bluuebunny/crossref_metadata_2025 huggingface dataset:
Including Preference in Anthropometry-Driven Models for Design
Authors: Garneau Christopher J. , Parkinson Matthew B.
Published: September 2009

In the design of artifacts that interact with people, the spatial dimensions of the target user population are often used to determine the requirements of the engineered artifact. The expected variability in body dimensions (called “anthropometry”) is used to indicate how much adjustability or how many sizes are required to accommodate the intended user population. However, the quantification of anthropometric variability alone is not sufficient to make these kinds of assessments in many situations. For example, two vehicle drivers with similar body dimensions might have different preferred locations for the seat. In these situations, preference can be broken down into two components: that explained by body size and the variability that remains. By quantifying the magnitude of both sources, preference can be included in modeling strategies and design decision-making. This improves the accuracy of models and predictions, and can facilitate the application of design automation tools such as optimization and robust design methodologies, resulting in products that are safer, cost effective, and more accessible to broader populations (including people with disabilities). In contrast, failure to include variability in preference that is not attributable to anthropometry can produce misleading results that under- or over-approximate accommodation and prescribe inappropriate amounts of adjustability. A simulation-based approach for modeling both sources of variability and conducting designing for human variability (DfHV) assessments is presented. A stochastic component based on the residual variance in regression analysis relating body dimensions to experimental data is included in the predictive model. This ensures that a distribution of preferred configurations is produced for any given set of body dimensions. The effect of including both components of preference is quantified by comparing this approach to two traditional DfHV approaches in the context of a simple, univariate case study to determine the appropriate allocation of adjustability to achieve a desired accommodation level.
Fatigue Crack Growth Prediction Under Random Peaks and Sequence Loading
Authors: Alawi H.
Published: September 2009

Fatigue crack growth under random amplitude and sequence loading with peaks following the Rayleigh probability density function is simulated using the probabilistic model. Another attempt at fatigue life prediction under the above loads is made by converting random loads in to equivalent constant amplitude. Prediction results are compared with experimental findings. Empirical data for fatigue crack growth under random loads at different frequencies are compared with the results of prediction using the above techniques. Experimental results of three steels are used in this study to compare with the findings of the above prediction techniques. These steels are AISI 1018, AISI 4340 and stainless pH 17-7. It is seen that the probabilistic model produces reliable results. It conservatively predicts fatigue crack growth when no delay mechanism to retard crack growth is introduced.
Similarity Analysis Applied to the Die Casting Process
Authors: Eckert E. R. G.
Published: September 2009

Detailed studies of the filling process of the die with liquid metal and the solidification are necessary to put this technology on a firm scientific basis. An experimental study of the fluid flow, heat transfer, and solidification encounters, however, enormous difficulties. It is extremely fast [in order of milliseconds], the small scale of the die makes local measurements difficult, and the temperature range and the nature of the liquid metal does not lend itself readily to experimentation. This paper explores whether similarity analysis is useful for the design of model experiments which reduce these difficulties and which reproduce the actual occurrence faithfully. The study is carried out in two steps. During the initial period, the whole cavity of the die is available for the fluid. Reynolds and Weber numbers which have to have the same value for the model experiment and for the die casting process permit the use of any fluid and of a large scale model which decreases the injection velocity and increases the filling time. During the later period of the filling process the cavity available for the liquid is reduced by the solidified metal. The energy conservation equation results in two more dimensionless numbers, the Prandtl and Jakob numbers which prescribe that model experiments have now to use a liquid metal but use of a metal with a low melting point and of a large scale decrease again the required injection velocity and increase the filling time by orders of magnitude, conditions beneficial for detailed and accurate experiments.
Low-Cycle Fatigue Properties of Steels and Their Weld Metals
Authors: Itoh Y. Z. , Kashiwaya H.
Published: September 2009

Completely reversed, strain-controlled, low-cycle fatigue behavior at room temperature is investigated for steels and their weld metals. Weld metal specimens were taken from multi-pass weld metal deposited by shield metal arc welding (SMAW) and gas metal arc welding (GMAW), such that their gage length consisted entirely of the weld metal. Results indicate that there is a trend toward reduction in the low-cycle fatigue life of weld metals as compared with the base metals. In low carbon steel weld metals, the tendency described above is explained in terms of local plastic strain concentration by lack of uniformity of the multi-pass weld metals. The weld metals do not have the same mechanical properties anywhere as confirmed by hardness distribution, and the fatigue crack grows preferentially through the temper softened region in the multi-pass welds. In Type 308 stainless steel weld metals, the ductility reduction causes reductions in low-cycle fatigue life. This study leads to the conclusion that fairly accurate estimates of the low-cycle fatigue life of weld metals can be obtained using Manson’s universal slope method. However, life estimates of the Type 304 stainless steel is difficult due to a lack of ductility caused by a deformation-induced martensitic transformation.
A Stochastic Nonlinear Constitutive Law for Concrete
Authors: Fafitis A. , Won Y. H.
Published: September 2009

An incremental three-dimensional stress-strain relationship for concrete with induced anisotropy has been developed. The nonlinearity and path-dependency are modeled by expressing the elastic moduli at each increment as function of the octahedral and deviatoric strains, based on a uniaxial stochastic model developed earlier. Predictions of multiaxial response under proportional and nonproportional loading are in good agreement with experimental results.
Alterations in Two-Component Regulatory Systems of
phoPQ
and
pmrAB
Are Associated with Polymyxin B Resistance in Clinical Isolates of
Pseudomonas aeruginosa
Authors: Barrow Kaddy , Kwon Dong H.
Published: September 2009

