance of the three modules measured at the laboratories was in excellent agreement. The largest difference in measured results between the two laboratories was noted in the response of the modules to incident angles that exceed 75deg.
Polyamines Increase Antibiotic Susceptibility in
Pseudomonas aeruginosa
Authors: Kwon Dong H. , Lu Chung-Dar
Published: April 2006

Pseudomonas aeruginosa
is an opportunistic human pathogen. Treatment is complicated by frequent acquired resistance to antipseudomonal therapies. Polyamines (cadaverine, putrescine, spermidine, and spermine) are ubiquitous polycationic compounds essential for all living organisms. In a dose-dependent manner, polyamines increased the susceptibility of
P. aeruginosa
to 14 β-lactam antibiotics, chloramphenicol, nalidixic acid, and trimethoprim as demonstrated by a reduction in MIC of up to 64-fold. This effect was partially antagonized (25 to 50%) by the presence of 10 mM of Mg
2+
or Ca
2+
. In contrast, the effects of the outer membrane permeabilizers, polymyxin B nonapeptide and EDTA, were completely abolished by 3 mM Mg
2+
or Ca
2+
. Changes on the outer membrane barrier by these compounds were assessed by activity measurements of periplasmic β-lactamase. The results showed that while EDTA and polymyxin B serve as outer membrane disorganizing agents as expected, exogenous spermidine and spermine did not exhibit any apparent effect on outer membrane permeability or rupture. In summary, these results strongly suggest that the increased antibiotic susceptibility by polyamines is exerted by a mechanism that differs from that of EDTA and polymyxin B. Polyamines might be potentially useful in antipseudomonal therapies by increasing the effectiveness of certain β-lactam antibiotics.
Cellular Accumulation and Activity of Quinolones in Ciprofloxacin-Resistant J774 Macrophages
Authors: Michot Jean-Michel , Heremans Marie F. , Caceres Nancy E. , Mingeot-Leclercq Marie-Paule , Tulkens Paul M. , Van Bambeke Françoise
Published: April 2006

Ciprofloxacin is the substrate for a multidrug resistance-related protein (MRP)-like multidrug transporter in J774 mouse macrophages, which also modestly affects levofloxacin but only marginally affects garenoxacin and moxifloxacin (J.-M. Michot et al., Antimicrob. Agents Chemother.
49:
2429-2437, 2005). Two clones of ciprofloxacin-resistant cells were obtained by a stepwise increase in drug concentration (from 34 to 51 to 68 mg/liter) in the culture fluid. Compared to wild-type cells, ciprofloxacin-resistant cells showed (i) a markedly reduced ciprofloxacin accumulation (12% of control) and (ii) a two- to threefold lower sensitivity to the enhancing effect exerted by MRP-inhibitors (probenecid and MK571) on ciprofloxacin accumulation or by ciprofloxacin itself. ATP-depletion brought ciprofloxacin accumulation to similarly high levels in both wild-type and ciprofloxacin-resistant cells. Garenoxacin and moxifloxacin accumulation remained unaffected, and levofloxacin showed an intermediate behavior. DNA and protein synthesis were not impaired in ciprofloxacin-resistant cells for ciprofloxacin concentrations up to 100 mg/liter (∼85 and 55% inhibition, respectively, in wild-type cells). In
Listeria monocytogenes
-infected ciprofloxacin-resistant cells, 12-fold higher extracellular concentrations of ciprofloxacin were needed to show a bacteriostatic effect in comparison with wild-type cells. The data suggest that the resistance mechanism is mediated by an overexpression and/or increased activity of the MRP-like ciprofloxacin transporter expressed at a basal level in wild-type J774 macrophages, which modulates both the intracellular pharmacokinetics and activity of ciprofloxacin.
Preclinical Safety and Efficacy Assessments of Dendrimer-Based (SPL7013) Microbicide Gel Formulations in a Nonhuman Primate Model
Authors: Patton D. L. , Cosgrove Sweeney Y. T. , McCarthy T. D. , Hillier S. L.
Published: April 2006

