bluuebunny/crossref_metadata_2025 huggingface dataset:
A Gis‐Based Approach to Watershed Classification for Nebraska Reservoirs1
Authors: Bulley Henry N.N. , Merchant James W. , Marx David B. , Holz John C. , Holz Aris A.
Published: May 2007

Abstract:  The U.S. Environmental Protection Agency is charged with establishing standards and criteria for assessing lake water quality. It is, however, increasingly evident that a single set of national water quality standards that do not take into account regional hydrogeologic and ecological differences will not be viable as lakes clearly have different inherent capacities to meet such standards. We demonstrate a GIS‐based watershed classification strategy for identifying groups of Nebraska reservoirs that have similar potential capacity to attain a certain level of water quality standard. A preliminary cluster analysis of 78 reservoirs was performed to determine the potential number of Nebraska reservoir groups. Subsequently, a Classification Trees method was used to refine number of classes, describe the structure of reservoir watershed classes, and to develop a predictive model that relates watershed conditions to reservoir classes. Results suggest that Nebraska reservoirs can be represented by nine classes and that soil organic matter content in the watershed is the most important single variable for segregating the reservoirs. The cross‐validation prediction error rate of the Classification Tree model was 26.3%. Because all geospatial data used in this work are available nationally, the method could be adopted throughout the U.S. Hence, this GIS‐based watershed classification approach could provide water resources managers an effective decision‐support tool in managing reservoir water quality.
Time Series Analysis of Nebraska Daily Rainfall Data to Simulate Atrazine Runoff1
Authors: Adelman D.D. , Stansbury J.S.
Published: May 2007

Abstract:  Measured atrazine concentrations in Nebraska surface water have been shown to exceed water‐quality standards, posing risks to humans and to the ecosystem. To assess this risk, atrazine runoff was simulated at the field‐scale in Nebraska based on the pesticide component of the AGNPS model. This project’s objective was to determine the frequency that the atrazine concentration at the field outlet exceeded three different atrazine water‐quality criteria. The simulation was conducted for different farm management practices, soil moisture conditions, and five Nebraska topographic regions. If the criteria were exceeded, a risk to the drinking water consumer or freshwater aquatic life was hypothesized to exist. Three pesticide fate and transport processes were simulated with the model. Degradation was simulated using first‐order kinetics. Adsorption/desorption was modeled assuming a linear soil‐water partitioning coefficient. Advection (runoff) was based primarily on the USDA‐NRCS curve number method. Daily rainfall from the National Weather Service was used to compute the soil moisture conditions for the 1985‐2000 growing seasons. After each runoff event, the pesticide runoff concentration was compared with each of the three atrazine water‐quality criteria. The results show that environmental receptors (i.e., freshwater aquatic species) are exposed to unacceptable atrazine runoff concentrations in 20‐50% of the runoff events.
Dynamic Modeling of Ground‐Water Quality Using Bayesian Techniques1
Authors: Shihab Khalil , Chalabi Nida
Published: May 2007

Abstract:  Water industry experts have been arguing that the traditional techniques are not an accurate means of measuring water contamination. This is mainly because these techniques emphasize neither the stochastic nature of the water contamination process nor the precision and the accuracy of the tested methods used by environmental laboratories. In this work, we describe the development and application of prototype Dynamic Bayesian Networks (DBNs) that model ground‐water quality to determine the impact of chemical contaminants on ground‐water quality in the Salalah area, which is allocated to the south of Oman. We also present a new technique for data pre‐processing because it is needed for the treatment of ground‐water datasets that are used as the data source to learn the probabilities for dynamic decision models. Among more than 20 wells in area, only four wells were selected to be analyzed and the results show that we achieved an acceptable level of efficiency.
Effects of Impervious Cover at Multiple Spatial Scales on Coastal Watershed Streams1
Authors: Schiff Roy , Benoit Gaboury
Published: May 2007

Abstract:  The spatial scale and location of land whose development has the strongest influence on aquatic ecosystems must be known to support land use decisions that protect water resources in urbanizing watersheds. We explored impacts of urbanization on streams in the West River watershed, New Haven, Connecticut, to identify the spatial scale of watershed imperviousness that was most strongly related to water chemistry, macroinvertebrates, and physical habitat. A multiparameter water quality index was used to characterize regional urban nonpoint source pollution levels. We identified a critical level of 5% impervious cover, above which stream health declined. Conditions declined with increasing imperviousness and leveled off in a constant state of impairment at 10%. Instream variables were most correlated (0.77 ≤ |r| ≤ 0.92, p < 0.0125) to total impervious area (TIA) in the 100‐m buffer of local contributing areas (∼5‐km2 drainage area immediately upstream of each study site). Water and habitat quality had a relatively consistent strong relationship with TIA across each of the spatial scales of investigation, whereas macroinvertebrate metrics produced noticeably weaker relationships at the larger scales. Our findings illustrate the need for multiscale watershed management of aquatic ecosystems in small streams flowing through the spatial hierarchies that comprise watersheds with forest‐urban land use gradients.
Concurrent Tobacco Use in a Random Sample of UK‐Resident Bangladeshi Men
Authors: Croucher Raymond E. , Islam Syed S. , Pau Allan K.
Published: May 2007

The literature on concurrent tobacco (CCT) use, i.e., regularly using both smoked and chewed tobacco, is sparse.

Objectives: This study aims to establish the point prevalence of CCT use in a randomly selected sample of UK‐resident Bangladeshi males, compare CCT users with other tobacco users (smokers alone and chewers alone), and model the factors for CCT use and chewing tobacco use alone.