Polymyxins are often the only option to treat acquired multidrug-resistant
Pseudomonas aeruginosa
. Polymyxin susceptibility in
P. aeruginosa
PAO1 is associated with the lipopolysaccharide structure that is determined by
arnBCADTEF
and modulated by
phoPQ
and
pmrAB
. We examined five clonally unrelated clinical isolates of polymyxin B-resistant
P. aeruginosa
to investigate the molecular basis of polymyxin resistance. All isolates grew with 4 μg/ml polymyxin B (MIC, 8 μg/ml), whereas
P. aeruginosa
PAO1 grew with 0.25 μg/ml polymyxin B (MIC, 0.5 μg/ml). The resistant isolates were converted to susceptible ones (the MICs fell from 8 to 0.5 μg/ml) following the introduction of
phoPQ
(four isolates) and
pmrAB
(one isolate), which had been cloned from strain PAO1. DNA sequence analysis revealed that a single-nucleotide substitution in three isolates replaced a single amino acid of PhoQ, the deletion of 17 nucleotides in one isolate truncated the protein of PhoQ, and two nucleotide substitutions in one isolate replaced two amino acids of PmrB. The involvement of these amino acid substitutions or the truncated protein of PhoQ and PmrB in polymyxin B resistance was confirmed using strain PAO1 lacking
phoPQ
or
pmrAB
that was transformed by
phoPQ
or
pmrAB
containing the amino acid substitutions or the truncated protein. The resistant clinical isolates were sensitized by the inactivation of
arnBCADTEF
(the MICs fell from 8 to 0.5 μg/ml). These results suggest that polymyxin B resistance among clinical isolates of
P. aeruginosa
is associated with alterations in two-component regulatory systems of
phoPQ
or
pmrAB
.
Therapeutic Drug Monitoring of Posaconazole: a Monocentric Study with 54 Adults
Authors: Lebeaux David , Lanternier Fanny , Elie Caroline , Suarez Felipe , Buzyn Agnès , Viard Jean-Paul , Bougnoux Marie-Elisabeth , Lecuit Marc , Jullien Vincent , Lortholary Olivier
Published: September 2009

Posaconazole is a potent broad-spectrum triazole antifungal. Little is known about the prevalence and risk factors for low plasma posaconazole concentrations (PPCs). We retrospectively reviewed all adult patients whose PPCs were measured after at least 5 days of treatment between April 2006 and July 2008 at the Hôpital Necker Enfants Malades. A low PPC was defined as a concentration lower than 500 ng/ml. Fifty-four patients were included: 36 receiving prophylactic (200 mg three times a day) and 18 receiving curative (400 mg twice a day) posaconazole therapy. The prevalence of low PPCs was 44% (16/36) in the prophylaxis group and 22% (4/18) in the curative-treatment group. In the prophylaxis group, low PPCs tended to be more frequent in cases of digestive disease (62.5% versus 30%;
P
= 0.051) and were significantly more frequent among patients with diarrhea (71.4% versus 27%;
P
= 0.009) or mucositis (100% versus 33%;
P
= 0.004). In the curative-treatment group, low PPCs were significantly more frequent in cases of diarrhea (75% versus 7%;
P
= 0.018). In the prophylaxis group, the only two patients who subsequently developed invasive fungal infections exhibited low PPCs. The only adverse event was hepatotoxicity for 2/54 patients (3.7%), which was not related to high plasma drug concentrations. In conclusion, low PPC is common, significantly more frequent in cases of diarrhea or mucositis, and potentially associated with subsequent invasive fungal infection. Therapeutic drug monitoring of posaconazole is therefore mandatory for immunosuppressed adults, at least for those with gastrointestinal disorders.
Unbound Cephalothin Pharmacokinetics in Adult Burn Patients Are Related to the Elapsed Time after Injury
Authors: Dalley Andrew J. , Deans Renae , Lipman Jeffrey , Venkatesh Bala , Rudd Michael , Roberts Michael S. , Cross Sheree E.
Published: September 2009

Cephalothin (cefalotin) pharmacokinetics were evaluated for nine severely burned patients (42% ± 9% mean burn areas) and five healthy volunteers by using non-plasma-protein-bound concentration-time profiles. Burn patients gave increased mean residence times (36%) and reduced total clearances (25%). Mean residence times and distribution volumes increased between 1 and 4 days posttrauma, suggesting that burn patient pharmacokinetics change during the initial fluid resuscitation phase of treatment.
A Naturally Occurring Rgg Variant in Serotype M3
Streptococcus pyogenes
Does Not Activate
speB
Expression Due to Altered Specificity of DNA Binding
Authors: Kappeler Kyle V. , Anbalagan Srivishnupriya , Dmitriev Alexander V. , McDowell Emily J. , Neely Melody N. , Chaussee Michael S.
Published: September 2009