Three gel formulations (1%, 3%, and 5% [wt/wt]) of SPL7013, a dendrimer known to have antiviral (anti-human immunodeficiency virus and anti-herpes simplex virus) activities, completed a range of preclinical tests in the pigtailed macaque models for vaginally and rectally applied topical microbicide safety assessments. The vaginal safety profile of the 3% SPL7013 gel formulation was equal to that of the 1% formulation but was superior to that of the 5% formulation. The 3% SPL7013 gel was further evaluated for rectal safety and for antichlamydial efficacy with cervical challenge with
Chlamydia trachomatis
. This first-generation dendrimer-based product was shown to be safe to the vaginal and rectal microenvironments with repeated daily use. However, a single intravaginal application of the 3% (wt/wt) SPL7013 gel did not provide protection from the acquisition of cervical chlamydial infection.
Long-Term Multiple-Dose Pharmacokinetics of Human Monoclonal Antibodies (MAbs) against Human Immunodeficiency Virus Type 1 Envelope gp120 (MAb 2G12) and gp41 (MAbs 4E10 and 2F5)
Authors: Joos Beda , Trkola Alexandra , Kuster Herbert , Aceto Leonardo , Fischer Marek , Stiegler Gabriela , Armbruster Christine , Vcelar Brigitta , Katinger Hermann , Günthard Huldrych F.
Published: April 2006

While certain antibodies directed against the human immunodeficiency virus (HIV) envelope have the potential to suppress virus replication in vitro, the impact of neutralizing antibodies in vivo remains unclear. In a recent proof-of-concept study, the broadly neutralizing monoclonal antibodies 2G12, 4E10, and 2F5 exhibited inhibitory activities in vivo, as exemplified by a delay of the viral rebound following the interruption of antiretroviral therapy. Unexpectedly, the antiviral effect seen was most prominently due to 2G12 activity. To further investigate whether differential HIV-inhibitory activity was due to different pharmacokinetic properties of the antibodies, we performed a formal pharmacokinetic analysis with 14 patients. Repeated infusions at high dose levels were well tolerated by the patients and did not elicit an endogenous immune response against the monoclonal antibodies. The pharmacokinetic parameters of all three antibodies correlated with each other. Mean estimates were 0.047, 0.035, and 0.044 liter/kg for the central volume of distribution of 2G12, 4E10, and 2F5, respectively, and 0.0018, 0.0058, and 0.0077 liter/kg · day for the systemic clearance of 2G12, 4E10, and 2F5, respectively. Monoclonal antibody 2G12 had a significantly longer elimination half-life (21.8 ± 7.2 days [
P
< 0.0001]) than monoclonal antibodies 4E10 (5.5 ± 2.2 days) and 2F5 (4.3 ± 1.1 days). The comprehensive pharmacokinetic data from this long-term multiple-dose phase II study were coherent with those from previous short-term phase I studies, as assessed by compartmental and noncompartmental techniques. The anti-HIV type 1 antibodies studied showed distribution and elimination kinetics similar to those seen for other human-like antibodies. Further studies examining tissue concentrations to explain the differential in vivo activity of the anti-gp120 antibody compared with those of the two anti-gp41 antibodies are warranted.
Novel Effects of Azithromycin on Tight Junction Proteins in Human Airway Epithelia
Authors: Asgrimsson Valthor , Gudjonsson Thorarinn , Gudmundsson Gudmundur Hrafn , Baldursson Olafur
Published: April 2006

The macrolide antibiotic azithromycin improves lung function and prognosis among patients with cystic fibrosis or diffuse panbronchiolitis, independently of bacterial eradication. Anti-inflammatory effects have been implicated, but data from in vivo studies are scarce, and the link between abnormal electrolyte content in airway surface liquid and bronchial infections remains uncertain. In the present study, we treated human airway epithelia on filter supports with azithromycin and monitored transepithelial electrical resistance. We found that azithromycin increased transepithelial electrical resistance of airway epithelia in a dose-dependent manner. Immunocytochemistry and Western blotting showed that addition of azithromycin changed the locations of proteins in cell cultures and induced processing of the tight junction proteins claudin-1 and claudin-4, occludin, and junctional adhesion molecule-A. These effects were reversible, and no effect was seen when cells were treated with penicillin or erythromycin. The data indicate that azithromycin increases the transepithelial electrical resistance of human airway epithelia by changing the processing of tight junction proteins. The results are novel and may help explain the beneficial effects of azithromycin in patients with cystic fibrosis, diffuse panbronchiolitis, and community-acquired pneumonia.
Pharmacokinetics of a New, Orally Available Ceftriaxone Formulation in Physical Complexation with a Cationic Analogue of Bile Acid in Rats
Authors: Lee Seulki , Kim Sang Kyoon , Lee Dong Yun , Chae Su Young , Byun Youngro
Published: April 2006

Oral administration of ceftriaxone associated with a bile acid-based new oral carrier, cholylethylenediamine, in 50% propylene glycol to rats at doses of 25 and 50 mg/kg of body weight resulted in a significant increase in intestinal absorption, as evidenced by 55% improvement in the bioavailability, whereas ceftriaxone alone showed a bioavailability of less than 1%.
Erythromycin and Clindamycin Resistance in Group B Streptococcal Clinical Isolates
Authors: Gygax Scott E. , Schuyler Jessica A. , Kimmel Lauren E. , Trama Jason P. , Mordechai Eli , Adelson Martin E.
Published: April 2006

