bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure of sodium above 100 GPa by single-crystal x-ray diffraction
Authors: McMahon M. I. , Gregoryanz E. , Lundegaard L. F. , Loa I. , Guillaume C. , Nelmes R. J. , Kleppe A. K. , Amboage M. , Wilhelm H. , Jephcoat A. P.
Published: October 2007

At pressures above a megabar (100 GPa), sodium crystallizes in a number of complex crystal structures with unusually low melting temperatures, reaching as low as 300 K at 118 GPa. We have utilized this unique behavior at extreme pressures to grow a single crystal of sodium at 108 GPa, and have investigated the complex crystal structure at this pressure using high-intensity x-rays from the new Diamond synchrotron source, in combination with a pressure cell with wide angular apertures. We confirm that, at 108 GPa, sodium is isostructural with the
cI
16 phase of lithium, and we have refined the full crystal structure of this phase. The results demonstrate the extension of single-crystal structure refinement beyond 100 GPa and raise the prospect of successfully determining the structures of yet more complex phases reported in sodium and other elements at extreme pressures.
Encoding and Maintaining Reference in Oral Discourse
Authors: Canoz Florence , Vion Monique
Published: October 2007

This study deals with information management and reference encoding modes in oral discourse production. Three potentially influential factors were the distance between the first occurrence of an item and its later occurrences, a topic change that takes the focus off that item, and the span of the conceptual information available for verbalization. French‐speaking adult subjects were asked to tell stories from comic strips to a listener who was unfamiliar with them. The frames in each strip were presented simultaneously or in succession. Four versions were generated for each comic strip: a given version was either short (three frames) or long (eight frames), and either did or did not have a topic change. The results showed that the target character was usually marked as a given, regardless of the version. This was more often true, however, when the topic did not change. When the character was treated as a given, referent accessibility marking was dependent on (1) topic change alone when the frames were presented simultaneously, and (2) topic change and comic strip length when the frames were presented in succession. The discussion analyzes the results in terms of the allocation of cognitive resources to maintaining coreference and to assisting addressees in their processing.
The Course of Representation in Memory During the Comprehension of Paragraphs
Authors: Hyodo Muneyoshi , Ny Jean‐François Le , Achour L'Hacène
Published: October 2007

The course of the representation built in memory from a text during comprehension of paragraphs was studied by a probe technique (immediate item recognition). Three experiments showed that response times, the main variable, gradually increase as a function of the lag between the probe (a word or an atomic proposition) and its target in the text. In Experiment 3 the same result was also found with a priming technique. The absence of any kick‐up over the course of time was confirmed by several additional analyses of individual data. The results were only weakly consistent with models assuming two distinct memory stores, in particular a specific “short‐term memory store,” but highly consistent with models involving semantic activation and subsequent gradual deactivation.
Is Written Language Production More Difficult Than Oral Language Production? A Working Memory Approach
Authors: Bourdin Béatrice , Fayol Michel
Published: October 2007

Is written language production more difficult than oral language production? Probably, yes. But why?

Several experiments were conducted in order to test the impact of low‐level activities involved in writing on the performance of higher‐level activities also involved in writing. Three assumptions were made: (1) the capacity of working‐memory is limited, (2) every component of writing has a cognitive load, and (3) every increase in the load devoted to the activity of one component would lead to a decrease in the remaining resources available for the other components. These low‐level activities are more resource‐consuming in children than in adults because children have not yet automated these activities. So, it was hypothezised that the difficulties encountered by children in dealing with the low‐level activities would have a negative impact on the performance of higher activities.

To test that hypothesis, a serial recall paradigm was used. Adults and children were asked to recall series of words, either orally or in writing. The results showed that: (1) serial recall of children, but not of adults, was weaker with writing as compared to speaking; (2) the slowness of writing relative to speaking did not explain these results; and (3) the difficulties of graphic and of orthographic transcription were partially responsible for these results.

These results are discussed in the general framework of production models.
Typicality of Interpersonal Situations: The Role of Affect in Determining Contextual Variations in Typicality Norms
Authors: Mallet Pascal , Cordier Françoise
Published: October 2007

This study deals with the relationship between affect and cognition. This relationship is conceptualized in the terms of Bower's (Bower & Cohen, 1982) theory. Subjects (early adolescents aged 12 or 14, boy or girl) were asked to imagine themselves as the actor in an interpersonal situation. The situation was either intimate or non‐intimate, and the hypothetical partner was either a boy or a girl. The subject's task was to produce a series of sentences expressing the behaviours considered representative of each situation.

The results indicated (1) the existence of a typicality hierarchy (whose characteristics are examined here) and (2) variations in this hierarchy according to the affective tone of the situation (intimate or non‐intimate). We explain how the cultural, interpersonal situation norms acquired by adolescents can account for these variations. Thus, contrary to what some authors contend, variations in typicality are not random.
Prevalence of and Risk Factors for Methicillin-ResistantStaphylococcus aureusCarriage at Hospital Admission
Authors: Casas Irma , Sopena Nieves , Esteve Maria , Quesada Maria Dolores , Andrés Isabel , Matas Lourdes , Blanco Silvia , Pedro-Botet Maria Luisa , Caraballo Montse , Ausina Vicente , Sabrià Miquel
Published: October 2007