The transcriptional regulator Rgg of
Streptococcus pyogenes
is essential for expression of the secreted cysteine protease SpeB. Although all isolates of
S. pyogenes
possess the
speB
gene, not all of them produce the protein in vitro. In a murine model of infection, the absence of SpeB production is associated with invasive disease. We speculated that naturally occurring mutations in
rgg
, which would also abrogate SpeB production, may be present in invasive isolates of
S. pyogenes
. Examination of the inferred Rgg sequences available in public databases revealed that the
rgg
gene in strain MGAS315 (a serotype M3 strain associated with invasive disease) encodes a proline at amino acid position 103 (Rgg
103P
); in contrast, all other strains encode a serine at this position (Rgg
103S
). A caseinolytic assay and Western blotting indicated that strain MGAS315 does not produce SpeB in vitro. Gene-swapping experiments showed that the
rgg
gene of MGAS315 is solely responsible for the lack of SpeB expression. In contrast to Rgg
103S
, Rgg
103P
does not bind to the
speB
promoter in gel shift assays, which correlates with a lack of
speB
expression. Despite its inability to activate
speB
expression, Rgg
103P
retains the ability to bind to DNA upstream of
norA
and to influence its expression. Overall, this study illustrates how variation at the
rgg
locus may contribute to the phenotypic diversity of
S. pyogenes
.
Distinctive Profiles of Infection and Pathology in Hamsters Infected with
Clostridium difficile
Strains 630 and B1
Authors: Goulding David , Thompson Harold , Emerson Jenny , Fairweather Neil F. , Dougan Gordon , Douce Gill R.
Published: September 2009

Currently, the Golden Syrian hamster is widely considered an important model of
Clostridium difficile
disease, as oral infection of this animal pretreated with antibiotics reproduces many of the symptoms observed in humans. Two
C. difficile
strains, B1 and 630, showed significant differences in the progression and severity of disease in this model. B1-infected hamsters exhibited more severe pathology and a shorter time to death than hamsters infected with 630. Histological changes in the gut did not correlate with absolute numbers of
C. difficile
bacteria, but there were clear differences in the distribution of bacteria within gut tissues. Light, scanning, and transmission electron microscopy revealed high numbers of B1 bacteria at the mucosal surface of the tissue, whereas 630 bacteria were more frequently associated with the crypt regions. Both B1 and 630 bacteria were frequently observed within polymorphonuclear leukocytes, although, interestingly, a space frequently separated B1 bacteria from the phagosome wall, a phenomenon not observed with 630. However, pilus-like structures were detected on 630 located in the crypts of the gut tissue. Furthermore, B1 bacteria, but not 630 bacteria, were found within nonphagocytic cells, including enterocytes and muscle cells.
Bcl-2 Regulates the Onset of Shiga Toxin 1-Induced Apoptosis in THP-1 Cells
Authors: Lee Moo-Seung , Cherla Rama P. , Leyva-Illades Dinorah , Tesh Vernon L.
Published: September 2009

Shiga toxins (Stxs), which are proteins expressed by the enteric pathogens
Shigella dysenteriae
serotype 1 and some serotypes of
Escherichia coli
, are potent protein synthesis inhibitors. Stx-producing organisms cause bloody diarrhea with the potential to progress to acute renal failure and central nervous system complications. Studies using animal models of these diseases have shown that Stxs are major virulence factors, and purified toxins have been shown to be capable of killing many types of cells in vitro. We showed that Stx type 1 (Stx1) rapidly induced apoptosis in undifferentiated, monocytic THP-1 cells through a mechanism involving the endoplasmic reticulum (ER) stress response. Rapid apoptosis correlated with increased expression of C/EBP homologous protein (CHOP), TRAIL, and DR5, while expression of the antiapoptotic factor Bcl-2 was downregulated. Stx1 treatment of differentiated, macrophage-like THP-1 cells was associated with cytokine production and delayed apoptosis. The mechanisms contributing to cell maturation-dependent differences in responses to Stx1 are unknown. We show here that in macrophage-like cells, Stx1 activated the proximal ER stress sensors RNA-dependent protein kinase-like ER kinase and inositol-requiring ER signal kinase 1α but did not activate activating transcription factor 6. Proapoptotic signaling pathways mediated by CHOP and by Bax and Bak were activated by Stx1. However, the toxin also activated prosurvival signaling through increased expression, mitochondrial translocation, and alternative phosphorylation of Bcl-2.
Role for theBurkholderia pseudomalleiCapsular Polysaccharide Encoded by thewcbOperon in Acute Disseminated Melioidosis
Authors: Warawa Jonathan M. , Long Dan , Rosenke Rebecca , Gardner Don , Gherardini Frank C.
Published: September 2009

The capsular polysaccharide ofBurkholderia pseudomalleiis an essential virulence determinant that is required for protection from host serum cidal activity and opsonophagocytosis. In this study, the immune response directed against aB. pseudomalleicapsule mutant (JW270) was investigated in an acute respiratory murine model. JW270 was significantly attenuated in this model (∼2 logs) to levels resembling those of avirulentBurkholderia thailandensis. At lethal doses, JW270 colonized the lung, liver, and spleen at levels similar to the wild-type strain levels and was found to trigger reduced pathology in the liver and spleen. Several cytokine responses were altered in these tissues, and importantly, the levels of gamma interferon were reduced in the livers and spleens of JW270-infected mice but not in the lungs. These results suggest that the capsular polysaccharide ofB. pseudomalleiis a critical virulence determinant in respiratory tract infections and that it is an important antigen for generating the Th1 immune response commonly observed in systemic melioidosis. Furthermore, the data suggest that host recognition ofB. pseudomalleicapsular polysaccharide in the lungs may not be as important to the disease outcome as the innate immune response in the peripheral organs.
Evaluation of a New Test, GenoType HelicoDR, for Molecular Detection of Antibiotic Resistance inHelicobacter pylori
Authors: Cambau Emmanuelle , Allerheiligen Vera , Coulon Céline , Corbel Céline , Lascols Christine , Deforges Lionel , Soussy Claude-James , Delchier Jean-Charles , Megraud Francis
Published: September 2009