Methods: A cross‐sectional bilingual interview survey collecting data on age, marital status, social class, employment status, home ownership and overcrowding, self‐assessed health and chronic illness episodes, social capital, nicotine dependence, and oral pain was used. Carbon monoxide readings validated smoked tobacco use. Logistic regressions were used for data analysis.

Results: The initial response rate was 59 percent. Sample mean age was 40.7 years. CCT prevalence was estimated at 22 percent, practiced by older respondents of limited educational status. CCT users more likely had only average or poor self‐rated health and more likely reported current oral pain compared with tobacco smokers. A wife chewing tobacco distinguished CCT users, as compared with tobacco smokers alone.

Conclusions: In this sample of adult Bangladeshi males, CCT use was prevalent. CCT users more likely had a partner who was also a tobacco chewer, as compared with tobacco smokers.
Development of a Word Recognition Instrument to Test Health Literacy in Dentistry: The REALD‐30 – A Brief Communication
Authors: Lee Jessica Y. , Rozier R. Gary , Lee Shoou‐Yih Daniel , Bender Deborah , Ruiz Rafael E.
Published: May 2007

Objective: This study aims to develop and pilot test a dental word recognition instrument.

Methods: The development of our instrument was based on the Rapid Estimate of Adult Literacy in Medicine (REALM), an efficient word recognition instrument used to assess health literacy in the medical arena. Our instrument, Rapid Estimate of Adult Literacy in Dentistry (REALD‐30), consisted of 30 common dental words with various degrees of difficulty. It was administered to 202 English‐speaking adults recruited from outpatient medical clinics. We examined the instrument’s internal reliability using Cronbach’s alpha and its validity by correlating the REALD‐30 score to two dental outcomes (perceived dental health status and oral health‐related quality of life) and medical health literacy.

Results: REALD‐30 scores were significantly correlated with REALM scores. REALD‐30 was significantly related to perceived dental health status in the bivariate analysis. It also was significantly related to oral health‐related quality of life in a multivariate analysis. In contrast, medical health literacy was not related to either of the dental outcome measures.

Conclusions: The new REALD‐30 instrument displays good reliability but only partial validity. Results suggest that dental health literacy may be distinct from medical health literacy and may have an independent effect on dental health outcomes.
Global Desertification: Building a Science for Dryland Development
Authors: Reynolds James F. , Smith D. Mark Stafford , Lambin Eric F. , Turner B. L. , Mortimore Michael , Batterbury Simon P. J. , Downing Thomas E. , Dowlatabadi Hadi , Fernández Roberto J. , Herrick Jeffrey E. , Huber-Sannwald Elisabeth , Jiang Hong , Leemans Rik , Lynam Tim , Maestre Fernando T. , Ayarza Miguel , Walker Brian
Published: May 2007

In this millennium, global drylands face a myriad of problems that present tough research, management, and policy challenges. Recent advances in dryland development, however, together with the integrative approaches of global change and sustainability science, suggest that concerns about land degradation, poverty, safeguarding biodiversity, and protecting the culture of 2.5 billion people can be confronted with renewed optimism. We review recent lessons about the functioning of dryland ecosystems and the livelihood systems of their human residents and introduce a new synthetic framework, the Drylands Development Paradigm (DDP). The DDP, supported by a growing and well-documented set of tools for policy and management action, helps navigate the inherent complexity of desertification and dryland development, identifying and synthesizing those factors important to research, management, and policy communities.
The Child as Scientific Object
Authors: Cahan Emily D.
Published: May 2007

Science in the Service of Children, 1893-1935
.
By Alice Boardman Smuts
. Yale University Press, New Haven, CT, 2006. 395 pp. $55. ISBN 9780300108972.

Describing the development of the field of child study during the early 20th century, Smuts discusses the rise of psychological research, "scientific" child rearing, and the intersection of science and policy-making.
Ultralow Friction of Carbonate Faults Caused by Thermal Decomposition
Authors: Han Raehee , Shimamoto Toshihiko , Hirose Takehiro , Ree Jin-Han , Ando Jun-ichi
Published: May 2007

High-velocity weakening of faults may drive fault motion during large earthquakes. Experiments on simulated faults in Carrara marble at slip rates up to 1.3 meters per second demonstrate that thermal decomposition of calcite due to frictional heating induces pronounced fault weakening with steady-state friction coefficients as low as 0.06. Decomposition produces particles of tens of nanometers in size, and the ultralow friction appears to be associated with the flash heating on an ultrafine decomposition product. Thus, thermal decomposition may be an important process for the dynamic weakening of faults.
Seroprevalence of Bactericidal and Anti-Outer Membrane Vesicle Antibodies to
Neisseria meningitidis
Group B in England
Authors: Trotter Caroline , Findlow Jamie , Balmer Paul , Holland Ann , Barchha Rita , Hamer Nick , Andrews Nick , Miller Elizabeth , Borrow Ray
Published: May 2007