To determine the prevalence of and risk factors for methicillin-resistantStaphylococcus aureus(MRSA) carriage at the time of admission to our hospital, we screened the medical records of 1,128 patients for demographic and clinical data. The antimicrobial resistance pattern and genotype of MRSA isolates were studied. The prevalence of MRSA carriage at hospital admission was 1.4%. Older patients and patients previously admitted to healthcare centers were the most likely to have MRSA carriage at admission.
Inconsistency in Classical Electrodynamics?
Authors: Muller F. A.
Published: October 2007

In a recent issue of this journal, M. Frisch claims to have proven that classical electrodynamics is an inconsistent physical theory. We argue that he has applied classical electrodynamics inconsistently. Frisch also claims that all other classical theories of electromagnetic phenomena, when consistent and in some sense an approximation of classical electrodynamics, are haunted by “serious conceptual problems” that defy resolution. We argue that this claim is based on a partisan if not misleading presentation of theoretical research in classical electrodynamics.
Clostridium difficile-Associated Disease in Patients in a Small Rural Hospital
Authors: Kuntz Jennifer L. , Cavanaugh Joseph E. , Becker Laura K. , Ward Melissa A. , Appelgate Dianna M. , Herwaldt Loreen A. , Polgreen Philip M.
Published: October 2007

Objective.

To determine the risk factors for Clostridium difficile–associated disease (CDAD) in a 25-bed rural hospital and to compare antimicrobial use ratios at the study hospital with those at a large academic medical center.

Design.

Case-control study.

Setting.

A 25-bed rural hospital in Iowa during the period from August 2002 through January 2005.

Patients.

A total of 17 case patients with CDAD and 34 control patients matched for age (ie, within 10 years of the case patient's age), sex, and admission date (ie, within 2 weeks of the case patient's admission date).

Methods.

Retrospective medical record review was performed to obtain data on antimicrobial exposures during the 6 weeks before hospital admission for both case and control patients. Exact conditional logistic regression was used for univariable and multivariable analyses. Antimicrobial use ratios were calculated to compare the rates of antimicrobial use for case and control patients at the study hospital with the rates for patients evaluated in a study of CDAD at a nearly 700-bed teaching hospital.

Results.

Case patients had a larger cumulative number of days of antimicrobial use (P = .004), and they received a larger total number of antimicrobial agents during hospitalization (P = .001). Antimicrobial use ratios were higher for both case and control patients at the smaller hospital, compared with the larger hospital.

Conclusions.

CDAD at a small rural hospital was not associated with exposure to the antimicrobial classes that are typically associated with CDAD, but was instead related to the total number of antimicrobials used to treat patients. The rate of antimicrobial use for case and control patients was about 40% higher at the small rural hospital, compared with the corresponding rates at a large academic medical center.
Outbreak of Burkholderia cepacia Bloodstream Infection at an Outpatient Hematology and Oncology Practice
Authors: Abe Karon , D'Angelo Melissa Tobin , Sunenshine Rebecca , Noble-Wang Judith , Cope James , Jensen Bette , Srinivasan Arjun
Published: October 2007

We investigated an outbreak of infection in 10 patients with blood cultures positive for B. cepacia. All patients had indwelling intravenous catheters. Though we did not identify the source of the organism, our findings support the hypothesis that cross-contamination of multidose medications through the use of the same needle and syringe was a contributing factor.
Increasing Prevalence of Gastrointestinal Colonization With Ceftazidime-Resistant Gram-Negative Bacteria Among Intensive Care Unit Patients
Authors: Thom Kerri A. , Johnson Judith A. , Strauss Sandra M. , Furuno Jon P. , Perencevich Eli N. , Harris Anthony D.
Published: October 2007

Background.

The occurrence of nosocomial infections due to third-generation cephalosporin–resistant gram-negative bacteria is increasing. Gastrointestinal colonization is an important reservoir for antibiotic-resistant bacteria, and it often precedes clinical infection.

Objective.

To estimate the prevalence of gastrointestinal colonization with ceftazidime-resistant gram-negative bacteria among intensive care unit (ICU) patients at a university-affiliated tertiary-care hospital during 2 distinct periods and to assess whether, at any time during the index hospitalization, colonized patients had a clinical culture positive for the same organism that was recovered from surveillance culture.

Setting.

Two ICUs at the University of Maryland Medical Center, a 656-bed tertiary-care hospital located in Baltimore, Maryland. Both ICUs provide care to adult patients.

Methods.

We performed a cross-sectional study of adult patients admitted to the medical ICU or the surgical ICU from June 14 to July 14, 2003, and from June 14 to July 14, 2006. Perirectal swab samples were obtained for surveillance culture on admission to the intensive care unit, weekly thereafter, and at discharge. Each culture sample was plated onto MacConkey agar supplemented with ceftazidime.

Results.

In 2003, a total of 33 (18.8%) of 176 patients were colonized with ceftazidime-resistant gram-negative bacilli; in 2006, 60 (31.4%) of 191 patients were (P<.01). This increase was largely driven by an increase in ceftazidime-resistantKlebsiellaisolates (which accounted for 6.4% of isolates in 2003 and for 22.8% in 2006;P<.01). In 2003, a total of 16 (48.5%) of 33 colonized patients had a clinical culture positive for the same organism that was recovered from the perirectal surveillance culture, compared with 22 (36.6%) of 60 colonized patients in 2006 (P= .28).

Conclusion.