The eradication rate ofHelicobacter pyloriby standard therapy is decreasing due to antibiotic resistance, mainly to clarithromycin. Our aim was to provide a new molecular test to guide the treatment of new and relapsed cases. We first studied 126H. pyloristrains for phenotypic (MIC) and genotypic resistance to clarithromycin (rrlmutation) and levofloxacin (gyrAmutation) and then developed a DNA strip genotyping test on the basis of the correlation results and literature data. Clinical strains (n= 92) and gastric biopsy specimens containingH. pylori(n= 105) were tested blindly with the new molecular test GenoType HelicoDR. The presence of mutations or the absence of hybridization with wild-type sequences was predictive, inrrlfor clarithromycin resistance in 91 cases (mostly the A2147G mutation) and ingyrAfor levofloxacin resistance in 58 cases (mutations at codon 87 or 91). Genotyping revealed a mix of genotypes in 33% of the cases, reflecting a coinfection or selection for resistant mutants. The sensitivity and specificity of detecting resistance were 94% and 99% for clarithromycin and 87% and 98.5% for levofloxacin, respectively. The concordance scores were 0.96 for clarithromycin and 0.94 for levofloxacin. With global resistance rates of 46% for clarithromycin and 25% for levofloxacin, which were observed for consecutive positive biopsy specimens from 2007 and 2008, the positive and negative predictive values for detecting resistance were 99% and 94% for clarithromycin and 96% and 96% for fluoroquinolone. GenoType HelicoDR is efficient at detecting mutations predictive of antibiotic resistance inH. pyloriwhen applied to strains or directly to gastric biopsy specimens.
Transgenic Expression of the 3D Polymerase Inhibits Theiler's Virus Infection and Demyelination
Authors: Kerkvliet Jason , Zoecklein Laurie , Papke Louisa , Denic Aleksandar , Bieber Allan J. , Pease Larry R. , David Chella S. , Rodriguez Moses
Published: September 2009

The RNA-dependent RNA polymerase 3Dpolis required for the elongation of positive- and negative-stranded picornavirus RNA. During the course of investigating the effect of the transgenic expression of viral genes on the host immune response, we evaluated the viral load present in the host after infection. To our surprise, we found that 3D transgenic expression in genetically susceptible FVB mice led to substantially lower viral loads after infection with Theiler's murine encephalomyelitis virus (TMEV). As a result, spinal cord damage caused by chronic viral infection in the central nervous system was reduced in FVB mice that expressed 3D. This led to the preservation of large-diameter axons and motor function in these mice. The 3D transgene also lowered early viral loads when expressed in FVB-Dbmice resistant to persistent TMEV infection. The protective effect of 3D transgenic expression was not altered in FVB-Rag−/−.3D mice that are deficient in T and B cells, thus ruling out a mechanism by which the overexpression of 3D enhanced the adaptive immune clearance of the virus. Understanding how endogenously overexpressed 3D polymerase inhibits viral replication may lead to new strategies for targeting therapies to all picornaviruses.
Evolutionary Dynamics of GII.4 Noroviruses over a 34-Year Period
Authors: Bok Karin , Abente Eugenio J. , Realpe-Quintero Mauricio , Mitra Tanaji , Sosnovtsev Stanislav V. , Kapikian Albert Z. , Green Kim Y.
Published: September 2009

Noroviruses are a major cause of epidemic gastroenteritis in children and adults, and GII.4 has been the predominant genotype since its first documented occurrence in 1987. This study examined the evolutionary dynamics of GII.4 noroviruses over more than three decades to investigate possible mechanisms by which these viruses have emerged to become predominant. Stool samples (
n
= 5,424) from children hospitalized at the Children's Hospital in Washington, DC, between 1974 and 1991 were screened for the presence of noroviruses by a custom multiplex real-time reverse transcription-PCR. The complete genome sequences of five GII.4 noroviruses (three of which predate 1987 by more than a decade) in this archival collection were determined and compared to the sequences of contemporary strains. Evolutionary analysis determined that the GII.4 VP1 capsid gene evolved at a rate of 4.3 × 10
−3
nucleotide substitutions/site/year. Only six sites in the VP1 capsid protein were found to evolve under positive selection, most of them located in the shell domain. No unique mutations were observed in or around the two histoblood group antigen (HBGA) binding sites in the P region, indicating that this site has been conserved since the 1970s. The VP1 proteins from the 1974 to 1977 noroviruses contained a unique sequence of four consecutive amino acids in the P2 region, which formed an exposed protrusion on the modeled capsid structure. This protrusion and other observed sequence variations did not affect the HBGA binding profiles of recombinant virus-like particles derived from representative 1974 and 1977 noroviruses compared with more recent noroviruses. Our analysis of archival GII.4 norovirus strains suggests that this genotype has been circulating for more than three decades and provides new ancestral strain sequences for the analysis of GII.4 evolution.
Mouse Hepatitis Virus Stem-Loop 2 Adopts a uYNMG(U)a-Like Tetraloop Structure That Is Highly Functionally Tolerant of Base Substitutions
Authors: Liu Pinghua , Li Lichun , Keane Sarah C. , Yang Dong , Leibowitz Julian L. , Giedroc David P.
Published: September 2009