Erythromycin (EM) and clindamycin (CM) susceptibility testing was performed on 222 clinical isolates of group B
Streptococcus
. A multiplex PCR assay was used to detect the
ermB
,
ermTR
, and
mefA/E
antibiotic resistance genes. These results were compared to the phenotypes as determined by the standard EM/CM double disk diffusion assay.
Increasing Prevalence and Diversity of Metallo-β-Lactamases in
Pseudomonas
spp.,
Acinetobacter
spp., and
Enterobacteriaceae
from Korea
Authors: Yong Dongeun , Choi Yeoung Seon , Roh Kyoung Ho , Kim Chang Ki , Park Youn Hee , Yum Jong Hwa , Lee Kyungwon , Chong Yunsop
Published: April 2006

Among imipenem-nonsusceptible isolates, acquired metallo-β-lactamase genes were detected in 36 of 581 (6.2%)
Pseudomonas aeruginosa
isolates, 42 of 44 (95.4%) other
Pseudomonas
species, and 136 of 513 (26.5%)
Acinetobacter
species from 2003 to 2004 at a Korean hospital. Overall,
bla
VIM-2
-like genes were the most prevalent and were also detected in
Enterobacteriaceae
, including
Klebsiella pneumoniae
.
Processing of the Bovine Spongiform Encephalopathy-Specific Prion Protein by Dendritic Cells
Authors: Rybner-Barnier Catherine , Jacquemot Catherine , Cuche Céline , Doré Grégory , Majlessi Laleh , Gabellec Marie-Madeleine , Moris Arnaud , Schwartz Olivier , Di Santo James , Cumano Ana , Leclerc Claude , Lazarini Françoise
Published: April 2006

Dendritic cells (DC) are suspected to be involved in transmissible spongiform encephalopathies, including bovine spongiform encephalopathy (BSE). We detected the disease-specific, protease-resistant prion protein (PrPbse) in splenic DC purified by magnetic cell sorting 45 days after intraperitoneal inoculation of BSE prions in immunocompetent mice. We showed that bone marrow-derived DC (BMDC) from wild-type or PrP-null mice acquired both PrPbseand prion infectivity within 2 h of in vitro culture with a BSE inoculum. BMDC cleared PrPbsewithin 2 to 3 days of culture, while BMDC infectivity was only 10-fold diminished between days 1 and 6 of culture, suggesting that the infectious unit in BMDC is not removed at the same rate as PrPbseis removed from these cells. Bone marrow-derived plasmacytoid DC and bone marrow-derived macrophages (BMM) also acquired and degraded PrPbsewhen incubated with a BSE inoculum, with kinetics very similar to those of BMDC. PrPbsecapture is probably specific to antigen-presenting cells since no uptake of PrPbsewas observed when splenic B or T lymphocytes were incubated with a BSE inoculum in vitro. Lipopolysaccharide activation of BMDC or BMM prior to BSE infection resulted in an accelerated breakdown of PrPbse. Injected by the intraperitoneal route, BMDC were not infectious for alymphoid recombination-activated gene 20/common cytokine γ chain-deficient mice, suggesting that these cells are not capable of directly propagating BSE infectivity to nerve endings.
Cyclophilin A Renders Human Immunodeficiency Virus Type 1 Sensitive to Old World Monkey but Not Human TRIM5α Antiviral Activity
Authors: Keckesova Zuzana , Ylinen Laura M. J. , Towers Greg J.
Published: April 2006