Our data suggest that gastrointestinal colonization with ceftazidime-resistant gram-negative bacilli is common, that its prevalence is increasing, and that colonization may result in clinical cultures positive for these bacilli.
Endocytic Trafficking of Sphingomyelin Depends on Its Acyl Chain Length
Authors: Koivusalo Mirkka , Jansen Maurice , Somerharju Pentti , Ikonen Elina
Published: October 2007

To study the principles of endocytic lipid trafficking, we introduced pyrene sphingomyelins (PyrSMs) with varying acyl chain lengths and domain partitioning properties into human fibroblasts or HeLa cells. We found that a long-chain, ordered-domain preferring PyrSM was targeted Hrs and Tsg101 dependently to late endosomal compartments and recycled to the plasma membrane in an NPC1- and cholesterol-dependent manner. A short-chain, disordered domain preferring PyrSM recycled more effectively, by using Hrs-, Tsg101- and NPC1-independent routing that was insensitive to cholesterol loading. Similar chain length-dependent recycling was observed for unlabeled sphingomyelins (SMs). The findings 1) establish acyl chain length as an important determinant in the endocytic trafficking of SMs, 2) implicate ESCRT complex proteins and NPC1 in the endocytic recycling of ordered domain lipids to the plasma membrane, and 3) introduce long-chain PyrSM as the first fluorescent lipid tracing this pathway.
Cooperative Assembly of CYK-4/MgcRacGAP and ZEN-4/MKLP1 to Form the Centralspindlin Complex
Authors: Pavicic-Kaltenbrunner Visnja , Mishima Masanori , Glotzer Michael
Published: October 2007

Cytokinesis in metazoan cells requires a set of antiparallel microtubules that become bundled upon anaphase onset to form a structure known as the central spindle. Bundling of these microtubules requires a protein complex, centralspindlin, that consists of the CYK-4/MgcRacGAP Rho-family GTPase-activating protein and the ZEN-4/MKLP1 kinesin-6 motor protein. Centralspindlin, but not its individual subunits, is sufficient to bundle microtubules in vitro. Here, we present a biochemical and genetic dissection of centralspindlin. We show that each of the two subunits of centralspindlin dimerize via a parallel coiled coil. The two homodimers assemble into a high-affinity heterotetrameric complex by virtue of two low-affinity interactions. Conditional mutations in the regions that mediate complex assembly can be readily suppressed by numerous second site mutations in the interacting regions. This unexpected plasticity explains the lack of primary sequence conservation of the regions critical for this essential protein–protein interaction.
Identification of Yeast IQGAP (Iqg1p) as an Anaphase-Promoting-Complex Substrate and Its Role in Actomyosin-Ring-Independent Cytokinesis
Authors: Ko Nolan , Nishihama Ryuichi , Tully Gregory H. , Ostapenko Denis , Solomon Mark J. , Morgan David O. , Pringle John R.
Published: October 2007

In the yeast Saccharomyces cerevisiae, a ring of myosin II forms in a septin-dependent manner at the budding site in late G1. This ring remains at the bud neck until the onset of cytokinesis, when actin is recruited to it. The actomyosin ring then contracts, septum formation occurs concurrently, and cytokinesis is soon completed. Deletion of MYO1 (the only myosin II gene) is lethal on rich medium in the W303 strain background and causes slow-growth and delayed-cell-separation phenotypes in the S288C strain background. These phenotypes can be suppressed by deletions of genes encoding nonessential components of the anaphase-promoting complex (APC/C). This suppression does not seem to result simply from a delay in mitotic exit, because overexpression of a nondegradable mitotic cyclin does not suppress the same phenotypes. Overexpression of either IQG1 or CYK3 also suppresses the myo1Δ phenotypes, and Iqg1p (an IQGAP protein) is increased in abundance and abnormally persistent after cytokinesis in APC/C mutants. In vitro assays showed that Iqg1p is ubiquitinated directly by APC/CCdh1via a novel recognition sequence. A nondegradable Iqg1p (lacking this recognition sequence) can suppress the myo1Δ phenotypes even when expressed at relatively low levels. Together, the data suggest that compromise of APC/C function allows the accumulation of Iqg1p, which then promotes actomyosin-ring-independent cytokinesis at least in part by activation of Cyk3p.
The Function of Mitochondria in Presynaptic Development at the Neuromuscular Junction
Authors: Lee Chi Wai , Peng H. Benjamin
Published: October 2007

Mitochondria with high membrane potential (ΔΨm) are enriched in the presynaptic nerve terminal at vertebrate neuromuscular junctions, but the exact function of these localized synaptic mitochondria remains unclear. Here, we investigated the correlation between mitochondrial ΔΨmand the development of synaptic specializations. Using mitochondrial ΔΨm-sensitive probe JC-1, we found that ΔΨmin Xenopus spinal neurons could be reversibly elevated by creatine and suppressed by FCCP. Along naïve neurites, preexisting synaptic vesicle (SV) clusters were positively correlated with mitochondrial ΔΨm, suggesting a potential regulatory role of mitochondrial activity in synaptogenesis. Indicating a specific role of mitochondrial activity in presynaptic development, mitochondrial ATP synthase inhibitor oligomycin, but not mitochondrial Na+/Ca2+exchanger inhibitor CGP-37157, inhibited the clustering of SVs induced by growth factor–coated beads. Local F-actin assembly induced along spinal neurites by beads was suppressed by FCCP or oligomycin. Our results suggest that a key role of presynaptic mitochondria is to provide ATP for the assembly of actin cytoskeleton involved in the assembly of the presynaptic specialization including the clustering of SVs and mitochondria themselves.
p21 Inhibits Cdk1 in the Absence of Cdk2 to Maintain the G1/S Phase DNA Damage Checkpoint
Authors: Satyanarayana Ande , Hilton Mary Beth , Kaldis Philipp
Published: October 2007