Stem-loop 2 (SL2) of the 5′-untranslated region of the mouse hepatitis virus (MHV) contains a highly conserved pentaloop (C47-U48-U49-G50-U51) stacked on a 5-bp stem. Solution nuclear magnetic resonance experiments are consistent with a 5′-uYNMG(U)a or uCUYG(U)a tetraloop conformation characterized by an
anti
-C47-
syn
-G50 base-pairing interaction, with U51 flipped out into solution and G50 stacked on A52. Previous studies showed that U48C and U48A substitutions in MHV SL2 were lethal, while a U48G substitution was viable. Here, we characterize viruses harboring all remaining single-nucleotide substitutions in the pentaloop of MHV SL2 and also investigate the degree to which the sequence context of key pentaloop point mutations influences the MHV replication phenotype. U49 or U51 substitution mutants all are viable; C47 substitution mutants also are viable but produce slightly smaller plaques than wild-type virus. In contrast, G50A and G50C viruses are severely crippled and form much smaller plaques. Virus could not be recovered from G50U-containing mutants; rather, only true wild-type revertants or a virus, G50U/C47A, containing a second site mutation were recovered. These functional data suggest that the Watson-Crick edges of C47 and G50 (or A47 and U50 in the G50U/C47A mutant) are in close enough proximity to a hydrogen bond with U51 flipped out of the hairpin. Remarkably, increasing the helical stem stability rescues the previously lethal mutants U48C and G50U. These studies suggest that SL2 functions as an important, but rather plastic, structural element in stimulating subgenomic RNA synthesis in coronaviruses.
Identification and Characterization of Broadly Neutralizing Human Monoclonal Antibodies Directed against the E2 Envelope Glycoprotein of Hepatitis C Virus
Authors: Broering Teresa J. , Garrity Kerry A. , Boatright Naomi K. , Sloan Susan E. , Sandor Frantisek , Thomas William D. , Szabo Gyongyi , Finberg Robert W. , Ambrosino Donna M. , Babcock Gregory J.
Published: September 2009

Nearly all livers transplanted into hepatitis C virus (HCV)-positive patients become infected with HCV, and 10 to 25% of reinfected livers develop cirrhosis within 5 years. Neutralizing monoclonal antibody could be an effective therapy for the prevention of infection in a transplant setting. To pursue this treatment modality, we developed human monoclonal antibodies (HuMAbs) directed against the HCV E2 envelope glycoprotein and assessed the capacity of these HuMAbs to neutralize a broad panel of HCV genotypes. HuMAb antibodies were generated by immunizing transgenic mice containing human antibody genes (HuMAb mice; Medarex Inc.) with soluble E2 envelope glycoprotein derived from a genotype 1a virus (H77). Two HuMAbs, HCV1 and 95-2, were selected for further study based on initial cross-reactivity with soluble E2 glycoproteins derived from genotypes 1a and 1b, as well as neutralization of lentivirus pseudotyped with HCV 1a and 1b envelope glycoproteins. Additionally, HuMAbs HCV1 and 95-2 potently neutralized pseudoviruses from all genotypes tested (1a, 1b, 2b, 3a, and 4a). Epitope mapping with mammalian and bacterially expressed proteins, as well as synthetic peptides, revealed that HuMAbs HCV1 and 95-2 recognize a highly conserved linear epitope spanning amino acids 412 to 423 of the E2 glycoprotein. The capacity to recognize and neutralize a broad range of genotypes, the highly conserved E2 epitope, and the fully human nature of the antibodies make HuMAbs HCV1 and 95-2 excellent candidates for treatment of HCV-positive individuals undergoing liver transplantation.
Identification of Proteins fromPrunus persicaThat Interact with Peach Latent Mosaic Viroid
Authors: Dubé Audrey , Bisaillon Martin , Perreault Jean-Pierre
Published: September 2009

Peach latent mosaic viroid (PLMVd) is a small, single-stranded, circular RNA pathogen that infectsPrunus persicatrees. As with all other known viroids, the PLMVd genome does not encode any proteins. Consequently, it must interact with host cellular factors in order to ensure its life cycle. With the objective of identifying cellular proteins that interact with PLMVd, Northwestern hybridizations were performed using partially purified peach leaf extracts. Mass spectrometric analysis of the detected RNA-protein complexes led to the identification of six putative RNA-binding proteins. One of these was found to be elongation factor 1-alpha (eEF1A), and because of its known involvement in the replication and translation of various RNA viruses, further characterizations were performed. Initially, the existence of this interaction received support from an experiment that immunoprecipitated the eEF1A from a crude extract of infected peach leaves, coupled with reverse transcription-PCR detection of the PLMVd. Subsequently, eEF1A interaction with PLMVd strands of both polarities was confirmed in vitro by electrophoresis mobility shift assays, fluorescence spectroscopy, and the prediction of an altered PLMVd RNase mapping profile in the presence of the protein. The potential contribution of eEF1A to the molecular biology of PLMVd, including for viroid replication, is discussed.
Reticuloendotheliosis Virus Strain T Induces miR-155, Which Targets JARID2 and Promotes Cell Survival
Authors: Bolisetty Mohan T. , Dy George , Tam Wayne , Beemon Karen L.
Published: September 2009