Outer membrane vesicle (OMV) and recombinant protein-based vaccines targeted against multiple strains of group B meningococci are under development. The serum bactericidal antibody (SBA) assay has been designated the surrogate of protection, but the exact cutoff has not been determined. We measured the SBA titers in 2,415 serum samples and the anti-OMV IgG antibody concentrations in 2,672 serum samples representative of the English population to establish a baseline of natural immunity. SBA and anti-OMV IgG antibody titers are high in infants in the first 3 months of life, declining thereafter, presumably as maternal immunity wanes. About 6% of the subjects in the 1- to 11-year-old age group had SBA titers ≥4. During the teenage years, there was a marked increase in the percentage of subjects with SBA titers ≥4, rising to over 50% in 19-year-olds, with about 20% of older adults achieving this titer. The peak in SBA and anti-OMV IgG titers coincided with the peak in meningococcal carriage. Simple mathematical models confirm that the relationship between observed seroprevalence and carriage by age is consistent with carriage inducing SBA and that following an episode of carriage, SBA levels may remain elevated for many months. With the exception of children aged 3 to 11 months, there was no clear relationship between disease incidence and seroprevalence.
Needle-Free Skin Patch Delivery of a Vaccine for a Potentially Pandemic Influenza Virus Provides Protection against Lethal Challenge in Mice
Authors: Garg Sanjay , Hoelscher Mary , Belser Jessica A. , Wang Chong , Jayashankar Lakshmi , Guo Zhu , Durland Ross H. , Katz Jacqueline M. , Sambhara Suryaprakash
Published: May 2007

In the event of another influenza virus pandemic, strategies for effective mass vaccination will urgently be needed. We used a novel transdermal patch delivery technology, known as the PassPort system, to vaccinate mice with recombinant H5 hemagglutinin with or without immunomodulators. This needle-free form of vaccine delivery induced robust serum antibody responses that were augmented by different immunomodulators that stimulated the innate immune system and protected mice against lethal challenge with a highly pathogenic avian H5N1 influenza virus.
Phenotypic Prediction Rule for Community-Associated Methicillin-Resistant
Staphylococcus aureus
Authors: Popovich Kyle , Hota Bala , Rice Thomas , Aroutcheva Alla , Weinstein Robert A.
Published: May 2007

Recent studies have suggested that community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) infections are encroaching upon nosocomial settings. We assessed the performance characteristics of a rule using the antimicrobial phenotype to predict genotype. This rule could be applied for epidemiologic purposes to describe the trend in CA-MRSA infections over time.
Diagnosis of a Critical Respiratory Illness Caused by Human Metapneumovirus by Use of a Pan-Virus Microarray
Authors: Chiu Charles Y. , Alizadeh Ash A. , Rouskin Silvi , Merker Jason D. , Yeh Elaine , Yagi Shigeo , Schnurr David , Patterson Bruce K. , Ganem Don , DeRisi Joseph L.
Published: May 2007

A pan-virus DNA microarray (Virochip) was used to detect a human metapneumovirus (hMPV) strain associated with a critical respiratory tract infection in an elderly adult with chronic lymphocytic leukemia. This infection had previously eluded diagnosis despite extensive microbiological testing for possible etiologic agents. The patient's hMPV strain did not grow in viral culture, and only one of five specific reverse transcription-PCR assays for hMPV was positive.
emm
Types, Virulence Factors, and Antibiotic Resistance of Invasive
Streptococcus pyogenes
Isolates from Italy: What Has Changed in 11 Years?
Authors: Creti Roberta , Imperi Monica , Baldassarri Lucilla , Pataracchia Marco , Recchia Simona , Alfarone Giovanna , Orefici Graziella
Published: May 2007

To investigate the epidemiology and characteristics of invasive group A streptococcal (GAS) disease over 11 years in Italy, this study compared the
emm
types and the superantigen toxin genes
speA
and
speC
as well as the erythromycin, clindamycin, and tetracycline susceptibilities of 207 invasive GAS strains collected during two national enhanced surveillance periods (1994 to 1996 and 2003 to 2005) and the time between each set of surveillance periods. The present study demonstrated that
emm
1 strains were consistently responsible for about 20% of invasive GAS infections, while variations in the frequencies of the other types were noted, although the causes of most cases of invasive infections were restricted to
emm
1,
emm
3,
emm
4,
emm
6,
emm
12, and
emm
18. During the 1994 to 1996 surveillance period, an
emm
89 epidemic clone spread across the northern part of Italy. A restricted macrolide resistance phenotype-type distribution of the bacteriophage-encoded
speA
toxin as well as of macrolide resistance genes was noted over time. Indeed, the recent acquisition of macrolide resistance in previously susceptible
emm
types was observed.
Comparison of Various Blood Compartments and Reporting Units for the Detection and Quantification of Epstein-Barr Virus in Peripheral Blood
Authors: Hakim H. , Gibson C. , Pan J. , Srivastava K. , Gu Z. , Bankowski M. J. , Hayden R. T.
Published: May 2007

Epstein-Barr virus (EBV) infection is associated with a broad spectrum of disease. While quantification of EBV nucleic acid in the peripheral blood has been demonstrated to be useful for diagnosis and patient care, the optimal sample type and reporting format for such testing remain uncertain. Using quantitative real-time PCR (QRT-PCR), we evaluated EBV in whole blood (WB), peripheral blood mononuclear cells (PBMC), and plasma in 249 samples from 122 patients. In WB and PBMC, results were reported both in viral copies/ml and in copies/μg of total DNA. Trendings of quantitative values over time among the different sample types were compared. The sensitivities of QRT-PCR using WB and that using PBMC did not differ significantly (
P
= 0.33), and both were more sensitive than plasma alone (
P
< 0.0001). EBV viral load results from WB and PBMC paired sample types also showed a significant correlation (
P
< 0.05), as did results reported in copies/ml and copies/μg DNA for both WB and PBMC (
R
2
> 0.93). EBV viral loads detected using WB and PBMC trended very closely for the few patients who had multiple positive samples available for analysis. WB and PBMC show comparable sensitivities and a close quantitative correlation when assayed for EBV by QRT-PCR. The close correlation between copies/ml and copies/μg DNA also suggests that normalization to cell number or genomic DNA in cellular specimens may not be necessary.
Comparative In Vitro Antimicrobial Activity of Tigecycline, a New Glycylcycline Compound, in Freshly Prepared Medium and Quality Control
Authors: Brown Steven D. , Traczewski Maria M.
Published: May 2007