Cdk1 was proposed to compensate for the loss of Cdk2. Here we present evidence that this is possible due to premature translocation of Cdk1 from the cytoplasm to the nucleus in the absence of Cdk2. We also investigated the consequence of loss of Cdk2 on the maintenance of the G1/S DNA damage checkpoint. Cdk2−/−mouse embryonic fibroblasts in vitro as well as regenerating liver cells after partial hepatectomy (PH) in Cdk2−/−mice, arrest promptly at the G1/S checkpoint in response to γ-irradiation due to activation of p53 and p21 inhibiting Cdk1. Furthermore re-entry into S phase after irradiation was delayed in Cdk2−/−cells due to prolonged and impaired DNA repair activity. In addition, Cdk2−/−mice were more sensitive to lethal irradiation compared to wild-type and displayed delayed resumption of DNA replication in regenerating liver cells. Our results suggest that the G1/S DNA damage checkpoint is intact in the absence of Cdk2, but Cdk2 is important for proper repair of the damaged DNA.
Hypoxia-inducible Factor-1α Stabilization in Nonhypoxic Conditions: Role of Oxidation and Intracellular Ascorbate Depletion
Authors: Pagé Elisabeth L. , Chan Denise A. , Giaccia Amato J. , Levine Mark , Richard Darren E.
Published: October 2007

Hypoxia-inducible factor-1 (HIF-1) is a decisive element for the transcriptional regulation of many genes induced under low oxygen conditions. Under normal oxygen conditions, HIF-1α, the active subunit of HIF-1, is hydroxylated on proline residues by specific HIF prolyl-hydroxylases, leading to ubiquitination and degradation by the proteasome. In hypoxia, hydroxylation and ubiquitination are blocked and HIF-1α accumulates in cells. Recent studies have shown that in normal oxygen conditions G-protein–coupled receptor agonists, including angiotensin (Ang) II and thrombin, potently induce and activate HIF-1 in vascular smooth muscle cells. The current study identifies HIF-1α protein stabilization as a key mechanism for HIF-1 induction by Ang II. We show that hydroxylation on proline 402 is altered by Ang II, decreasing pVHL binding to HIF-1α and allowing HIF-1α protein to escape subsequent ubiquitination and degradation mechanisms. We show that HIF-1α stability is mediated through the Ang II–mediated generation of hydrogen peroxide and a subsequent decrease in ascorbate levels, leading to decreased HIF prolyl-hydroxylase activity and HIF-1α stabilization. These findings identify novel and intricate signaling mechanisms involved in HIF-1 complex activation and will lead to the elucidation of the importance of HIF-1 in different Ang II–related cell responses.
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
Authors: Song Jiangning , Yuan Zheng , Tan Hao , Huber Thomas , Burrage Kevin
Published: October 2007

Motivation: Disulfide bonds are primary covalent crosslinks between two cysteine residues in proteins that play critical roles in stabilizing the protein structures and are commonly found in extracy-toplasmatic or secreted proteins. In protein folding prediction, the localization of disulfide bonds can greatly reduce the search in conformational space. Therefore, there is a great need to develop computational methods capable of accurately predicting disulfide connectivity patterns in proteins that could have potentially important applications.

Results: We have developed a novel method to predict disulfide connectivity patterns from protein primary sequence, using a support vector regression (SVR) approach based on multiple sequence feature vectors and predicted secondary structure by the PSIPRED program. The results indicate that our method could achieve a prediction accuracy of 74.4% and 77.9%, respectively, when averaged on proteins with two to five disulfide bridges using 4-fold cross-validation, measured on the protein and cysteine pair on a well-defined non-homologous dataset. We assessed the effects of different sequence encoding schemes on the prediction performance of disulfide connectivity. It has been shown that the sequence encoding scheme based on multiple sequence feature vectors coupled with predicted secondary structure can significantly improve the prediction accuracy, thus enabling our method to outperform most of other currently available predictors. Our work provides a complementary approach to the current algorithms that should be useful in computationally assigning disulfide connectivity patterns and helps in the annotation of protein sequences generated by large-scale whole-genome projects.

Availability: The prediction web server and Supplementary Material are accessible at http://foo.maths.uq.edu.au/~huber/disulfide

Contact:  kb@maths.uq.edu.au

Supplementary information: Supplementary data are available at Bioinformatics online.
Inhibitory Effects of Coptidis rhizoma and Berberine on Cocaine‐Induced Sensitization
Authors: Lee Bombi , Yang Chae Ha , Hahm Dae-Hyun , Choe Eun Sang , Lee Hye-Jung , Pyun Kwang-Ho , Shim Insop
Published: October 2007