TRIM5α is an important mediator of antiretroviral innate immunity influencing species-specific retroviral replication. Here we investigate the role of the peptidyl prolyl isomerase enzyme cyclophilin A in TRIM5α antiviral activity. Cyclophilin A is recruited into nascent human immunodeficiency virus type 1 (HIV-1) virions as well as incoming HIV-1 capsids, where it isomerizes an exposed proline residue. Here we show that cyclophilin A renders HIV-1 sensitive to restriction by TRIM5α in cells from Old World monkeys, African green monkey and rhesus macaque. Inhibition of cyclophilin A activity with cyclosporine A, or reducing cyclophilin A expression with small interfering RNA, rescues TRIM5α-restricted HIV-1 infectivity. The effect of cyclosporine A on HIV-1 infectivity is dependent on TRIM5α expression, and expression of simian TRIM5α in permissive feline cells renders them able to restrict HIV-1 in a cyclosporine A-sensitive way. We use an HIV-1 cyclophilin A binding mutant (CA G89V) to show that cyclophilin A has different roles in restriction by Old World monkey TRIM5α and owl monkey TRIM-Cyp. TRIM-Cyp, but not TRIM5α, recruits its tripartite motif to HIV-1 capsid via cyclophilin A and, therefore, HIV-1 G89V is insensitive to TRIM-Cyp but sensitive to TRIM5α. We propose that cyclophilin A isomerization of a proline residue in the TRIM5α sensitivity determinant of the HIV-1 capsid sensitizes it to restriction by Old World monkey TRIM5α. In humans, where HIV-1 has adapted to bypass TRIM5α activity, the effects of cyclosporine A are independent of TRIM5α. We speculate that cyclophilin A alters HIV-1 sensitivity to a TRIM5α-independent innate immune pathway in human cells.
In Vivo Interactions of Ecotropic and Polytropic Murine Leukemia Viruses in Mixed Retrovirus Infections
Authors: Evans Leonard H. , Lavignon Marc , Peterson Karin , Hasenkrug Kim , Robertson Shelly , Malik Frank , Virtaneva Kimmo
Published: April 2006

Mixed retrovirus infections are the rule rather than the exception in mice and other species, including humans. Interactions of retroviruses in mixed infections and their effects on disease induction are poorly understood. Upon infection of mice, ecotropic retroviruses recombine with endogenous proviruses to generate polytropic viruses that utilize different cellular receptors. Interactions among the retroviruses of this mixed infection facilitate disease induction. Using mice infected with defined mixtures of the ecotropic Friend murine leukemia virus (F-MuLV) and different polytropic viruses, we demonstrate several dramatic effects of mixed infections. Remarkably, inoculation of F-MuLV with polytropic MuLVs completely suppressed the generation of new recombinant viruses and dramatically altered disease induction. Coinoculation of F-MuLV with one polytropic virus significantly lengthened survival times, while inoculation with another polytropic MuLV induced a rapid and severe neurological disease. In both instances, the level of the polytropic MuLV was increased 100- to 1,000-fold, whereas the ecotropic MuLV level remained unchanged. Surprisingly, nearly all of the polytropic MuLV genomes were packaged within F-MuLV virions (pseudotyped) very soon after infection. At this time, only a fractional percentage of cells in the mouse were infected by either virus, indicating that the coinoculated viruses had infected the same small subpopulation of susceptible cells. The profound amplification of polytropic MuLVs in coinfected mice may be facilitated by pseudotyping or, alternatively, by transactivation of the polytropic virus in the coinfected cells. This study illustrates the complexity of the interactions between components of mixed retrovirus infections and the dramatic effects of these interactions on disease processes.
Adeno-Associated Virus Type 2 Increases Proteosome-Dependent Degradation of p21WAF1in a Human Papillomavirus Type 31b-Positive Cervical Carcinoma Line
Authors: Alam Samina , Sen Ellora , Brashear Heidi , Meyers Craig
Published: April 2006

Adeno-associated virus type 2 (AAV2) seropositivity is negatively correlated with the development of human papillomavirus (HPV)-associated cervical cancer. We have begun analysis of the molecular mechanisms underlying AAV2-mediated oncosuppression through cell cycle regulation in HPV-infected keratinocytes isolated from a low-grade cervical lesion. AAV2 superinfection of HPV type 31b (HPV31b)-positive cells at early times postinfection resulted in degradation of the cyclin-dependent kinase (CDK) inhibitor p21WAF1protein in a proteosome-dependent manner. Downstream consequences of lowering p21WAF1levels included a proportional loss of cyclin E/CDK2 complexes bound to p21WAF1. The loss of stable p21WAF1/cyclin E/CDK2 complexes coincided with an increase in CDK2-associated kinase activity and cyclin E levels. Both events have the potential to enhance the G1/S transition point mediated by active cyclin E/CDK2 complexes. Concurrently, cyclin A and E2F levels were decreased, conditions reminiscent of delayed entrance into the S phase of the cell cycle. On the other hand, infection of primary human foreskin keratinocytes with AAV2 resulted in upregulation of p21WAF1protein levels, reminiscent of a block in G1phase progression. We propose that by downregulating p21WAF1, AAV2 initiates cell cycle activities leading to enhanced G1/S phase-like conditions which may be favorable for AAV2-specific functions and may lead to downstream interference with HPV-associated cervical cancer progression.
The K65R Mutation in Human Immunodeficiency Virus Type 1 Reverse Transcriptase Exhibits Bidirectional Phenotypic Antagonism with Thymidine Analog Mutations
Authors: Parikh Urvi M. , Bacheler Lee , Koontz Dianna , Mellors John W.
Published: April 2006