The oncogenic microRNA miR-155 is upregulated by several oncogenic viruses. The precursor of miR-155, termedbic, was first observed to cooperate withmycin chicken B-cell lymphomas induced by avian leukosis proviral integrations. We identified another oncogenic retrovirus, reticuloendotheliosis virus strain T (REV-T), that upregulates miR-155 in chicken embryo fibroblasts. We also observed very high levels of miR-155 in REV-T-induced B-cell lymphomas. To study the role of miR-155 in these tumors, we identified JARID2/Jumonji, a cell cycle regulator and part of a histone methyltransferase complex, as a target of miR-155. The overexpression of miR-155 decreased levels of endogenous JARID2 mRNA. We confirmed that miR-155 directly targets both human and chicken JARID2 by assaying the repression of reporters containing the JARID2 3′-untranslated regions. Further, the overexpression of a sponge complementary to miR-155 in a tumor cell line increased endogenous JARID2 mRNA levels. The overexpression of JARID2 in chicken fibroblasts led to decreased cell numbers and an increase in apoptotic cells. The overexpression of miR-155 rescued cells undergoing cytopathic effect caused by infection with subgroup B avian retroviruses. Therefore, we propose that miR-155 has a prosurvival function that is mediated through the downregulation of targets including JARID2.
Dephosphorylation of eIF2α Mediated by the γ
1
34.5 Protein of Herpes Simplex Virus 1 Facilitates Viral Neuroinvasion
Authors: Verpooten Dustin , Feng Zongdi , Valyi-Nagy Tibor , Ma Yijie , Jin Huali , Yan Zhipeng , Zhang Cuizhu , Cao Youjia , He Bin
Published: September 2009

The γ
1
34.5 protein, a virulence factor of herpes simplex viruses, redirects protein phosphatase 1 to dephosphorylate the α subunit of translation initiation factor 2 (eIF2α). Additionally, it inhibits the induction of antiviral genes by TANK-binding kinase 1. Nevertheless, its precise role in vivo remains to be established. Here we show that eIF2α dephosphorylation by γ
1
34.5 is crucial for viral neuroinvasion. V
193
E and F
195
L substitutions in γ
1
34.5 abrogate viral replication in the eye and spread to the trigeminal ganglia and brain. Intriguingly, inhibition of antiviral gene induction by γ
1
34.5 is not sufficient to exhibit viral virulence.
Maribavir Inhibits Epstein-Barr Virus Transcription in Addition to Viral DNA Replication
Authors: Wang Fu-Zhang , Roy Debasmita , Gershburg Edward , Whitehurst Christopher B. , Dittmer Dirk P. , Pagano Joseph S.
Published: September 2009

Although many drugs inhibit the replication of Epstein-Barr virus (EBV) in cell culture systems, there is still no drug that is effective and approved for use in primary EBV infection. More recently, maribavir (MBV), an
l
-ribofuranoside benzimidazole, has been shown to be a potent and nontoxic inhibitor of EBV replication and to have a mode of action quite distinct from that of acyclic nucleoside analogs such as acyclovir (ACV) that is based primarily on MBV's ability to block the phosphorylation of target proteins by EBV and human cytomegalovirus protein kinases. However, since the antiviral mechanisms of the drug are complex, we have carried out a comprehensive analysis of the effects of MBV on the RNA expression levels of all EBV genes with a quantitative real-time reverse transcription-PCR-based array. We show that in comparisons with ACV, the RNA expression profiles produced by the two drugs are entirely different, with MBV causing a pronounced inhibition of multiple viral mRNAs and with ACV causing virtually none. The results emphasize the different modes of action of the two drugs and suggest that the action of MBV may be linked to indirect effects on the transcription of EBV genes through the interaction of BGLF4 with multiple viral proteins.
STABILITY OF EXCESS DEMAND FUNCTIONS WITH RESPECT TO A STRONG VERSION OF WALD'S AXIOM
Authors: AN PHAN THANH , BINH VUONG THI THAO
Published: September 2009

In this paper, a use of s-quasimonotonicity [introduced in Optimization, Vol. 55 (2006)] in an economics model is presented. We introduce a strong version of Wald's Axiom of excess demand functions [Formula: see text], namely "there exists σ > 0 such that p, q ∈ P, qT Z(p) - δ ≤ 0,|δ| < σ, and Z(q) ≠ Z(p) imply pTZ(q) + δ > 0". Under some assumptions, Z satisfies the strong version of Wald's Axiom iff -Z is a s-quasimonotone function. Consequently, an excess demand function Z satisfies the strong version of Wald's Axiom iff -Z is stable with respect to the pseudomonotonicity property (i.e. there exists ∊ > 0 such that -Z + a fulfills the pseudomonotonicity property for all a ∈ ℝn satisfying ‖a‖ < ∊). Some properties on the measure of the strong version of Wald's Axiom of excess demand functions are also presented.
THE SARS CRISIS IN HONG KONG: A FEMINIST CHALLENGE TO SOCIAL POLICY
Authors: LEUNG LAI-CHING
Published: September 2009

This paper concerns the risk that women faced during the outbreak of Severe Acute Respiratory Syndrome (SARS) in Hong Kong in 2003. The concept of a "risk society", which is developed by Ulrich Beck, has made a major contribution to our understanding of the SARS crisis. He points out that risk is not equally distributed among all people in society, but adheres to patterns that are based on class and gender. He also suggests that the increasing trend of individualization has created a set of obligations and responsibilities to people, any individuals who failed to avoid risk are seen as personal failure and to be blamed. During the SARS crisis, women were more likely to be infected by the virus, as the primary care takers of the family, in the community, and being health care workers in hospitals. However, women were at risk not only due to their role as carers, but the dominant and authoritative discourses that undermined their claims for protection. This paper attempts to deconstruct the discourses of the roles of women in health crises, and to discuss how the discourses interplay with other social structures to construct a "reality", to marginalise and silent women in a crisis situation.
Cellulolytic Systems in Insects
Authors: Watanabe Hirofumi , Tokuda Gaku
Published: September 2009