Substantial evidence suggests that the behavioral and reinforcing effects of cocaine can be mediated by the central dopaminergic systems. Repeated injections of cocaine produce an increase in locomotor activity and the expression of tyrosine hydroxylase (TH) in the main dopaminergic areas. Protoberberine alkaloids affect neuronal functions. Coptidis rhizoma (CR) and its main compound, berberine (BER) reduced the dopamine content in the central nervous system. In order to investigate the effects of CR or BER on the repeated cocaine‐induced neuronal and behavioral alterations, we examined the influence of CR or BER on the repeated cocaine‐induced locomotor activity and the expression of TH in the brain by using immunohistochemistry. Male SD rats were given repeated injections of saline or cocaine hydrochloride (15 mg/kg, i.p. for 10 consecutive days) followed by one challenge injection on the 4th day after the last daily injection. Cocaine challenge (15 mg/kg, i.p) produced a larger increase in locomotor activity and expression of TH in the central dopaminergic areas. Pretreatment with CR (50, 100, 200 and 400 mg/kg, p.o.) and BER (200 mg/kg, p.o.) 30 min before the daily injections of cocaine significantly inhibited the cocaine‐induced locomotor activity as well as TH expression in the central dopaminergic areas. Our data demonstrate that the inhibitory effects of CR and BER on the repeated cocaine‐induced locomotor activity were closely associated with the reduction of dopamine biosynthesis and post‐synaptic neuronal activity. These results suggest that CR and BER may be effective for inhibiting the behavioral effects of cocaine by possibly modulating the central dopaminergic system.
Phytic Acid Exposure Alters AflatoxinB1‐Induced Reproductive and Oxidative Toxicity in Albino Rats (Rattus norvegicus)
Authors: Abu El-Saad Abdelaziz S. , Mahmoud Hamada M.
Published: October 2007

The increased use of feed in Egypt′s aquaculture and animal industries raises concerns about the possible presence of mycotoxins in feedstuffs. The use of alternative medicine, such as botanicals and nutritional supplements, has become popular with inflammatory cases. The present study aimed to testify the role played by phytic acid (IP6) in enhancing the reproductive and oxidative toxicity induced in aflatoxinB1 (AFB1) treated white male albino rats (Rattus norvegicus) throughout treatment and withdrawal periods. One hundred and twenty white male albino rats were grouped into four groups. Group 1, was injected with 300 μg kg−1 body wt of AFB1 once every 3 days for 15 days and left uninjected for another 15 days to study the withdrawal effect. Group 2, was injected with 300 μg kg−1 body wt of AFB1 once every 3 days for 15 days and treated simultaneously with IP6 daily for another 15 days. Group 3, was treated daily with IP6 (40 mg kg−1 body wt) for 15 days and with no treatment for other 15 days. Group 4, injected with equivalent volume of sterile phosphate buffer saline solution as a control group. Sera were taken at the experimental intervals and assayed for testosterone hormone, follicular‐stimulating hormone (FSH) and luteinizing hormone (LH) to determine the toxicological impact of AFB1 and the possibility of amelioration by phytic acid on the reproductive performance of the studied animal. The effects of AFB1 treatment on the absolute and relative weight of testis as well as its histopathologic effect on the testis and the possibility of amelioration by IP6 treatment were evaluated. The activities of enzymatic and non‐enzymatic anti‐oxidants, in addition to lipid peroxidation were measured in the testis’ homogenate of AFB1‐treated rats. A decrease in sex hormone levels, an increase in testicular lipid peroxidation product levels and a significant decrease in testicular glutathione content, catalase and total peroxidase and superoxide dismutase activities were recorded. The histopathologic alterations revealed a degeneration and highly mitotic division within the spermatogenic nuclei, in addition to some karyomegaly and nuclear pyknosis. It is concluded that the reduction in the toxicity of free radicals by phytic acid might be responsible for the protective influence observed.
Experimental study of impact oscillator with one-sided elastic constraint
Authors: Ing James , Pavlovskaia Ekaterina , Wiercigroch Marian , Banerjee Soumitro
Published: October 2007

In this paper, extensive experimental investigations of an impact oscillator with a one-sided elastic constraint are presented. Different bifurcation scenarios under varying the excitation frequency near grazing are shown for a number of values of the excitation amplitude. The mass acceleration signal is used to effectively detect contacts with the secondary spring. The most typical recorded scenario is when a non-impacting periodic orbit bifurcates into an impacting one via grazing mechanism. The resulting orbit can be stable, but in many cases it loses stability through grazing. Following such an event, the evolution of the attractor is governed by a complex interplay between smooth and non-smooth bifurcations. In some cases, the occurrence of coexisting attractors is manifested through discontinuous transition from one orbit to another through boundary crisis. The stability of non-impacting and impacting period-1 orbits is then studied using a newly proposed experimental procedure. The results are compared with the predictions obtained from standard theoretical stability analysis and a good correspondence between them is shown for different stiffness ratios. A mathematical model of a damped impact oscillator with one-sided elastic constraint is used in the theoretical studies.
Reconstructing slow-time dynamics from fast-time measurements
Authors: Chelidze David , Liu Ming
Published: October 2007

This paper considers a dynamical system subjected to damage evolution in variable operating conditions to illustrate the reconstruction of slow-time (damage) dynamics using fast-time (vibration) measurements. Working in the reconstructed fast-time phase space, phase space warping-based feature vectors are constructed for slow-time damage identification. A subspace of the feature space corresponding to the changes in the operating conditions is identified by applying smooth orthogonal decomposition (SOD) to the initial set of feature vectors. Damage trajectory is then reconstructed by applying SOD to the feature subspace not related to the changes in the operating conditions. The theory is validated experimentally using a vibrating beam, with a variable nonlinear potential field, subjected to fatigue damage. It is shown that the changes in the operating condition (or the potential field) can be successfully separated from the changes caused by damage (or fatigue) accumulation and SOD can identify the slow-time damage trajectory.
Severe acute respiratory syndrome coronavirus Orf3a protein interacts with caveolin
Authors: Padhan Kartika , Tanwar Charu , Hussain Amjad , Hui Pui Yan , Lee Man Yan , Cheung Chung Yan , Peiris Joseph Sriyal Malik , Jameel Shahid
Published: October 2007