The K65R mutation in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is selected in vitro by manyd-nucleoside analog RT inhibitors (NRTI) but has been rarely detected in treated patients. In recent clinical trials, the K65R mutation has emerged frequently in patients experiencing virologic failure on antiretroviral combinations that do not include 3′-azidothymidine (AZT). The reason for this change is uncertain. To gain insight, we examined trends in the frequency of K65R in a large genotype database, the association of K65R with thymidine analog mutations (TAMs) and other NRTI mutations, and the viral susceptibility profile of HIV-1 with K65R alone and in combination with TAMs. Among >60,000 clinical samples submitted for genotype analysis that contained one or more NRTI resistance mutations, the frequency of K65R increased from 0.4% in 1998 to 3.6% in 2003. Among samples with K65R, a strong negative association was evident with the TAMs M41L, D67N, L210W, T215Y/F, and K219Q/E (P< 0.005) but not with other NRTI mutations, including the Q151M complex. This suggested that K65R and TAMs are antagonistic. To test this possibility, we generated recombinant HIV-1 encoding K65R in two different TAM backgrounds: M41L/L210W/T215Y and D67N/K70R/T215F/K219Q. K65R reduced AZT resistance from >50-fold to <2.5-fold in both backgrounds. In addition, TAMs antagonized the phenotypic effect of K65R, reducing resistance to tenofovir, abacavir, 2′,3′-dideoxycytidine, dideoxyinosine, and stavudine. In conclusion, K65R and TAMs exhibit bidirectional phenotypic antagonism. This antagonism likely explains the negative association of these mutations in genotype databases, the rare emergence of K65R with antiretroviral therapies that contain AZT, and its more frequent emergence with combinations that exclude AZT.
Genome of Crocodilepox Virus
Authors: Afonso C. L. , Tulman E. R. , Delhon G. , Lu Z. , Viljoen G. J. , Wallace D. B. , Kutish G. F. , Rock D. L.
Published: April 2006

Here, we present the genome sequence, with analysis, of a poxvirus infecting Nile crocodiles (
Crocodylus niloticus
) (crocodilepox virus; CRV). The genome is 190,054 bp (62% G+C) and predicted to contain 173 genes encoding proteins of 53 to 1,941 amino acids. The central genomic region contains genes conserved and generally colinear with those of other chordopoxviruses (ChPVs). CRV is distinct, as the terminal 33-kbp (left) and 13-kbp (right) genomic regions are largely CRV specific, containing 48 unique genes which lack similarity to other poxvirus genes. Notably, CRV also contains 14 unique genes which disrupt ChPV gene colinearity within the central genomic region, including 7 genes encoding GyrB-like ATPase domains similar to those in cellular type IIA DNA topoisomerases, suggestive of novel ATP-dependent functions. The presence of 10 CRV proteins with similarity to components of cellular multisubunit E3 ubiquitin-protein ligase complexes, including 9 proteins containing F-box motifs and F-box-associated regions and a homologue of cellular anaphase-promoting complex subunit 11 (Apc11), suggests that modification of host ubiquitination pathways may be significant for CRV-host cell interaction. CRV encodes a novel complement of proteins potentially involved in DNA replication, including a NAD
+
-dependent DNA ligase and a protein with similarity to both vaccinia virus F16L and prokaryotic serine site-specific resolvase-invertases. CRV lacks genes encoding proteins for nucleotide metabolism. CRV shares notable genomic similarities with molluscum contagiosum virus, including genes found only in these two viruses. Phylogenetic analysis indicates that CRV is quite distinct from other ChPVs, representing a new genus within the subfamily
Chordopoxvirinae
, and it lacks recognizable homologues of most ChPV genes involved in virulence and host range, including those involving interferon response, intracellular signaling, and host immune response modulation. These data reveal the unique nature of CRV and suggest mechanisms of virus-reptile host interaction.
The Unique IR2 Protein of Equine Herpesvirus 1 Negatively Regulates Viral Gene Expression
Authors: Kim Seong K. , Ahn Byung C. , Albrecht Randy A. , O'Callaghan Dennis J.
Published: April 2006