The in vitro spectra of activity of tigecycline and tetracycline were determined for 2,490 bacterial isolates representing 50 different species or phenotypic groups. All isolates were tested simultaneously by broth microdilution using freshly prepared Mueller-Hinton broth and by disk diffusion. Portions of these data were submitted to the Food and Drug Administration (FDA) in support of the sponsor's application for new drug approval. In a separate study, MIC and disk diffusion quality control ranges were determined. The tigecycline MICs at which 50%/90% of bacteria were inhibited were (in μg/ml) as follows: for
Streptococcus
spp., 0.06/0.12; for
Moraxella catarrhalis
, 0.06/0.12; for
Staphylococcus
spp., 0.12/0.25; for
Enterococcus
spp., 0.12/0.25; for
Listeria monocytogenes
, 0.12/0.12; for
Neisseria meningitidis
, 0.12/0.25; for
Haemophilus
spp., 0.25/0.5; for
Enterobacteriaceae
, 0.05/2.0; for non-
Enterobacteriaceae
, 0.5/8.0. Tigecycline was consistently more potent than tetracycline against all species studied. The data from this study confirm the FDA-approved MIC and disk diffusion breakpoints for tigecycline for
Streptococcus
spp. other than
Streptococcus pneumoniae
, enterococci, and
Enterobacteriaceae
. Provisional breakpoints for
Haemophilus
spp. and
S. pneumoniae
are proposed based on the data from this study. The following MIC and/or disk diffusion quality control ranges are proposed:
Staphylococcus aureus
ATCC 29213, 0.03 to 0.25 μg/ml;
S. aureus
ATCC 25923, 20 to 25 mm;
Escherichia coli
ATCC 25922, 0.03 to 0.25 μg/ml and 20 to 27 mm;
Pseudomonas aeruginosa
ATCC 27853, 9 to 13 mm,
Enterococcus faecalis
ATCC 29212, 0.03 to 0.12 μg/ml;
S. pneumoniae
ATCC 49619, 0.015 to 0.12 μg/ml and 23 to 29 mm;
Haemophilus influenzae
ATCC 49247, 0.06 to 0.5 μg/ml and 23 to 31 mm; and
Neisseria gonorrhoeae
ATCC 49226, 30 to 40 mm.
X-Box-Binding Protein 1 Activates Lytic Epstein-Barr Virus Gene Expression in Combination with Protein Kinase D
Authors: Bhende Prasanna M. , Dickerson Sarah J. , Sun Xiaoping , Feng Wen-Hai , Kenney Shannon C.
Published: May 2007

Epstein-Barr virus (EBV) establishes a latent form of infection in memory B cells, while antibody-secreting plasma cells often harbor the lytic form of infection. The switch between latent and lytic EBV infection is mediated by the two viral immediate-early proteins BZLF1 (Z) and BRLF1 (R), which are not expressed in latently infected B cells. Here we demonstrate that a cellular transcription factor that plays an essential role in plasma cell differentiation, X-box-binding protein 1 (XBP-1), also activates the transcription of the two EBV immediate-early gene promoters. In reporter gene assays, XBP-1 alone was sufficient to activate the R promoter, whereas the combination of XBP-1 and protein kinase D (PKD) was required for efficient activation of the Z promoter. Most importantly, the expression of XBP-1 and activated PKD was sufficient to induce lytic viral gene expression in EBV-positive nasopharyngeal carcinoma cells and lymphoblastoid cells, while an XBP-1 small interfering RNA inhibited constitutive lytic EBV gene expression in lymphoblastoid cells. These results suggest that the plasma cell differentiation factor XBP-1, in combination with activated PKD, can mediate the reactivation of EBV, thereby allowing the viral life cycle to be intimately linked to plasma cell differentiation.
The Translocation Motif of Hepatitis B Virus Envelope Proteins Is Dispensable for Infectivity
Authors: Lepère Charlotte , Régeard Morgane , Le Seyec Jacques , Gripon Philippe
Published: May 2007

The early events of hepatitis B virus (HBV) infection remain unclear. In 2006, Stoeckl et al. proposed a new entry mechanism involving a translocation motif (TLM) present in the pre-S2 domain of envelope proteins (L. Stoeckl, A. Funk, A. Kopitzki, B. Brandenburg, S. Oess, H. Will, H. Sirma, and E. Hildt, Proc. Natl. Acad. Sci. USA 103:6730-6734, 2006). After receptor binding and internalization into the endosomal compartment, this motif would allow the translocation of HBV particles through the endosomal membrane into the cytosol. In this study we have used two different mutated viruses containing a truncated TLM and showed their ability to infect human hepatocytes in primary culture, thus demonstrating the dispensability of the TLM for HBV infectivity.
The Stable 2-Kilobase Latency-Associated Transcript of Herpes Simplex Virus Type 1 Can Alter the Assembly of the 60S Ribosomal Subunit and Is Exported from Nucleus to Cytoplasm by a CRM1-Dependent Pathway
Authors: Atanasiu Doina , Fraser Nigel W.
Published: May 2007