Theorf3a(also called X1 or U274) gene is the largest unique open reading frame in the severe acute respiratory syndrome coronavirus genome and has been proposed to encode a protein with three transmembrane domains and a large cytoplasmic domain. Recent work has suggested that the 3a protein may play a structural role in the viral life cycle, although the mechanisms for this remain uncharacterized. Here, the expression of the 3a protein in variousin vitrosystems is shown, it has been localized to the Golgi region and its membrane topology in transfected cells has been confirmed. Three potential caveolin-1-binding sites were reported to be present in the 3a protein. By using various biochemical, biophysical and genetic techniques, interaction of the 3a protein with caveolin-1 is demonstrated. Any one of the potential sites in the 3a protein was sufficient for this interaction. These results are discussed with respect to the possible roles of the 3a protein in the viral life cycle.
The Npro product of classical swine fever virus and bovine viral diarrhea virus uses a conserved mechanism to target interferon regulatory factor-3
Authors: Seago Julian , Hilton Louise , Reid Elizabeth , Doceul Virginie , Jeyatheesan Janan , Moganeradj Kartykayan , McCauley John , Charleston Bryan , Goodbourn Stephen
Published: October 2007

Classical swine fever virus(CSFV) is a member of the genusPestivirusin the familyFlaviviridae. The Nproproduct of CSFV targets the host's innate immune response and can prevent the production of type I interferon (IFN). The mechanism by which CSFV orchestrates this inhibition was investigated and it is shown that, like the related pestivirus bovine viral diarrhea virus (BVDV), this involves the Nproprotein targeting interferon regulatory factor-3 (IRF-3) for degradation by proteasomes and thus preventing IRF-3 from activating transcription from the IFN-βpromoter. Like BVDV, the steady-state levels of IRF-3 mRNA are not reduced markedly by CSFV infection or Nprooverexpression. Moreover, IFN-αstimulation of CSFV-infected cells induces the antiviral protein MxA, indicating that, as in BVDV-infected cells, the JAK/STAT pathway is not targeted for inhibition.
Estimating the temporal relationship between PrPSc detection and incubation period in experimental bovine spongiform encephalopathy of cattle
Authors: Arnold M. E. , Ryan J. B. M. , Konold T. , Simmons M. M. , Spencer Y. I. , Wear A. , Chaplin M. , Stack M. , Czub S. , Mueller R. , Webb P. R. , Davis A. , Spiropoulos J. , Holdaway J. , Hawkins S. A. C. , Austin A. R. , Wells G. A. H.
Published: October 2007

This study examines tissues from sequential-kill, time-course pathogenesis studies to refine estimates of the age at which disease-specific PrP (PrPSc) can first be detected in the central nervous system (CNS) and related peripheral nervous system ganglia of cattle incubating bovine spongiform encephalopathy (BSE). Such estimates are important for risk assessments of the age at which these tissues should be removed from cattle at slaughter to prevent human and animal exposure to BSE infection. Tissues were examined from cattle dosed orally with 100 or 1 g BSE-infected brain. Incubation period data for the doses were obtained from attack rate and the sequential-kill studies. A statistical model, fitted by maximum likelihood, accounted for the differences in the lognormal incubation period and the logistic probability of infection between different dose groups. Initial detection of PrPSc during incubation was invariably in the brainstem and the earliest was at 30 and 44 months post-exposure for the 100 g- and 1 g-dosed sequential-kill study groups, respectively. The point at which PrPSc in 50 % of the animals would be detected by immunohistochemistry applied to medulla–obex was estimated at 9.6 and 1.7 months before clinical onset for the 100 g- and 1 g-dosed cattle, respectively, with a low probability of detection in any of the tissues examined at more than 12 months before clinical onset. PrPSc was detected inconsistently in dorsal root ganglia, concurrent with or after detection in CNS, and not at all in certain sympathetic nervous system ganglia.
Early and late gene expression in pepper huasteco yellow vein virus
Authors: Shimada-Beltrán Harumi , Rivera-Bustamante Rafael F.
Published: October 2007

Viral infections usually take place in an orderly manner and can be divided into at least two phases: an early and a late stage. In geminiviruses, plant viruses with a circular, single-stranded DNA genome, expression of viral genes involves complex regulation strategies that suggest the existence of a pattern of temporal gene expression. In this work, the transcription of pepper huasteco yellow vein virus (PHYVV) genes was studied. Green fluorescent protein replacements and RT-PCR analyses were used to monitor PHYVV gene expression chronologically in suspension cells and plant tissue. A model is proposed to describe the order of geminivirus gene expression, where the genes that encode Rep, TrAP and REn are expressed during an early stage of infection. The genes that encode the coat protein and the nuclear shuttle protein are expressed during the late stage of infection.
Transcription-termination-mediated immunity and its prevention in bacteriophage SfV of Shigella flexneri
Authors: Roberts Fleur , Allison Gwen E. , Verma Naresh K.
Published: October 2007