The IR2 protein (IR2P) is a truncated form of the immediate-early protein (IEP) lacking the essential acidic transcriptional activation domain (TAD) and serine-rich tract and yet retaining binding domains for DNA and TFIIB and nuclear localization signal (NLS). Analysis of the
IR2
promoter indicated that the
IR2
promoter was upregulated by the EICP0P. The IR2P was first detected in the nucleus at 5 h postinfection in equine herpesvirus 1 (EHV-1)-infected HeLa and equine NBL6 cells. Transient-transfection assays revealed that (i) the IR2P by itself downregulated EHV-1 early promoters (
EICP0
,
TK
,
EICP22
, and
EICP27
) in a dose-dependent manner; (ii) the IR2P abrogated the IEP and the EICP27P (UL5) mediated transactivation of viral promoters in a dose-dependent manner; and (iii) the IR2P, like the IEP itself, also downregulated the
IE
promoter, indicating that the IEP TAD is not necessary to downregulate the
IE
promoter. In vitro interaction assays revealed that the IR2P interacts with TATA box-binding protein (TBP). The essential domain(s) of the IR2P that mediate negative regulation were mapped to amino acid residues 1 to 706, indicating that the DNA-binding domain and the NLS of the IR2P may be important for the downregulation. In transient-transfection and virus growth assays, the IR2P reduced EHV-1 production by 23-fold compared to virus titers achieved in cells transfected with the empty vector. Overall, these studies suggest that the IR2P downregulates viral gene expression by acting as a dominant-negative protein that blocks IEP-binding to viral promoters and/or squelching the limited supplies of TFIIB and TBP.
X-Ray Crystallographic Structure of the Norwalk Virus Protease at 1.5-Å Resolution
Authors: Zeitler Corinne E. , Estes Mary K. , Venkataram Prasad B. V.
Published: April 2006

Norwalk virus (NV), a member of the
Caliciviridae
family, is the major cause of acute, epidemic, viral gastroenteritis. The NV genome is a positive sense, single-stranded RNA that encodes three open reading frames (ORFs). The first ORF produces a polyprotein that is processed by the viral cysteine protease into six nonstructural proteins. We have determined the structure of the NV protease to 1.5 and 2.2 Å from crystals grown in the absence or presence, respectively, of the protease inhibitor AEBSF [4-(2-aminoethyl)-benzenesulfonyl fluoride]. The protease, which crystallizes as a stable dimer, exhibits a two-domain structure similar to those of other viral cysteine proteases with a catalytic triad composed of His 30, Glu 54, and Cys 139. The native structure of the protease reveals strong hydrogen bond interactions between His 30 and Glu 54, in the favorable
syn
configuration, indicating a role of Glu 54 during proteolysis. Mutation of this residue to Ala abolished the protease activity, in a fluorogenic peptide substrate assay, further substantiating the role of Glu 54 during proteolysis. These observations contrast with the suggestion, from a previous study of another norovirus protease, that this residue may not have a prominent role in proteolysis (K. Nakamura, Y. Someya, T. Kumasaka, G. Ueno, M. Yamamoto, T. Sato, N. Takeda, T. Miyamura, and N. Tanaka, J. Virol. 79:13685-13693, 2005). In the structure from crystals grown in the presence of AEBSF, Glu 54 undergoes a conformational change leading to disruption of the hydrogen bond interactions with His 30. Since AEBSF was not apparent in the electron density map, it is possible that these conformational changes are due to subtle changes in pH caused by its addition during crystallization.
The Epstein-Barr Virus BMRF1 Gene Is Essential for Lytic Virus Replication
Authors: Neuhierl Bernhard , Delecluse Henri-Jacques
Published: April 2006

The Epstein-Barr virus (EBV) BMRF1 protein is a DNA polymerase processivity factor. We have deleted the BMRF1 open reading frame from the EBV genome and assessed the ΔBMRF1 EBV phenotype. ΔBMRF1 viruses were replication deficient, but the wild-type phenotype could be restored by BMRF1
trans
-complementation. The replication-deficient phenotype included impaired lytic DNA replication and late protein expression. ΔBMRF1 and wild-type viruses were undistinguishable in terms of their ability to transform primary B cells. Our results provide genetic evidence that BMRF1 is essential for lytic replication of the EBV genome.
Identification and Characterization of Novel Adeno-Associated Virus Isolates in ATCC Virus Stocks
Authors: Schmidt Michael , Grot Emmanuelle , Cervenka Peter , Wainer Sandra , Buck Charles , Chiorini John A.
Published: April 2006

Adeno-associated viruses (AAVs) depend on a helper virus for efficient replication. To identify novel AAV isolates, we screened a diverse set of virus isolates for the presence of AAV DNA. AAVs found in 10 simian adenovirus isolates showed greater than 96% homology to AAV1 and AAV6 but had distinct biological properties. Two representatives of this group, AAV(VR-195) and AAV(VR-355), were studied in more detail. While the novel AAVs had high sequence homologies and required sialic acid for cell binding and transduction, differences were observed in lectin competition, resulting in distinct tropisms in human cancer cell lines.
GAMOW–TELLER SUM RULE IN RELATIVISTIC NUCLEAR MODELS
Authors: KURASAWA HARUKI , SUZUKI TOSHIO
Published: April 2006