During latency of herpes simplex virus type 1 in the neurons of the peripheral nervous system, the major transcript detected is the 2-kb latency-associated transcript (LAT) intron. During lytic infection, this intron has been shown to associate with ribosomes, suggesting a role in modifying the translational machinery of infected cells. In this study we show, using LAT-transfected cells, that the interaction of the intron with the 60S ribosomal subunit leads to irreversible changes in the sedimentation profile of this subunit in the nucleus. Furthermore, the 2-kb LAT intron is transported to the cytoplasm as part of the 60S ribosomal subunit, using a CRM1-dependent pathway.
Quantitative Analysis of Human Immunodeficiency Virus Type 1-Infected CD4+Cell Proteome: Dysregulated Cell Cycle Progression and Nuclear Transport Coincide with Robust Virus Production
Authors: Chan Eric Y. , Qian Wei-Jun , Diamond Deborah L. , Liu Tao , Gritsenko Marina A. , Monroe Matthew E. , Camp David G. , Smith Richard D. , Katze Michael G.
Published: May 2007

Relatively little is known at the functional genomic level about the global host response to human immunodeficiency virus type 1 (HIV-1) infection. Microarray analyses by several laboratories, including our own, have revealed that HIV-1 infection causes significant changes in host mRNA abundance and regulation of several cellular biological pathways. However, it remains unclear what consequences these changes bring about at the protein level. Here we report the expression levels of ∼3,200 proteins in the CD4+CEMx174 cell line after infection with the LAI strain of human immunodeficiency virus type 1 (HIV-1); the proteins were assessed using liquid chromatography-mass spectrometry coupled with stable isotope labeling and the accurate mass and time tag approach. Furthermore, we found that 687 (21%) proteins changed in abundance at the peak of virus production at 36 h postinfection. Pathway analysis revealed that the differential expression of proteins was concentrated in select biological pathways, exemplified by ubiquitin-conjugating enzymes in ubiquitination, carrier proteins in nucleocytoplasmic transport, cyclin-dependent kinase in cell cycle progression, and pyruvate dehydrogenase of the citrate cycle pathways. Moreover, we observed changes in the abundance of proteins with known interactions with HIV-1 viral proteins. Our proteomic analysis captured changes in the host protein milieu at the time of robust virus production, depicting changes in cellular processes that may contribute to virus replication. Continuing analyses are expected to focus on blocking virus replication by targeting these pathways and their effector proteins.
The TAR Hairpin of Human Immunodeficiency Virus Type 1 Can Be Deleted When Not Required for Tat-Mediated Activation of Transcription
Authors: Das Atze T. , Harwig Alex , Vrolijk Martine M. , Berkhout Ben
Published: May 2007

The human immunodeficiency virus type 1 (HIV-1) RNA genome contains a terminal repeat (R) region that encodes the transacting responsive (TAR) hairpin, which is essential for Tat-mediated activation of gene expression. TAR has also been implicated in several other processes during viral replication, including translation, dimerization, packaging, and reverse transcription. However, most studies in which replication of TAR-mutated viruses was analyzed were complicated by the dominant negative effect of the mutations on transcription. We therefore used an HIV-1 variant that does not require TAR for transcription to reinvestigate the role of TAR in HIV-1 replication. We demonstrate that this virus can replicate efficiently upon complete deletion of TAR. Furthermore, evolution of a TAR-deleted variant in long-term cultures indicates that HIV-1 requires a stable stem-loop structure at the start of the viral transcripts in which the 5′-terminal nucleotides are base paired. This prerequisite for efficient replication can be fulfilled by the TAR hairpin but also by unrelated stem-loop structures. We therefore conclude that TAR has no essential function in HIV-1 replication other than to accommodate Tat-mediated activation of transcription.
Generation of Infectious Molecular Clones of Simian Immunodeficiency Virus from Fecal Consensus Sequences of Wild Chimpanzees
Authors: Takehisa Jun , Kraus Matthias H. , Decker Julie M. , Li Yingying , Keele Brandon F. , Bibollet-Ruche Fréderic , Zammit Kenneth P. , Weng Zhiping , Santiago Mario L. , Kamenya Shadrack , Wilson Michael L. , Pusey Anne E. , Bailes Elizabeth , Sharp Paul M. , Shaw George M. , Hahn Beatrice H.
Published: May 2007

Studies of simian immunodeficiency viruses (SIVs) in their endangered primate hosts are of obvious medical and public health importance, but technically challenging. Although SIV-specific antibodies and nucleic acids have been detected in primate fecal samples, recovery of replication-competent virus from such samples has not been achieved. Here, we report the construction of infectious molecular clones of SIVcpz from fecal viral consensus sequences. Subgenomic fragments comprising a complete provirus were amplified from fecal RNA of three wild-living chimpanzees and sequenced directly. One set of amplicons was concatenated using overlap extension PCR. The resulting clone (TAN1.24) contained intact genes and regulatory regions but was replication defective. It also differed from the fecal consensus sequence by 76 nucleotides. Stepwise elimination of all missense mutations generated several constructs with restored replication potential. The clone that yielded the most infectious virus (TAN1.910) was identical to the consensus sequence in both protein and long terminal repeat sequences. Two additional SIVcpz clones were constructed by direct synthesis of fecal consensus sequences. One of these (TAN3.1) yielded fully infectious virus, while the second one (TAN2.69) required modification at one ambiguous site in the viral
pol
gene for biological activity. All three reconstructed proviruses produced infectious virions that replicated in human and chimpanzee CD4
+
T cells, were CCR5 tropic, and resembled primary human immunodeficiency virus type 1 isolates in their neutralization phenotype. These results provide the first direct evidence that naturally occurring SIVcpz strains already have many of the biological properties required for persistent infection of humans, including CD4 and CCR5 dependence and neutralization resistance. Moreover, they outline a new strategy for obtaining medically important “SIV isolates” that have thus far eluded investigation. Such isolates are needed to identify viral determinants that contribute to cross-species transmission and host adaptation.
Murine Cytomegalovirus Major Immediate-Early Enhancer Region Operating as a Genetic Switch in Bidirectional Gene Pair Transcription
Authors: Simon Christian O. , Kühnapfel Birgit , Reddehase Matthias J. , Grzimek Natascha K. A.
Published: May 2007