The temperate phage SfV encodes the genes responsible for the serotype conversion of Shigella flexneri strains from serotype Y to 5a. Bacteriophages often encode proteins that prevent subsequent infection by homologous phages; the mechanism by which this is accomplished is referred to as superinfection immunity. The serotype conversion mediated following lysogenization of SfV is one such mechanism. Another mechanism is the putative λ-like CI protein within SfV. This study reports the characterization of a third superinfection mechanism, transcription termination, in SfV. The presence of a small immunity-mediating RNA molecule, called CI RNA, and its essential role in the establishment of immunity, is shown. The novel role of the gene orf77, located immediately downstream from the transcription termination region, in inhibiting the establishment of CI RNA-mediated immunity is also presented.
Complete nucleotide sequence of Middelburg virus, isolated from the spleen of a horse with severe clinical disease in Zimbabwe
Authors: Attoui Houssam , Sailleau Corinne , Mohd Jaafar Fauziah , Belhouchet Mourad , Biagini Philippe , Cantaloube Jean François , de Micco Philippe , Mertens Peter , Zientara Stephan
Published: October 2007

The complete nucleotide sequence of Middelburg virus (MIDV) was determined for strain MIDV-857 from Zimbabwe. The isolation of this virus in 1993 from a horse that died showing severe clinical signs represents the first indication that MIDV can cause severe disease in equids. Full-length cDNA copies of the viral genome were successfully synthesized by an innovative RT-PCR amplification approach using an ‘anchor primer’ combined with the SMART methodology described previously for the synthesis of full-length cDNA copies from genome segments of dsRNA viruses. The MIDV-857 genome is 11 674 nt, excluding the 5′-terminal cap structure and poly(A) tail (which varies in length from approximately 180 to approximately 220 residues). The organization of the genome is like that of other alphaviruses, including a read-through stop codon between the nsP3 and nsP4 genes. However, phylogenetic analyses of the structural protein amino acid sequences suggested that the MIDV E1 gene was generated by recombination with a Semliki Forest virus-like virus. This hypothesis was supported by bootscanning analysis using a recombination-detection program. The 3′ untranslated region of MIDV-857 also contains a 112 nt duplication. This study reports the first full-length sequence of MIDV, which was obtained from a single RT-PCR product.
Mapping of putative virulence motifs on infectious salmon anemia virus surface glycoprotein genes
Authors: Kibenge Frederick S. B. , Kibenge Molly J. T. , Wang Yingwei , Qian Biao , Hariharan Shebel , McGeachy Sandi
Published: October 2007

Infectious salmon anemia virus (ISAV) is classified in the genus Isavirus of the family Orthomyxoviridae. Although virulence variation of ISAV can be demonstrated experimentally in fish, virus strain identification is ambiguous because the correlates of pathogenicity and/or antigenicity of ISAV are not well defined. Thirteen ISAV isolates characterized for their ability to kill fish were used to search for markers of virulence on the virus surface glycoprotein genes; haemagglutinin-esterase (HE) and fusion (F) protein genes. A single amino acid change N164D in the putative globular head of the HE protein, and a deletion/insertion of ≤13 aa with the presence of a specific motif 352FNT354 in the highly polymorphic region spanning residues 337V to M372 in the HE protein stalk, in combination with a specific motif 265YP266 very close to the trypsin-cleavage site 267RA/G268 of the precursor F0 protein were correlated with reduced cytopathogenicity and reduced virulence for Atlantic salmon. Phylogenetic analysis suggests that the original ancestral ISAV was virulent. The virulence of the North American genotype has not changed much, whereas the European genotype evolved into two genogroups, the real-European genogroup that is still virulent and the European-in-North America genogroup, which is of lower virulence. A novel phylogenetic software program, backtrack, estimated that the North American and European genotypes diverged between 1879 and 1891, whereas the European-in-North America genogroup diverged from the real-European genogroup between 1976 and 1988. This direction of evolution supports insertion of specific motifs in the HE protein, resulting in ISAV attenuation.
Gene-expression profiles of a hepatitis B small surface antigen-secreting cell line reveal upregulation of lymphoid enhancer-binding factor 1
Authors: Tian Xiaochen , Zhao Chao , Ren Jun , Ma Zhang-Mei , Xie You-Hua , Wen Yu-Mei
Published: October 2007

The genome of hepatitis B virus (HBV) consists of four open reading frames, encoding the envelope proteins (Pre-S/S), the core proteins (Pre-C/C), the polymerase (P) and the transactivating X protein (X). In the sera of HBV-infected patients, hepatitis B surface antigen (HBsAg) particles without the viral genome can outnumber virions by more than 1000-fold. To analyse the interactions between HBsAg and host cells, global gene-expression profiles of a small HBsAg (SHBs)-secreting stable cell line (HepG2-S-G2) and its counterpart control cell line (HepG2-Neo-F4) were compared. Marked upregulation of lymphoid enhancer-binding factor 1 (LEF-1), a transcription factor in the Wnt pathway, was found in SHBs-expressing cells and was confirmed by interference experiments with small interfering RNA. However, compared with the control cells, HepG2-S-G2 did not show higher proliferative competence in culture or increased tumorigenesis in nude mice. A possible mechanism to explain the discrepancy between the upregulation of LEF-1 and the lack of increased tumorigenesis is SHBs expression resulting in altered expression and distribution of LEF-1 protein in cell compartments and upregulation of LEF-1 isoforms that could suppress, rather than enhance, the Wnt pathway.
Exposure of ichnovirus particles to digitonin leads to enhanced infectivity and induces fusion from without in an in vitro model system
Authors: Stoltz Don , Lapointe Renée , Makkay Andrea , Cusson Michel
Published: October 2007