Relativistic corrections are investigated to the Gamow–Teller (GT) sum rule with respect to the difference between the β- and β+ transition strengths in nuclei. Since the sum rule requires the complete set of the nuclear states, the relativistic corrections come from the anti-nucleon degrees of freedom. In the relativistic mean field approximation, the total GT strengths carried by the nucleon sector is quenched by about 12% in nuclear matter, while by about 8% in finite nuclei, compared to the sum rule value. The coupling between the particle-hole states with the nucleon–antinucleon states is also discussed with the relativistic random phase approximation, where the divergence of the response function is renormalized with use of the counterterms in the Lagrangian. It is shown that the approximation to neglect the divergence, like the no-sea approximation extensively used so far, is unphysical, from the sum-rule point of view.
TRANSLATING RELATIONAL SCHEMA WITH CONSTRAINTS INTO XML SCHEMA
Authors: FONG JOSEPH , FONG ANTHONY , WONG H. K. , YU PHILIP
Published: April 2006

With XML adopted as the technology trend on the Internet, and with investment in the current relational database systems, companies must convert their relational data into XML documents for data transmission on the Internet. In the process, to preserve the users' relational data requirements of data constraints into the converted XML documents, we must define a meaningful root element for each XML document. The construction of an XML document is based on the root element and its relevant elements. The root element can be selected from a relational entity table in the existing relational database, which depends on the requirements to present the business behind. The relevant elements are mapped from the related entities, based on the navigability of the chosen entity. The derived root and relevant elements can form a Data Type Definition Graph (DTD-graph) of an XML conceptual schema diagram which can be mapped into a Data Type Definition (DTD) of an XML schema. The result is a translated XML schema with semantic constraints transferred from a relational conceptual schema of an Extended Entity Relationship (EER) model. The data conversion from relational data to the XML documents can be done after the schema translation. The relational data are loaded into XML documents according to the translated DTD.
COSMOLOGICAL MODELS WITH VARIABLE GRAVITATIONAL AND COSMOLOGICAL CONSTANTS IN R2GRAVITY
Authors: DEBNATH P. S. , PAUL B. C.
Published: April 2006

We consider the evolution of a flat Friedmann–Roberstson–Walker Universe in a higher derivative theory, including αR2terms for the Einstein–Hilbert action in the presence of variable gravitational and cosmological constants. We study the evolution of the gravitational and cosmological constants in the radiation and matter domination era of the universe. We present new cosmological solutions which are physically interesting for model building.
A COLLABORATIVE SOFTWARE CODE INSPECTION: THE DESIGN AND EVALUATION OF A REPEATABLE COLLABORATION PROCESS IN THE FIELD
Authors: DE VREEDE GERT-JAN , KONERI PUSHPA G. , DEAN DOUGLAS L. , FRUHLING ANN L. , WOLCOTT PETER
Published: April 2006

The use of software products in today's world has increased dramatically making quality an important aspect of software development. There is a continuous need to develop processes to control and increase software quality. Software code inspection is one way to pursue this goal. This paper presents a collaborative code inspection process that was designed during an action research study using Collaboration Engineering principles and techniques. Our inspection process was implemented as a sequence of thinkLets, chunks of facilitation skill, that were subsequently field tested in a traditional paper-based and Group Support System (GSS)-based environment. Four inspections were performed on four different pieces of software code in two different organizations. Results show that regardless of the implementation, the process was found to be successful in uncovering many major, minor, and false-positive defects in inspected pieces of code. Overall observations and feedback suggest that the collaborative inspection process was considered to be productive and satisfactory. GSS inspections were more effective, especially in terms of major defects. GSS inspections were also found to be more efficient. Finally, the GSS inspections outperformed the paper inspections from a practical perspective: logging and managing defects in a GSS was far superior.
USING PATTERNS TO EMPOWER END-USERS — THE OREGON SOFTWARE DEVELOPMENT PROCESS FOR GROUPWARE
Authors: SCHÜMMER TILL , LUKOSCH STEPHAN , SLAGTER ROBERT
Published: April 2006