Enhancers are defined as DNA elements that increase transcription when placed in any orientation relative to a promoter. The major immediate-early (MIE) enhancer region of murine cytomegalovirus is flanked by transcription units
ie1/3
and
ie2
, which are transcribed in opposite directions. We have addressed the fundamental mechanistic question of whether the enhancer synchronizes transcription of the bidirectional gene pair (synchronizer model) or whether it operates as a genetic switch, enhancing transcription of either gene in a stochastic alternation (switch model). Clonal analysis of cytokine-triggered, transcription factor-mediated MIE gene expression from latent viral genomes provided evidence in support of the switch model.
Poliovirus Induces Bax-Dependent Cell Death Mediated by c-Jun NH
2
-Terminal Kinase
Authors: Autret Arnaud , Martin-Latil Sandra , Mousson Laurence , Wirotius Aurélie , Petit Frédéric , Arnoult Damien , Colbère-Garapin Florence , Estaquier Jérôme , Blondel Bruno
Published: May 2007

Poliovirus (PV) is the causal agent of paralytic poliomyelitis, a disease that involves the destruction of motor neurons associated with PV replication. In PV-infected mice, motor neurons die through an apoptotic process. However, mechanisms by which PV induces cell death in neuronal cells remain unclear. Here, we demonstrate that PV infection of neuronal IMR5 cells induces cytochrome
c
release from mitochondria and loss of mitochondrial transmembrane potential, both of which are evidence of mitochondrial outer membrane permeabilization. PV infection also activates Bax, a proapoptotic member of the Bcl-2 family; this activation involves its conformational change and its redistribution from the cytosol to mitochondria. Neutralization of Bax by vMIA protein expression prevents cytochrome
c
release, consistent with a contribution of PV-induced Bax activation to mitochondrial outer membrane permeabilization. Interestingly, we also found that c-Jun NH
2
-terminal kinase (JNK) is activated soon after PV infection and that the PV-cell receptor interaction alone is sufficient to induce JNK activation. Moreover, the pharmacological inhibition of JNK by SP600125 inhibits Bax activation and cytochrome
c
release. This is, to our knowledge, the first demonstration of JNK-mediated Bax-dependent apoptosis in PV-infected cells. Our findings contribute to our understanding of poliomyelitis pathogenesis at the cellular level.
GENERALIZED FORMULATIONS OF MAXWELL'S EQUATIONS FOR NUMERICAL VLASOV–MAXWELL SIMULATIONS
Authors: BARTHELMÉ RÉGINE , CIARLET PATRICK , SONNENDRÜCKER ERIC
Published: May 2007

When solving numerically approximations of the Vlasov–Maxwell equations, the source terms in Maxwell's equations coming from the numerical solution of the Vlasov equation do not generally satisfy the continuity equation which is required for Maxwell's equations to be well-posed. Hence it is necessary to introduce generalized Maxwell's equations which remain well-posed when there are errors in the sources. Different such formulations have been introduced previously. The aim of this paper is to perform their mathematical analysis and verify the existence and uniqueness of the solution.
THE NEUMANN SIEVE PROBLEM AND DIMENSIONAL REDUCTION: A MULTISCALE APPROACH
Authors: ANSINI NADIA , BABADJIAN JEAN-FRANÇOIS , ZEPPIERI CATERINA IDA
Published: May 2007

We perform a multiscale analysis for the elastic energy of a n-dimensional bilayer thin film of thickness 2δ whose layers are connected through an ε-periodically distributed contact zone. Describing the contact zone as a union of (n - 1)-dimensional balls of radius r ≪ ε (the holes of the sieve) and assuming that δ ≪ ε, we show that the asymptotic memory of the sieve (as ε → 0) is witnessed by the presence of an extra interfacial energy term. Moreover, we find three different limit behaviors (or regimes) depending on the mutual vanishing rate of δ and r. We also give an explicit nonlinear capacitary-type formula for the interfacial energy density in each regime.
DYNAMICS OF POLYDISPERSE IRREVERSIBLE ADSORPTION: A PHARMACOLOGICAL EXAMPLE
Authors: ERBAN RADEK , CHAPMAN S. JONATHAN , FISHER KERRY D. , KEVREKIDIS IOANNIS G. , SEYMOUR LEONARD W.
Published: May 2007

Many drug delivery systems suffer from undesirable interactions with the host immune system. It has been experimentally established that covalent attachment (irreversible adsorption) of suitable macromolecules to the surface of the drug carrier can reduce such undesirable interactions. A fundamental understanding of the adsorption process is still lacking. In this paper, the classical random irreversible adsorption model is generalized to capture certain essential processes involved in pharmacological applications, allowing for macromolecules of different sizes, partial overlapping of the tails of macromolecules, and the influence of reactions with the solvent on the adsorption process. Working in one dimension, an integro-differential evolution equation for the adsorption process is derived, and the asymptotic behavior of the surface area covered and the number of molecules attached to the surface are studied. Finally, equation-free dynamic renormalization tools are applied to study the asymptotically self-similar behavior of the adsorption statistics.
ON A TWO-SIDEDLY DEGENERATE CHEMOTAXIS MODEL WITH VOLUME-FILLING EFFECT
Authors: BENDAHMANE MOSTAFA , KARLSEN KENNETH H. , URBANO JOSÉ MIGUEL
Published: May 2007