Despite the presence of many carbohydrolytic activities in insects, their cellulolytic mechanisms are poorly understood. Whereas cellulase genes are absent from the genomes of Drosophila melanogaster or Bombyx mori, other insects such as termites produce their own cellulases. Recent studies using molecular biological techniques have brought new insights into the mechanisms by which the insects and their microbial symbionts digest cellulose in the small intestine. DNA sequences of cellulase and associated genes, as well as physiological and morphological information about the digestive systems of cellulase-producing insects, may allow the efficient use of cellulosic biomass as a sustainable energy source.
Advances in Estuarine Physics
Authors: MacCready Parker , Geyer W. Rockwell
Published: September 2009

Recent advances in our understanding of estuarine circulation and salinity structure are reviewed. We focus on well- and partially mixed systems that are long relative to the tidal excursion. Dynamics of the coupled system of width- and tidally averaged momentum and salt equations are now better understood owing to the development of simple numerical solution techniques. These have led to a greater appreciation of the key role played by the time dependency of the length of the salt intrusion. Improved realism in simplified tidally averaged physics has been driven by simultaneous advances in our understanding of the detailed dynamics within the tidal cycle and across irregular channel cross-sections. The complex interactions of turbulence, stratification, and advection are now understood well enough to motivate a new generation of physically plausible mixing parameterizations for the tidally averaged equations.
Sea Surface Temperature Variability: Patterns and Mechanisms
Authors: Deser Clara , Alexander Michael A. , Xie Shang-Ping , Phillips Adam S.
Published: September 2009

Patterns of sea surface temperature (SST) variability on interannual and longer timescales result from a combination of atmospheric and oceanic processes. These SST anomaly patterns may be due to intrinsic modes of atmospheric circulation variability that imprint themselves upon the SST field mainly via surface energy fluxes. Examples include SST fluctuations in the Southern Ocean associated with the Southern Annular Mode, a tripolar pattern of SST anomalies in the North Atlantic associated with the North Atlantic Oscillation, and a pan-Pacific mode known as the Pacific Decadal Oscillation (with additional contributions from oceanic processes). They may also result from coupled ocean-atmosphere interactions, such as the El Niño-Southern Oscillation phenomenon in the tropical Indo-Pacific, the tropical Atlantic Niño, and the cross-equatorial meridional modes in the tropical Pacific and Atlantic. Finally, patterns of SST variability may arise from intrinsic oceanic modes, notably the Atlantic Multidecadal Oscillation.
Maternal nutrient restriction during early fetal kidney development attenuates the renal innate inflammatory response in obese young adult offspring
Authors: Sharkey Don , Gardner David S. , Symonds Michael E. , Budge Helen
Published: September 2009

Obesity is an independent risk factor for developing chronic kidney disease. Toll-like receptor 4 (TLR4), interleukin (IL)-18, and uncoupling protein 2 (UCP2) are important components of the innate immune system mediating inflammatory renal damage. Early to midgestation maternal nutrient restriction appears to protect the kidney from the deleterious effects of early onset obesity, although the mechanisms remain unclear. We examined the combined effects of gestational maternal nutrient restriction during early fetal kidney development and early onset obesity on the renal innate immune response in offspring. Pregnant sheep were randomly assigned to a normal (control, 100%) or nutrient-restricted (NR, 50%) diet from days 30 to 80 gestation and 100% thereafter. Offspring were killed humanely at 7 days or, following rearing in an obesogenic environment, at 1 yr of age, and renal tissues were collected. IL-18 and TLR4 expression were strongly correlated irrespective of intervention. Seven-day NR offspring had significantly lower relative renal mass and IL-18 mRNA expression. At 1 yr of age, obesity resulted in increased mRNA abundance of TLR4, IL-18, and UCP2, coupled with tubular atrophy and greater immunohistological staining of glomerular IL-6 and medullary tumor necrosis factor (TNF)-α. NR obese offspring had a marked reduction of TLR4 abundance and renal IL-6 staining. In conclusion, maternal nutrient restriction during early fetal kidney development attenuates the effects of early onset obesity-related nephropathy, in part, through the downregulation of the innate inflammatory response. A better understanding of maternal nutrition and the in utero nutritional environment may offer therapeutic strategies aimed at reducing the burden of later kidney disease.
A Role for the Clock Gene Per1 in Prostate Cancer
Authors: Cao Qi , Gery Sigal , Dashti Azadeh , Yin Dong , Zhou Yan , Gu Jiang , Koeffler H. Phillip
Published: September 2009

Circadian rhythms regulate diverse physiologic processes, including homeostatic functions of steroid hormones and their receptors. Perturbations of these rhythms are associated with pathogenic conditions, such as depression, diabetes, and cancer. Androgens play an important role in both normal development and carcinogenesis of the prostate. In the present study, we investigated a potential role for the core clock factor Per1 in the pathogenesis of prostate cancer. Serum-shocked synchronized prostate cancer cells displayed disrupted circadian rhythms compared with the normal prostate tissue. Using Oncomine to perform a meta-analysis of microarray expression studies, we found that Per1 is down-regulated in human prostate cancer samples compared with normal prostates. Reporter assays showed that Per1 inhibited transactivation of the androgen receptor (AR) both in 293T cells overexpressing the AR and in the prostate cancer cell line LNCaP. Forced expression of Per1 in LNCaP cells diminished the expression of known androgen-sensitive genes following stimulation with dihydrotestosterone. We showed that Per1 physically interacted with AR; in addition, we found that Per1 itself is regulated by androgens in prostate cancer cells. Overexpression of Per1 in prostate cancer cells resulted in significant growth inhibition and apoptosis. Our results support the emerging role of circadian genes as key players in malignant transformation. Further elucidating the connections between clock genes and the AR pathway could benefit the development of new therapeutic strategies for prostate cancer as well as provide insights into chronotherapy as a way to optimize current therapies. [Cancer Res 2009;69(19):7619–25]
Lessons from Applied Ecology: Cancer Control Using an Evolutionary Double Bind
Authors: Gatenby Robert A. , Brown Joel , Vincent Thomas
Published: September 2009