Unlike most viruses, the mature ichnovirus particle possesses two unit membrane envelopes. Following loss of the outer membranein vivo, nucleocapsids are believed to gain entry into the cytosol via a membrane fusion event involving the inner membrane and the plasma membrane of susceptible host cells; accordingly, experimentally induced damage to the outer membrane might be expected to increase infectivity. Here, in an attempt to develop anin vitromodel system for studying ichnovirus infection, we show that digitonin-induced disruption of the virion outer membrane not only increases infectivity, but also uncovers an activity not previously associated with any polydnavirus: fusion from without.
High-level expression from two independent expression cassettes in replication-incompetent adenovirus type 35 vector
Authors: Vogels Ronald , Zuijdgeest David , van Meerendonk Michelle , Companjen Arjen , Gillissen Gert , Sijtsma Jeroen , Melis Irene , Holterman Lennart , Radosevic Katarina , Goudsmit Jaap , Havenga Menzo J. E.
Published: October 2007

Replication-incompetent adenovirus type 35 (rAd35) represents a potent vaccine carrier that elicits strong, antigen-specific T- and B-cell responses in diverse preclinical models. Moreover, Ad35 is rare in human populations, resulting in the absence of neutralizing antibodies against this carrier, in contrast to the commonly used rAd5. Therefore, rAd35 is being investigated as a vaccine carrier for a number of diseases for which an effective vaccine is needed, including malaria, AIDS and tuberculosis. However, it can be perceived that effective immunization will require insertion of multiple antigens into adenoviral vectors. We therefore wanted to create rAd35 vectors carrying double expression cassettes, to expand within one vector the number of insertion sites for foreign DNA encoding antigenic proteins. We show that it is possible to generate rAd35 vectors carrying two cytomegalovirus promoter-driven expression cassettes, provided that the polyadenylation signals in each expression cassette are not identical. We demonstrate excellent rAd35 vector stability and show that expression of a transgene is not influenced by the presence of a second expression cassette. Moreover, by using two model vaccine antigens, i.e. the human immunodeficiency virus-derived Env-gp120 protein and the Plasmodium falciparum-derived circumsporozoite protein, we demonstrate that potent T- and B-cell responses are induced to both antigens expressed from a single vector. Such rAd35 vectors thus expand the utility of rAd35 vaccine carriers for the development of vaccines against, for example, malaria, AIDS and tuberculosis.
Protein tyrosine phosphatase H1 is a target of the E6 oncoprotein of high-risk genital human papillomaviruses
Authors: Töpffer Stephanie , Müller-Schiffmann Andreas , Matentzoglu Konstantin , Scheffner Martin , Steger Gertrud
Published: October 2007

The E6 proteins of high-risk genital human papillomaviruses (HPV), such as HPV types 16 and 18, possess a conserved C-terminal PDZ-binding motif, which mediates interaction with some cellular PDZ domain proteins. The binding of E6 usually results in their ubiquitin-mediated degradation. The ability of E6 to bind to PDZ domain proteins correlates with the oncogenic potential. Using a yeast two-hybrid system, GST pull-down experiments and coimmunoprecipitations, we identified the protein tyrosine phosphatase H1 (PTPH1/PTPN3) as a novel target of the PDZ-binding motif of E6 of HPV16 and 18. PTPH1 has been suggested to function as tumour suppressor protein, since mutational analysis revealed somatic mutations in PTPH1 in a minor fraction of various human tumours. We show here that HPV16 E6 accelerated the proteasome-mediated degradation of PTPH1, which required the binding of E6 to the cellular ubiquitin ligase E6-AP and to PTPH1. The endogenous levels of PTPH1 were particularly low in HPV-positive cervical carcinoma cell lines. The reintroduction of the E2 protein into the HPV16-positive cervical carcinoma cell line SiHa, known to lead to a sharp repression of E6 expression and to induce growth suppression, resulted in an increase of the amount of PTPH1. Our data suggest that reducing the level of PTPH1 may contribute to the oncogenic activity of high-risk genital E6 proteins.
West Nile virus-induced cytoplasmic membrane structures provide partial protection against the interferon-induced antiviral MxA protein
Authors: Hoenen Antje , Liu Wenjun , Kochs Georg , Khromykh Alexander A. , Mackenzie Jason M.
Published: October 2007

The human MxA protein is a type I and III interferon (IFN)-induced protein with proven antiviral activity against RNA viruses. In this study, we investigated the effect of MxA expression on the replication of West Nile Virus strain Kunjin (WNVKUN). Pretreatment of A549 cells with IFN-α lead to increased expression of MxA, which contributed to inhibition of WNVKUN replication and secretion. However, in Vero cells stably expressing the MxA protein, WNVKUN replication, maturation and secretion was not inhibited. Biochemical and subcellular localization studies of WNVKUN proteins and MxA suggest that the MxA activity was not compromised by a flavivirus-encoded antagonist. Instead, we show that characteristic membranous structures induced during WNVKUN replication provide partial protection from MxA, possibly by ‘hiding’ WNVKUN replication components. This distinct compartmentalization of viral replication and components of the cellular antiviral response may be an evolutionary mechanism by which flaviviruses can hide from host surveillance.