We consider a fully parabolic model for chemotaxis with volume-filling effect and a nonlinear diffusion that degenerates in a two-sided fashion. We address the questions of existence of weak solutions and of their regularity by using, respectively, a regularization method and the technique of intrinsic scaling.
The roles of myosin ATPase activity and myosin light chain relative content in the slowing of type IIB fibers with hindlimb unweighting in rats
Authors: Zhong Sheng , Thompson LaDora V.
Published: May 2007

We tested the hypothesis that slowing of shortening velocity generated by type IIB fibers from hindlimb-unweighted (HU) rats resulted from a reduced ATPase activity and/or a reduction in the relative content of myosin light chain 3f isoform content (MLC3f). After 2, 3, and 4 wk of HU, maximal unloaded shortening velocity ( Vo) of single permeabilized semimembranosus muscle fibers was determined by the slack test. Subsequently, the myosin heavy chain and the relative content of MLC were determined by SDS-PAGE. The ratio of MLC3f to MLC2f was determined by densitometric analysis. In addition, myofibrils were prepared from permeabilized fibers (soleus and semimembranosus muscles) and assayed for resting myosin ATPase and Ca2+-activated myosin ATPase. After HU, Vo declined by 28–40% and the MLC3f/MLC2f ratio decreased by 32 to 48%. A significant correlation between the relative amount of MLC3f and Vo was found ( r = 0.48, P < 0.05). Resting myosin ATPase rates were not different between myofibrils prepared from corresponding muscles of control and HU rats ( P = 0.86). Ca2+-activated myosin ATPase activities also were not different between myofibrils prepared from corresponding muscles of control and HU rats ( P = 0.13). These data suggest that the slowing of maximal unloaded shortening velocity in type IIB fibers with HU is, at least in part, due to a relative change in the essential light chain composition, a decrease in the relative amount of MLC3f and most likely a concomitant increase in MLC1f. However, this reduction in Vo is independent of myosin ATPase activity.
Polyamines upregulate the mRNA expression of cationic amino acid transporter-1 in human retinal pigment epithelial cells
Authors: Kaneko Shiho , Okuda-Ashitaka Emiko , Ando Akira , Nishimura Kazuhiro , Igarashi Kazuei , Maeda Masahide , Furuta Kyoji , Suzuki Masaaki , Matsumura Miyo , Ito Seiji
Published: May 2007

We previously showed that ornithine was mainly transported via cationic amino acid transporter (CAT)-1 in human retinal pigment epithelial (RPE) cell line, human telomerase RT (hTERT)-RPE, and that CAT-1 was involved in ornithine cytotoxicity in ornithine-δ-aminotransferase (OAT)-deficient cell produced by a OAT specific inhibitor, 5-fluoromethylornithine (5-FMO). We showed here that CAT-1 mRNA expression was increased by ornithne in OAT-deficient RPE cells, which was reversed by an inhibitor of ornithine decarboxylase (ODC), α-difluoromethylornithine (DFMO). Polyamines, especially spermine, one of the metabolites of ODC, also enhanced the expression of CAT-1 mRNA. ODC mRNA expression was also increased by ornithine and polyamines, and gene silencing of ODC by siRNA decreased ornithine transport activity and its cytotoxicity. In addition, the mRNA of nuclear protein c-myc was also increased in 5-FMO- and ornithine-treated hTERT-RPE cells, and gene silencing of c-myc prevented the induction of CAT-1 and ODC. Increases in expression of CAT-1, ODC, and c-myc, and the inhibition of these stimulated expression by DFMO were also observed in primary porcine RPE cells. These results suggest that spermine plays an important role in stimulation of mRNA expression of CAT-1, which is a crucial role in ornithine cytotoxicity in OAT-deficient hTERT-RPE cells.
Neuropeptide substance P upregulates chemokine and chemokine receptor expression in primary mouse neutrophils
Authors: Sun Jia , Ramnath Raina Devi , Bhatia Madhav
Published: May 2007

Neuropeptides play an important role in the active communication between the nervous and immune systems. Substance P (SP) is a prominent neuropeptide involved in neurogenic inflammation and has been reported to exert various proinflammatory actions on inflammatory leukocytes including neutrophils. The present study further investigated the modulatory effect of SP (1 μM) on chemokine production and chemokine receptor expression in primary mouse neutrophils. Our results showed that SP primed neutrophils for chemotactic responses not only to the CXC chemokine macrophage inflammatory protein (MIP)-2/CXCL2 but also to the CC chemokine MIP-1α/CCL3. The activating effect of SP on neutrophils was further evidenced by upregulation of the CD11b integrin, the activation marker of neutrophils. SP induced both the mRNA and protein expression of the chemokines MIP-1α/CCL3 and MIP-2/CXCL2 in neutrophils and upregulated the chemokine receptors CC chemokine receptor (CCR)-1 and CXC chemokine receptor (CXCR)-2. This stimulatory effect on chemokine and chemokine receptor expression in neutrophils was further found to be neurokinin-1 receptor (NK-1R) specific. Pretreatment with selective NK-1R antagonists inhibited SP-triggered activation of neutrophils and chemokine and chemokine receptor upregulation. Moreover, SP-induced chemokine upregulation was NF-κB dependent. SP time dependently induced NF-κB p65 binding activity, IκBα degradation, and NF-κB p65 nuclear translocation in neutrophils. Inhibition of NF-κB activation with its inhibitor Bay11-7082 (10 μM) abolished SP-induced NF-κB binding activity and upregulation of MIP-1α/CCL3 and MIP-2/CXCL2 in neutrophils. Together, these results suggest that SP exerts a direct stimulatory effect on the expression of chemokines and chemokine receptors in mouse neutrophils. The effect is NK-1R mediated, involving NF-κB activation.
S6 kinase inactivation impairs growth and translational target phosphorylation in muscle cells maintaining proper regulation of protein turnover
Authors: Mieulet Virginie , Roceri Mila , Espeillac Catherine , Sotiropoulos Athanassia , Ohanna Mickael , Oorschot Viola , Klumperman Judith , Sandri Marco , Pende Mario
Published: May 2007