Fostering interaction between end-users and developers is one of the most important issues when developing groupware. Insufficient interaction leads to groupware systems that do not fulfill the group's requirements and thus to low acceptance. Furthermore, as group processes change dynamically the requirements are not static as well. Groupware system development and use, therefore, have to address users' changing needs. Current design methodologies insufficiently focus on this aspect. Therefore, we propose the Oregon Software Development Process (OSDP) that fosters end-user participation throughout the whole groupware life cycle, structures the interaction between end-users and developers, and emphasizes the use of a shared language between users and developers. We illustrate the application of the process with experiences made in an interdisciplinary development project of a collaborative learning platform.
Weak Expression of Focal Adhesion Kinase (pp125FAK) in Patients with Cervical Cancer Is Associated with Poor Disease Outcome
Authors: Gabriel Boris , zur Hausen Axel , Stickeler Elmar , Dietz Carola , Gitsch Gerald , Fischer Dagmar-C. , Bouda Jiri , Tempfer Clemens , Hasenburg Annette
Published: April 2006

Purpose: The pp125 focal adhesion kinase (FAK) plays a pivotal role in tumor cell signaling. FAK expression has been linked to tumor cell invasion and metastasis, but data on cervical cancer are inconclusive. Our goal was to investigate FAK expression in cervical cancer and to assess whether its expression correlates with prognosis.

Experimental Design: FAK expression was examined using immunohistochemistry with sections from 162 resected cervical cancer specimens. Kaplan-Meier survival curves were used to determine the significance of FAK expression in the prognosis of cervical cancer patients.

Results: Specific FAK expression was found in the tumor cells, whereas normal cervical epithelium showed barely any FAK expression. Of 162 invasive cervical cancer specimens, 55 (34%) revealed weak expression of FAK, whereas moderate and strong expression was found in 63 (39%) and 44 (27%) tumors, respectively. Patients with tumors expressing weak amounts of FAK were characterized by a significantly poorer overall survival compared with those with moderate and high intratumoral FAK expression (P = 0.002). Weak expression of FAK correlated with pelvic lymph node metastasis (P = 0.026) and recurrent disease (P = 0.013). Multivariate Cox regression analysis revealed decreased FAK expression and pelvic lymph node metastasis to be significant independent factors predictive of poor disease outcome (hazard ratio, 0.36; P = 0.005; hazard ratio, 2.38; P = 0.018, respectively).

Conclusions: Weak expression of FAK in invasive cervical cancer is a strong independent predictor of poor patient outcome. Further studies are warranted to elucidate whether FAK expression analysis is a suitable tool identifying patients at high risk even at an early clinical stage.
Human Melanoma Metastases Express Functional CXCR4
Authors: Scala Stefania , Giuliano Paola , Ascierto Paolo A. , Ieranò Caterina , Franco Renato , Napolitano Maria , Ottaiano Alessandro , Lombardi Maria L. , Luongo Monica , Simeone Ester , Castiglia Daniele , Mauro Francesca , De Michele Ileana , Calemma Rosa , Botti Gerardo , Caracò Corrado , Nicoletti Gianfranco , Satriano Rocco A. , Castello Giuseppe
Published: April 2006

Purpose: The chemokine receptor CXCR4 was identified as an independent predictor of poor prognosis in primary melanoma. The aim of the study was to investigate the role of CXCR4 in human melanoma metastases.

Experimental Design: CXCR4 expression was evaluated in melanoma metastases and in metastatic cell lines through immunohistochemistry, immunoblotting, immunofluorescence, and reverse transcription-PCR. The function of CXCR4 was tested in the presence of the ligand, CXCL12, through induction of extracellular signal-regulated kinase-1 and -2 (Erk-1 and -2) phosphorylation, proliferation, apoptosis, and migration capabilities.

Results: CXCR4 expression was detected in 33 out of 63 (52.4%) metastases from cutaneous melanomas. Metastatic melanoma cell lines expressed cell surface CXCR4; PES 43, Alo 40, and COPA cell lines showed the highest levels of CXCR4 (>90% of positive cells); PES 41, Alo 39, PES 47, POAG, and CIMA cell lines showed low to moderate degrees of expression (5-65% of positive cells). Other chemokine receptors, CCR7 and CCR10, were detected on the melanoma cell lines; CXCL12 activated Erk-1 and Erk-2, the whose induction was specifically inhibited by AMD3100 treatment. CXCL12 increased the growth in PES 41, PES 43, and PES 47 cells under suboptimal (1% serum) and serum-free culture conditions; AMD3100 (1 μmol/L) inhibited the spontaneous and CXCL12-induced proliferation. No rescue from apoptosis was shown but PES 41, PES 43, and PES 47 cells migrate toward CXCL12.

Conclusions: These findings indicate that CXCR4 is expressed and active in human melanoma metastases, suggesting that active inhibitors such as AMD3100 may be experienced in human melanoma.