Because the metastatic cascade is largely governed by the ability of malignant cells to adapt and proliferate at the distant tissue site, we propose that disseminated cancers are analogous in many important ways to the evolutionary and ecological dynamics of exotic species. Although pests can be decimated through the application of chemical toxins, this strategy virtually never achieves robust control as evolution of resistant phenotypes typically permits population recovery to pretreatment levels. In general, biological strategies that introduce predators, parasitoids, or pathogens have achieved more durable control of pest populations even after emergence of resistant phenotypes. From this we propose that long term outcome from any treatment strategy for invasive pests, including cancer, is not limited by evolution of resistance, but rather by the phenotypic cost of that resistance. If a cancerous cell's adaptation to therapy is achieved by upregulating xenobiotic metabolism or a redundant signaling pathway, the required investment in resources is small, and the original malignant phenotype remains essentially intact. As a result, the cancer cells' initial high level of fitness is little changed and unconstrained proliferation will resume once resistance evolves. Robust population control is possible if resistance to therapy requires a substantial and costly phenotypic adaptation that also significantly reduces the organism's fitness in its original niche: an evolutionary double bind. [Cancer Res 2009;69(19):7499–502]
Metformin Selectively Targets Cancer Stem Cells, and Acts Together with Chemotherapy to Block Tumor Growth and Prolong Remission
Authors: Hirsch Heather A. , Iliopoulos Dimitrios , Tsichlis Philip N. , Struhl Kevin
Published: September 2009

The cancer stem cell hypothesis suggests that, unlike most cancer cells within a tumor, cancer stem cells resist chemotherapeutic drugs and can regenerate the various cell types in the tumor, thereby causing relapse of the disease. Thus, drugs that selectively target cancer stem cells offer great promise for cancer treatment, particularly in combination with chemotherapy. Here, we show that low doses of metformin, a standard drug for diabetes, inhibits cellular transformation and selectively kills cancer stem cells in four genetically different types of breast cancer. The combination of metformin and a well-defined chemotherapeutic agent, doxorubicin, kills both cancer stem cells and non–stem cancer cells in culture. Furthermore, this combinatorial therapy reduces tumor mass and prevents relapse much more effectively than either drug alone in a xenograft mouse model. Mice seem to remain tumor-free for at least 2 months after combinatorial therapy with metformin and doxorubicin is ended. These results provide further evidence supporting the cancer stem cell hypothesis, and they provide a rationale and experimental basis for using the combination of metformin and chemotherapeutic drugs to improve treatment of patients with breast (and possibly other) cancers. [Cancer Res 2009;69(19):7507–11]
Wnt Antagonist Gene DKK2 Is Epigenetically Silenced and Inhibits Renal Cancer Progression through Apoptotic and Cell Cycle Pathways
Authors: Hirata Hiroshi , Hinoda Yuji , Nakajima Koichi , Kawamoto Ken , Kikuno Nobuyuki , Kawakami Kazumori , Yamamura Soichiro , Ueno Koji , Majid Shahana , Saini Sharanjot , Ishii Nobuhisa , Dahiya Rajvir
Published: September 2009

Purpose: Wnt/β-catenin signaling is involved in renal cancer. DKK2, a Wnt antagonist, is silenced in some cancers, although its function has not been investigated. We hypothesized that DKK2 may be epigenetically silenced and inhibits progression of renal cell carcinoma (RCC).

Experimental Design: RCC cell lines and a normal kidney cell line were used for methylation and chromatin immunoprecipitation assays. To assess various functions of DKK2, we established stable DKK2-transfected cells and examined them with regard to cell viability, colony formation, apoptosis, cell cycle, and invasive capability. A total of 52 patients with confirmed conventional RCC were enrolled in this study.

Results: RCC cell lines had decreased levels of DKK2, which were significantly increased after treatment with 5-Aza-2′-deoxycytidine alone or 5-Aza-2′-deoxycytidine and trichostatin A. In chromatin immunoprecipitation assay, the levels of acetyl H3, acetyl H4, and dimethylated H3K4 were decreased, whereas the level of dimethylated H3K9 was increased in RCC cell lines compared with HK2 cells. Increased methylation in RCC tissues was associated with higher grades, pathologic stages, and pathologic tumor in RCC. Functional analysis showed that the numbers of viable A498 cells were significantly decreased in DKK2-transfected cells compared with mock cells. The number of apoptotic cells and S/G2-M phase cells was significantly increased and decreased after DKK2 transfection, respectively. Corresponding to these results, Bcl2 and cyclin D1 expression were also decreased in DKK2-overexpressing cells.

Conclusion: DKK2 is epigenetically silenced by methylation in higher grades and stages of RCC. These results suggest that DKK2 inhibits renal cancer progression through apoptotic and cell cycle pathways. (Clin Cancer Res 2009;15(18):5678–87)