A defect in protein turnover underlies multiple forms of cell atrophy. Since S6 kinase (S6K)-deficient cells are small and display a blunted response to nutrient and growth factor availability, we have hypothesized that mutant cell atrophy may be triggered by a change in global protein synthesis. By using mouse genetics and pharmacological inhibitors targeting the mammalian target of rapamycin (mTOR)/S6K pathway, here we evaluate the control of translational target phosphorylation and protein turnover by the mTOR/S6K pathway in skeletal muscle and liver tissues. The phosphorylation of ribosomal protein S6 (rpS6), eukaryotic initiation factor-4B (eIF4B), and eukaryotic elongation factor-2 (eEF2) is predominantly regulated by mTOR in muscle cells. Conversely, in liver, the MAPK and phosphatidylinositol 3-kinase pathways also play an important role, suggesting a tissue-specific control. S6K deletion in muscle mimics the effect of the mTOR inhibitor rapamycin on rpS6 and eIF4B phosphorylation without affecting eEF2 phosphorylation. To gain insight on the functional consequences of these modifications, methionine incorporation and polysomal distribution were assessed in muscle cells. Rates and rapamycin sensitivity of global translation initiation are not altered in S6K-deficient muscle cells. In addition, two major pathways of protein degradation, autophagy and expression of the muscle-specific atrophy-related E3 ubiquitin ligases, are not affected by S6K deletion. Our results do not support a role for global translational control in the growth defect due to S6K deletion, suggesting specific modes of growth control and translational target regulation downstream of mTOR.
Reduced sickle erythrocyte dehydration in vivo by endothelin-1 receptor antagonists
Authors: Rivera Alicia
Published: May 2007

Elevated plasma levels of cytokines such as endothelin-1 (ET-1) have been shown to be associated with sickle cell disease (SCD). However, the role of ET-1 in the pathophysiology of SCD is not entirely clear. I now show that treatment of SAD mice, a transgenic mouse model of SCD, with BQ-788 (0.33 mg·kg−1·day−1 intraperitoneally for 14 days), an ET-1 receptor B (ETB) antagonist, induced a significant decrease in Gardos channel activity (1.7 ± 0.1 to 1.0 ± 0.4 mmol·1013 cell−1·h−1, n = 3, P = 0.019) and reduced the erythrocyte density profile by decreasing the mean density (D50; n = 4, P = 0.012). These effects were not observed in mice treated with BQ-123, an ET-1 receptor A (ETA) antagonist. A mixture of both antagonists induced a similar change in density profile as with BQ-788 alone that was associated with an increase in mean cellular volume and a decrease in corpuscular hemoglobin concentration mean. I also observed in vitro effects of ET-1 on human sickle erythrocyte dehydration that was blocked by BQ-788 and a mixture of ETB/ETA antagonists but not by ETA antagonist alone. These results show that erythrocyte hydration status in vivo is mediated via activation of the ETB receptor, leading to Gardos channel modulation in SCD.
Effect of the endothelin receptor antagonist bosentan on chronic hypoxia-induced morphological and physiological changes in rat carotid body
Authors: Chen Jia , He Liang , Liu Xuemei , Dinger Bruce , Stensaas Larry , Fidone Salvatore
Published: May 2007

Previous experiments have repeatedly demonstrated that exposure to chronic hypoxia (CH) elicits remarkable structural changes and chemosensory hypersensitivity in the mammalian carotid body. Moreover, recent studies have shown that CH upregulates the neuroactive peptide, endothelin (ET), in oxygen-sensitive type I cells. The present study examines the possible involvement of ET in adaptation by concurrently exposing rats to hypobaric CH (BP = 380 Torr) and bosentan, a potent nonpeptide antagonist that blocks ETA and ETB receptors. Carotid body weight indicated that 14 days of CH induced organ enlargement, a response that was blunted in bosentan-treated rats (CH: 2.54 ± 0.19-fold increase; CH plus bosentan: 1.92 ± 0.14-fold increase; P < 0.05). Morphometric studies revealed that bosentan substantially eliminated CH-induced hyperplasia of chemosensory cell lobules as well as expansion of the connective tissue matrix. Vascular dilation associated with CH was not altered by the drug. In untreated animals exposed to 3 days of CH, expression of proliferating cell nuclear antigen (PCNA), a marker of mitosis, was increased in lobules of oxygen-sensitive type I cells and in extralobular vascular and connective tissue cells. The incidence of PCNA expression was significantly ( P < 0.05) reduced in bosentan-treated animals. In vitro assessments of carotid sinus nerve (CSN) activity showed that enhancement of basal and hypoxia-evoked chemosensory activity following 9 days of CH was significantly ( P < 0.001) blunted by concurrent treatment with bosentan. Collectively, our data are consistent with the hypothesis that CH-induced adaptation in the carotid body is at least partially mediated by signaling pathways involving ET receptors.